Bacterial and archaea community present in the pine barrens forest of long Island, NY: Unusually high percentage of ammonia oxidizing bacteria

PLoS ONE

Volumn 6, Issue 10, 2011, Pages

  Shah, Vishal ^a   Shah, Shreya ^a   Kambhampati, Murty S ^b   Ambrose, Jeffery ^b   Smith, Nyesha ^b   Dowd, Scot E ^c   McDonnell, Kevin T ^a   Panigrahi, Bishnu ^a   Green, Timothy ^d  

^a DOWLING COLLEGE   (United States)

^b SOUTHERN UNIVERSITY AT NEW ORLEANS   (United States)

^c Research and Testing Laboratory   (United States)

^d BROOKHAVEN NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIA;

AMMONIA OXIDIZING BACTERIUM; ARTICLE; BACTERIUM IDENTIFICATION; CONTROLLED STUDY; FOREST; GEOGRAPHIC DISTRIBUTION; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROBIAL POPULATION DYNAMICS; NITROGEN CYCLE; NITROGEN CYCLING; NITROSOCALDUS; NITROSOVIBRIO; NONHUMAN; PROKARYOTES BY METABOLISM; PROTEOBACTERIA; PYROSEQUENCING; SOIL ANALYSIS; SOIL MICROFLORA; SPECIES COMPOSITION; UNITED STATES; ARCHAEBACTERIUM; BACTERIUM; BIODIVERSITY; CLASSIFICATION; CLUSTER ANALYSIS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; OXIDATION REDUCTION REACTION; TREE;

ARCHAEA; BACTERIA (MICROORGANISMS); NITROSOMONADALES; NITROSOVIBRIO;

AMMONIA; ARCHAEA; BACTERIA; BIODIVERSITY; CLUSTER ANALYSIS; NEW YORK; OXIDATION-REDUCTION; SOIL MICROBIOLOGY; TREES;

EID: 80054789633     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0026263     Document Type: Article

References (27)

1. Hill GT, Mitkowski NA, Aldrich-Wolfe L, Emele LR, Jurkonie DD, (2000) Methods for assessing the composition and diversity of soil microbial communities. Appl Soil Ecol 15: 25-36.
2. Pampulha ME, Ferreira Mass, Oliveira A, (2007) Effects of a phosphinothricin based herbicide on selected groups of soil microorganisms. J Basic Microbiol 47: 325-331.
3. Markley ML, (1998) Pine Barrens. Ecosystem and landscape pp. 81-93 Rutgers Univ. Press, New Brunswick.
4. McCormick J, Forman RT, (1998) Pine Barrens. Ecosystem and landscape pp. xxi-xxvii Rutgers Univ. Press, New Brunswick.
5. Boyd HP, (1991) A field guide to the Pine Barrens of New Jersey. Plexus Publishing, Inc., Medford.
6. Joffe JS, Watson CW, (1933) Soil profile studies. V. Mature Podzols. Soil Sci 35: 313-332.
7. Cheplick GP, Quinn JA, (1987) The role of seed depth litter and fire in the seedling establishment of Amphicarpic peanutgrass Amphicarpum-Purshii. Oecologia 73: 459-464.
8. Guillen G, Rainey G, Morin M, (2004) A simple rapid approach using coupled multivariate statistical methods, GIS and trajectory models to delineate areas of common oil spill risk. J Marine Systems 45: 221-235.
9. Dillner AM, Schauer JJ, Christensen WF, Cass GR, (2005) A quantitiative method for clustering size distributions of elements. Atmospheric Env 39: 1525-1537.
10. Aldenderfer MS, Blashfield RK, (1984) Cluster analysis. Sage University Press, Newbury Park.
11. Fierer N, Jackson RB, (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 103: 626-631.
12. Francis CA, Beman JM, Kuypers MMM, (2007) New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammoniaoxidation. ISME Journal 1: 19-27.
13. He J, Shen J, Zhang L, Zhu Y, Zheng Y, et al. (2007) Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices. Environmental Microbiology 9: 2364-2374.
14. Yao B, Cao J, Zhao C, Rengel Zed, (2011) Influence of ammonium and nitrate supply on growth, nitrate reductase activity and N-use efficiency in a natural hybrid pine and its parents. doi:10.1093/jpe/rtq033.
15. Batcher MS, (2006) Monitoring protocols for Central Pine Barrens Field Plots. Available:www.fern-li.org.
16. Kumar N, Shah V, Walker V, (2011) Perturbation of Arctic soil microbial community by metal nanoparticles. doi:10.1016/j.jhazmat.2011.04.005.
17. Dowd SE, Sun Y, Secor PR, Rhoads DD, Wolcott BM, et al. (2008) Survey of bacterial diversity in chronic wounds using pyrosequencing, DGGE, and full ribosome shotgun sequencing. BMC Microbiol 8: 43.
18. Callaway TR, Dowd SE, Edrington TS, Anderson RC, Krueger N, (2010) Evaluation of bacterial diversity in the rumen and feces of cattle fed different levels of dried distillers grains plus solubles using bacterial tag-encoded FLX amplicon pyrosequencing. J Animal Sci 88: 3977-3983.
19. Finegold SM, Dowd SE, Gontcharova V, Liu C, Henley KE, et al. (2010) Pyrosequencing study of fecal microflora of autistic and control children. Anaerobe 16: 444-453.
20. Gontcharova V, Youn E, Wolcott RD, Hollister EB, Gentry TJ, (2010) A Windows-Based Software for Batch Depletion of Chimeras from Bacterial 16S rRNA Gene Datasets. Open Microbiol J 4: 47-52.
21. Dowd SE, Zaragoza J, Rodriguez JR, Oliver MJ, Payton PR, (2005) Windows.NET network distributed basic local alignment search toolkit (W.ND-BLAST). BMC Bioinformatics 6: 93.
22. Smith DM, Snow DE, Rees E, Zischkau AM, Hanson JD, et al. (2010) Evaluation of the bacterial diversity of pressure ulcers using bTEFAP pyrosequencing. BMC Med Genomics 3: 1.
23. Handl S, Dowd SE, Garcia-Mazcorro JF, Steiner JM, Suchodolski JS, (2011) Massive parallel 16S rRNA gene pyrosequencing reveals highly diverse fecal bacterial and fungal communities in healthy dogs and cats. FEMS Microbiol Ecol 76: 301-310.
24. Lozupone CM, Lladser ME, Knights D, Stombaugh J, Knight R, (2011) UniFrac: an effective distance metric for microbial community comparison. ISME J 5: 169-172.
25. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, (2009) Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities. Appl Environ Microbiol 75: 7537-7541.
26. Garland JL, (1996) Analytical approaches to the characterization of samples of microbial communities using patterns of potential C source utilization. Soil Biol Biochem 28: 213-221.
27. Ferrier S, Manion G, Elith J, Richardson K, (2007) Using generalized dissimilarity modeling to analsyse and predict patterns of beta diversity in regional biodiversity assessment. Diversity Distrib 13: 252-264.