PMID- 16156736
OWN - NLM
STAT- MEDLINE
DCOM- 20051101
LR  - 20131121
IS  - 1462-2912 (Print)
IS  - 1462-2912 (Linking)
VI  - 7
IP  - 10
DP  - 2005 Oct
TI  - Bacterial communities associated with benthic organic matter in headwater stream 
      microhabitats.
PG  - 1633-40
AB  - Bacterial communities associated with a variety of benthic detritus types were 
      studied in three streams in the context of the chemical characteristics of the 
      sediment material and the stream water. A cell purification assay was developed 
      for a quantitative microscopic evaluation of bacterial community structure in 
      detritus samples by fluorescence in situ hybridization (FISH). The efficiency of 
      FISH with fluorescently monolabelled probes was compared with FISH with signal 
      amplification by catalysed reporter deposition (CARD-FISH). In detritus types 
      poor in organic carbon and nitrogen, the numbers of prokaryotes were related to 
      the chemical characteristics of the stream water column, whereas no such 
      relationship was found for detritus types rich in organic carbon and nitrogen. 
      These results might help to provide criteria for the selection of detritus types 
      for river ecosystem assessment and monitoring. The percentage of bacteria 
      detected by FISH with monolabelled probes was correlated with the detritus total 
      organic matter (OM). This is likely attributed to a higher ribosome content of 
      microbial cells on substrates rich in OM. Cell detection by CARD-FISH did not 
      show any correlation with OM content, indicating that this technique renders the 
      results more independent from the activity state of cells. Fluorescence in situ 
      hybridization with four group-specific probes suggested a relationship between 
      substrate quality and the composition of the microbial assemblages on the various 
      types of detritus. The improved protocol for cell purification and CARD-FISH may 
      facilitate future investigations on the relationship between the riverine benthic 
      detritus quality and microbial community composition.
FAU - Fazi, Stefano
AU  - Fazi S
AD  - CNR-Water Research Institute (IRSA), via Reno 1, 00198 Rome, Italy. 
      fazi@irsa.cnr.it
FAU - Amalfitano, Stefano
AU  - Amalfitano S
FAU - Pernthaler, Jakob
AU  - Pernthaler J
FAU - Puddu, Alberto
AU  - Puddu A
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - England
TA  - Environ Microbiol
JT  - Environmental microbiology
JID - 100883692
RN  - 0 (Organic Chemicals)
RN  - 7440-44-0 (Carbon)
RN  - N762921K75 (Nitrogen)
SB  - IM
MH  - Bacteria/cytology/genetics/*growth & development/isolation & purification
MH  - Carbon/metabolism
MH  - Centrifugation, Density Gradient
MH  - *Ecosystem
MH  - Geologic Sediments/chemistry/*microbiology
MH  - In Situ Hybridization, Fluorescence
MH  - Nitrogen/metabolism
MH  - Organic Chemicals/*metabolism
MH  - Rivers/chemistry/*microbiology
MH  - Water Movements
EDAT- 2005/09/15 09:00
MHDA- 2005/11/03 09:00
CRDT- 2005/09/15 09:00
PHST- 2005/09/15 09:00 [pubmed]
PHST- 2005/11/03 09:00 [medline]
PHST- 2005/09/15 09:00 [entrez]
AID - EMI857 [pii]
AID - 10.1111/j.1462-2920.2005.00857.x [doi]
PST - ppublish
SO  - Environ Microbiol. 2005 Oct;7(10):1633-40. doi: 10.1111/j.1462-2920.2005.00857.x.