Soil microbial communities associated with Douglas-fir and red alder stands at high- and low-productivity forest sites in Oregon, USA.
Communities of archaea, bacteria, and fungi were examined in forest soils located in the Oregon Coast Range and the inland Cascade Mountains. Soils from replicated plots of Douglas-fir (Pseudotsuga menziesii) and red alder (Alnus rubra) were characterized using fungal ITS (internal transcribed spacer region), eubacterial 16S rRNA, and archaeal 16S rRNA primers. Population size was measured with quantitative (Q)-PCR and composition was examined using length heterogeneity (LH)-PCR for fungal composition, terminal restriction fragment length (T-RFLP) profiles for bacterial and archaeal composition, and sequencing to identify dominant community members. Whereas fungal and archaeal composition varied between sites and dominant tree species, bacterial communities only varied between sites. The abundance of archaeal gene copy numbers was found to be greater in coastal compared to montane soils accounting for 11% of the prokaryotic community. Crenarchaea groups 1.1a-associated, 1.1b, 1.1c, and 1.1c-associated were putatively identified. A greater abundance of Crenarchaea 1.1b indicator fragments was found in acidic (pH 4) soils with low C:N ratios under red alder. In coastal soils, 25% of fungal sequences were putatively identified as basidiomycetous yeasts belonging to the genus Cryptococcus. Although the function of these yeasts in soil is not known, they could significantly contribute to decomposition processes in coastal soils distinguished by rapid tree growth, high N content, low pH, and frequent water-saturation events.
Yarwood
Stephanie A
SA
Department of Microbiology, Oregon State University, Nash Hall 220, Corvallis, OR 97331, USA. stephanie.yarwood@oregonstate.edu
Bottomley
Peter J
PJ
Myrold
David D
DD
D029661:Alnus / Q000382:microbiology*; D001105:Archaea / Q000145:classification / Q000235:genetics / Q000254:growth & development*; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000254:growth & development*; D058448:Biota; D019641:DNA, Archaeal / Q000235:genetics / Q000302:isolation & purification; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D004271:DNA, Fungal / Q000235:genetics / Q000302:isolation & purification; D017753:Ecosystem; D005658:Fungi / Q000145:classification / Q000235:genetics / Q000254:growth & development*; D018628:Gene Dosage; D009922:Oregon; D010802:Phylogeny; D012150:Polymorphism, Restriction Fragment Length; D028224:Pseudotsuga / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012988:Soil Microbiology; D014197:Trees / Q000382:microbiology
D019641:DNA, Archaeal; D004269:DNA, Bacterial; D004271:DNA, Fungal; D012336:RNA, Ribosomal, 16S
J Bacteriol. 1988 Feb;170(2):720-6
2448289
Microb Ecol. 2006 Jul;52(1):90-103
16708262
Appl Environ Microbiol. 2005 Mar;71(3):1501-6
15746353
Environ Microbiol. 2005 Dec;7(12):1985-95
16309395
Nucleic Acids Res. 1989 Oct 11;17(19):7843-53
2798131
Microb Ecol. 2008 Oct;56(3):448-59
18253776
Mycol Res. 2007 May;111(Pt 5):549-71
17572335
Environ Microbiol. 2003 Jan;5(1):36-47
12542711
Appl Environ Microbiol. 1997 Jan;63(1):139-44
16535478
Environ Microbiol. 2008 Nov;10(11):3093-105
18764871
Environ Microbiol. 2005 Mar;7(3):337-47
15683394
Appl Environ Microbiol. 2008 Mar;74(5):1620-33
18192411
Microb Ecol. 2005 Oct;50(3):463-73
16328649
Environ Microbiol. 2008 Nov;10(11):2966-78
18707610
Environ Microbiol. 2008 Nov;10(11):2956-65
18393992
Ecol Lett. 2006 Oct;9(10):1127-35
16972876
Mycorrhiza. 2007 Nov;17(8):633-645
17638027
Arch Microbiol. 1995 Sep;164(3):165-72
7545384
Appl Environ Microbiol. 2006 Mar;72(3):1852-7
16517631
Appl Environ Microbiol. 2004 Sep;70(9):5057-65
15345382
Appl Environ Microbiol. 2006 Nov;72(11):7278-85
16936053
Appl Environ Microbiol. 1997 Feb;63(2):803-5
9023962
Microb Ecol. 2007 Oct;54(3):567-77
17546519
FEMS Microbiol Ecol. 2007 Apr;60(1):51-9
17263837
Appl Environ Microbiol. 2007 Nov;73(21):7059-66
17827313
FEMS Microbiol Ecol. 2007 Jun;60(3):442-8
17391330
Appl Environ Microbiol. 2006 Nov;72(11):6965-71
16950906
Environ Microbiol. 2006 Aug;8(8):1382-93
16872402
Bioinformatics. 2001 Aug;17(8):754-5
11524383
Environ Microbiol. 2004 Aug;6(8):769-79
15250879
ISME J. 2009 Mar;3(3):305-13
18987677
Environ Microbiol. 2008 Feb;10(2):534-41
18081854
Mol Ecol. 1993 Apr;2(2):113-8
8180733
Bioinformatics. 2003 Aug 12;19(12):1572-4
12912839
Environ Microbiol. 2003 Sep;5(9):787-97
12919414
Proc Natl Acad Sci U S A. 2005 Apr 5;102(14):5084-9
15784739
Appl Environ Microbiol. 2005 Jul;71(7):4117-20
16000830
Environ Microbiol. 2008 Apr;10(4):926-41
18218029
New Phytol. 2009 Oct;184(2):449-456
19703112
Nucleic Acids Res. 1997 Dec 15;25(24):4876-82
9396791
Nucleic Acids Res. 2007 Jan;35(Database issue):D169-72
17090583
Biotechnol Bioeng. 2005 Mar 20;89(6):670-9
15696537