PMID- 18487394
OWN - NLM
STAT- MEDLINE
DCOM- 20080731
LR  - 20211020
IS  - 1098-5336 (Electronic)
IS  - 0099-2240 (Print)
IS  - 0099-2240 (Linking)
VI  - 74
IP  - 14
DP  - 2008 Jul
TI  - Characterization of nitrifying, denitrifying, and overall bacterial communities 
      in permeable marine sediments of the northeastern Gulf of Mexico.
PG  - 4440-53
LID - 10.1128/AEM.02692-07 [doi]
AB  - Sandy or permeable sediment deposits cover the majority of the shallow ocean 
      seafloor, and yet the associated bacterial communities remain poorly described. 
      The objective of this study was to expand the characterization of bacterial 
      community diversity in permeable sediment impacted by advective pore water 
      exchange and to assess effects of spatial, temporal, hydrodynamic, and 
      geochemical gradients. Terminal restriction fragment length polymorphism (TRFLP) 
      was used to analyze nearly 100 sediment samples collected from two northeastern 
      Gulf of Mexico subtidal sites that primarily differed in their hydrodynamic 
      conditions. Communities were described across multiple taxonomic levels using 
      universal bacterial small subunit (SSU) rRNA targets (RNA- and DNA-based) and 
      functional markers for nitrification (amoA) and denitrification (nosZ). Clonal 
      analysis of SSU rRNA targets identified several taxa not previously detected in 
      sandy sediments (i.e., Acidobacteria, Actinobacteria, Chloroflexi, Cyanobacteria, 
      and Firmicutes). Sequence diversity was high among the overall bacterial and 
      denitrifying communities, with members of the Alphaproteobacteria predominant in 
      both. Diversity of bacterial nitrifiers (amoA) remained comparatively low and did 
      not covary with the other gene targets. TRFLP fingerprinting revealed changes in 
      sequence diversity from the family to species level across sediment depth and 
      study site. The high diversity of facultative denitrifiers was consistent with 
      the high permeability, deeper oxygen penetration, and high rates of aerobic 
      respiration determined in these sediments. The high relative abundance of 
      Gammaproteobacteria in RNA clone libraries suggests that this group may be poised 
      to respond to short-term periodic pulses of growth substrates, and this 
      observation warrants further investigation.
FAU - Mills, Heath J
AU  - Mills HJ
AD  - Department of Oceanography, Florida State University, Tallahassee, FL 32306-4470, 
      USA.
FAU - Hunter, Evan
AU  - Hunter E
FAU - Humphrys, Mike
AU  - Humphrys M
FAU - Kerkhof, Lee
AU  - Kerkhof L
FAU - McGuinness, Lora
AU  - McGuinness L
FAU - Huettel, Markus
AU  - Huettel M
FAU - Kostka, Joel E
AU  - Kostka JE
LA  - eng
SI  - GENBANK/DQ431855
SI  - GENBANK/DQ431856
SI  - GENBANK/DQ431857
SI  - GENBANK/DQ431858
SI  - GENBANK/DQ431859
SI  - GENBANK/DQ431860
SI  - GENBANK/DQ431861
SI  - GENBANK/DQ431862
SI  - GENBANK/DQ431863
SI  - GENBANK/DQ431864
SI  - GENBANK/DQ431865
SI  - GENBANK/DQ431866
SI  - GENBANK/DQ431867
SI  - GENBANK/DQ431868
SI  - GENBANK/DQ431869
SI  - GENBANK/DQ431870
SI  - GENBANK/DQ431871
SI  - GENBANK/DQ431872
SI  - GENBANK/DQ431873
SI  - GENBANK/DQ431874
SI  - GENBANK/DQ431875
SI  - GENBANK/DQ431876
SI  - GENBANK/DQ431877
SI  - GENBANK/DQ431878
SI  - GENBANK/DQ431879
SI  - GENBANK/DQ431880
SI  - GENBANK/DQ431881
SI  - GENBANK/DQ431882
SI  - GENBANK/DQ431883
SI  - GENBANK/DQ431884
SI  - GENBANK/DQ431885
SI  - GENBANK/DQ431886
SI  - GENBANK/DQ431887
SI  - GENBANK/DQ431888
SI  - GENBANK/DQ431889
SI  - GENBANK/DQ431890
SI  - GENBANK/DQ431891
SI  - GENBANK/DQ431892
SI  - GENBANK/DQ431893
SI  - GENBANK/DQ431894
SI  - GENBANK/DQ431895
SI  - GENBANK/DQ431896
SI  - GENBANK/DQ431897
SI  - GENBANK/DQ431898
SI  - GENBANK/DQ431899
SI  - GENBANK/DQ431900
SI  - GENBANK/DQ431901
SI  - GENBANK/DQ431902
SI  - GENBANK/DQ431903
SI  - GENBANK/DQ431904
SI  - GENBANK/DQ431905
SI  - GENBANK/DQ431906
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20080516
PL  - United States
TA  - Appl Environ Microbiol
JT  - Applied and environmental microbiology
JID - 7605801
RN  - 0 (DNA, Bacterial)
RN  - 0 (RNA, Bacterial)
RN  - 0 (RNA, Ribosomal)
SB  - IM
MH  - Atlantic Ocean
MH  - Bacteria/*classification/*isolation & purification
MH  - Base Sequence
MH  - DNA Fingerprinting
MH  - DNA, Bacterial/isolation & purification
MH  - Gene Library
MH  - Geologic Sediments/*microbiology
MH  - Molecular Sequence Data
MH  - Phylogeny
MH  - Polymorphism, Restriction Fragment Length
MH  - RNA, Bacterial/isolation & purification
MH  - RNA, Ribosomal/isolation & purification
MH  - Reverse Transcriptase Polymerase Chain Reaction
MH  - Sequence Analysis, DNA
MH  - Water Microbiology
PMC - PMC2493161
EDAT- 2008/05/20 09:00
MHDA- 2008/08/01 09:00
PMCR- 2009/01/01
CRDT- 2008/05/20 09:00
PHST- 2008/05/20 09:00 [pubmed]
PHST- 2008/08/01 09:00 [medline]
PHST- 2008/05/20 09:00 [entrez]
PHST- 2009/01/01 00:00 [pmc-release]
AID - AEM.02692-07 [pii]
AID - 2692-07 [pii]
AID - 10.1128/AEM.02692-07 [doi]
PST - ppublish
SO  - Appl Environ Microbiol. 2008 Jul;74(14):4440-53. doi: 10.1128/AEM.02692-07. Epub 
      2008 May 16.