Influence of geogenic factors on microbial communities in metallogenic Australian soils

ISME Journal

Volumn 6, Issue 11, 2012, Pages 2107-2118

  Reith, Frank ^a,b   Brugger, Joel ^a,c   Zammit, Carla M ^a,b   Gregg, Adrienne L ^b   Goldfarb, Katherine C ^d   Andersen, Gary L ^d   Desantis, Todd Z ^d   Piceno, Yvette M ^d   Brodie, Eoin L ^d   Lu, Zhenmei ^e,f   He, Zhili ^f   Zhou, Jizhong ^f   Wakelin, Steven A ^g  

^a UNIVERSITY OF ADELAIDE   (Australia)

^b CSIRO   (Australia)

^c SOUTH AUSTRALIAN MUSEUM   (Australia)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^e ZHEJIANG UNIVERSITY   (China)

^f UNIVERSITY OF OKLAHOMA   (United States)

^g AGRESEARCH LTD   (New Zealand)

Author keywords

Australia; bacteria; gold; landform; microarray; soil

Indexed keywords

METAL;

BACTERIUM; COMMUNITY STRUCTURE; GEOCHEMICAL METHOD; GEOGENIC SOURCE; GEOMORPHOLOGY; GOLD; LITHOLOGY; METALLOGENESIS; MICROBIAL COMMUNITY; PHYLOGENETICS; PHYLOGENY; POLYMORPHISM; SOIL CHEMISTRY; SOIL HORIZON; SOIL MICROORGANISM;

ARTICLE; AUSTRALIA; BACTERIUM; CHEMISTRY; CLASSIFICATION; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; PHYLOGENY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SOIL; SOIL POLLUTANT;

AUSTRALIA; BACTERIA; METALS; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; SOIL; SOIL MICROBIOLOGY; SOIL POLLUTANTS;

AUSTRALIA;

ALPHAPROTEOBACTERIA; BACILLUS (BACTERIUM); BACTERIA (MICROORGANISMS); CUPRIAVIDUS; CUPRIAVIDUS METALLIDURANS; FIRMICUTES; SPHINGOMONAS; SPHINGOMONAS SP.;

EID: 84867745288     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2012.48     Document Type: Article

References (45)

1. Abaye DA, Lawlor K, Hirsch PR, Brookes PC. (2005). Changes in the microbial community of an arable soil caused by long-term metal contamination. Europ J Soil Sci 56: 93-102.
2. Acosta-Martinez V, Dowd S, Sun Y, Allen V. (2008). Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biol Biochem 40: 2762-2770.
3. Anderson MJ, Gorley RN, Clarke KR. (2008). PERMANOVA + for PRIMER-Guide to software and statistical methods. Primer-E Ltd: Plymouth, UK.
4. Aspandiar MF, Anand RR, Gray DJ. (2008). Geochemical dispersion mechanisms through transported cover: implications for mineral exploration in Australia. Cooperative Research Centre for Landscape Evolution and Mineral Exploration, Open File Rep 246. Wembley West, Australia.
5. Ba°a°th E. (1989). Effects of heavy metals in soil on microbial processes and populations (a review).Water, Air, Soil Pol 47: 335-379.
6. Baker BJ, Banfield JF. (2003). Microbial communities in acid mine drainage. FEMS Microbiol Ecol 44: 139-152.
7. Bray JR, Curtis JT. (1957). An ordination of the upland forest communities of southern Wisconsin. Ecol Monograph 27: 325-349.
8. Brodie EL, DeSantis TZ, Joyner DC, Baek SM, Larsen JT, Andersen GL et al. (2006). Application of a highdensity oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Environ Microbiol 72: 6288-6298.
9. Castellanos T, Dohrmann AB, Imfeld G, Baumgarte S, Tebbe CC. (2009). Search of environmental descriptors to explain the variability of bacterial diversity from maize rhizospheres across a regional scale. Europ. J Soil Biol 45: 383-393.
10. Clarke KR. (1993). Non-parametric multivariate analysis of changes in community structure. Austral J Ecol 18: 117-143.
11. Clarke KR, Warwick RM. (2001). Change in Marine Communities: An Approach to Statistical Analysis and Interpretation. Primer-E Ltd: Plymouth, UK.
12. Denef VJ, Mueller RS, Banfield JF. (2010). AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature. ISME J 4: 599-610.
13. Dequiedt S, Thioulouse J, Jolivet C, Saby NPA, Lelievre M, Maron PA et al. (2009). Biogeographical patterns of soil bacterial communities. Environ Microbiol Rep 1: 251-255.
14. DeSantis TZ, Brodie EL, Moberg JP, Zubieta IX, Piceno YM, Andersen GL. (2007). High density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb Ecol 53: 371-383.
15. Drenovsky RE, Steenwerth KL, Jackson LE, Scow KM. (2010). Land use and climatic factors structure regional patterns in soil microbial communities. Glob Ecol Biogeo 19: 27-39.
16. Duxbury T, Bicknell B. (1983). Metal-tolerant bacterial populations from natural and metal-polluted soils. Soil Biol. Biochem 15: 243-250.
17. Fierer N, Jackson RB. (2006). The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci 103: 626-631.
18. Goldschmidt VM. (1954). Geochemistry. Oxford University Press: Oxford, UK.
19. He Z,Deng Y,Van Nostand JD, Tu Q, XuM, Hemme CL et al. (2010). Geochip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity. ISME J 4: 1-13.
20. Hu Q, Qi HY, Zeng JH, Zhang HX. (2007). Bacterial diversity in soils around a lead and zinc mine. J Environ Sci-China 19: 74-79.
21. Isbell RF. (2002). The Australian Soil Classification (Revised ed.) CSIRO Publishing Collingwood: Australia.
22. Jenny H. (1941). Factors of Soil Formation: A System of Quantitative Pedology. McCraw-Hill: New York, USA.
23. Kock D, Schippers A. (2008). Quantitative microbial community analysis of three different sulfidic mine tailing dumps generating acid drainage. Appl Environ Microbiol 74: 5211-5219.
24. Lauber CL, Strickland MS, Bradford MA, Fierer N. (2008). The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biol Biochem 40: 2407-2415.
25. Lazzaro A, Abegg C, Zeyer J. (2009). Bacterial community structure of glacier forefields on siliceous and calcareous bedrock. Europ J Soil Sci 60: 860-870.
26. McQueen KG. (2008). Regolith geochemistry. In: Scott KM, Pain CF (eds). Regolith Science. CSIRO Publishing: Melbourne, Australia, pp 73-104.
27. Mele P, Sawbridge T, Hayden H, Methe B, Stockwell T et al. (2010). How does surface soil geomorphology and landuse influence the soil microbial ecosystems in south eastern Australia. Insights gained from DNA sequencing of the soilmetagenome. Proceed. 19thWorld Congr. Soil Sci., Symposium 1.2.2, p. 12-15.
28. Pain CF. (2008). Regolith description and mapping. In: Scott KM, Pain CF (eds). Regolith Science. CSIRO Publishing: Melbourne, Australia, pp 281-306.
29. Reith F, Etschmann B, Grosse C, Moors H, Benotmane MA, Monsieurs P et al. (2009). Mechanisms of gold biomineralization in the bacterium Cupriavidus metallidurans. Proc Natl Acad Sci 106: 17757-17762.
30. Reith F, McPhail DC. (2006). Effect of resident microbiota on the solubilization of gold in soil from the Tomakin Park Gold Mine, New South Wales, Australia. Geochim Cosmochim Acta 70: 1421-1438.
31. Reith F, McPhail DC, Christy AG. (2005). Bacillus cereus, gold and associated elements in soil and regolith samples from Tomakin Park Gold Mine in south-eastern New South Wales, Australia. J Geochem Explor 85: 81-89.
32. Reith F, Rogers SL. (2008). Assessment of bacterial communities in auriferous and non-auriferous soils using genetic and functional fingerprinting. Geomicrobiol J 25: 203-215.
33. Reith F, Rogers SL, McPhail DC, Webb D. (2006). Biomineralization of gold: biofilms on bacterioform gold. Science 313: 233-236.
34. Schatz MC, Phillippy AM, Gajer P, DeSantis TZ, Andersen GL, Ravel J. (2010). Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray. Appl Environ Microbiol 76: 5636-5638.
35. Singh BK, Nazaries L, Munro S, Anderson IC, Campbell CD. (2006). Use of multiplex terminal restriction fragment length polymorphism for rapid and simultaneous analysis of different components of the soil microbial community. Appl Environ Microbiol 72: 7278-7285.
36. Torsvik V, Øvrea°s L. (2002). Microbial diversity and function in soil; from genes to ecosystems. Curr Opin Microbiol 3: 240-245.
37. Viles HA. (2011). Microbial geomorphology: a neglected link between life and landscape. Geomorphology, doi:10.1016/j.geomorph.2011.03.021.
38. Viles HA, Naylor LA, Carter NEA, Chaput D. (2008). Biogeomorphological disturbance regimes: progress in linking ecological and geomorphological systems. Earth Surf Process Landforms 33: 1419-1435.
39. Wagai R, Kitayama K, Satomura T, Fujinuma R, Balser T. (2011). Interactive influences of climate and parent material on soil microbial community structure in Bornean tropical foresy ecosystems. Ecol Res 26: 627-636.
40. Wakelin SA, Macdonald LM, Rogers SL, Gregg AL, Bolger TP, Baldock JA. (2008). Habitat selective factors influencing the structural composition and functional capacity of microbial communities in agricultural soils. Soil Biol Biochem 40: 803-813.
41. Wakelin SA, Anand RR, Reith F, Gregg AL, Noble RRP, Goldfarb KC et al. (2012a). Bacterial communities associated with a mineral weathering profile at a sulphidic mine tailings dump in arid Western Australia. FEMS Microbiol Ecol 79: 298-311.
42. Wakelin SA, Anand RR, Reith F, Macfarlane C, Rogers S. (2012b). Biogeochemical surface expression over a deep, overburden-covered VMS mineralization. J Geochem Explor 112: 262-271.
43. Wakelin SA, Chu GX, Broos K, Clarke KR, Liang YC, McLaughlin MJ. (2010a). Structural and functional response of soil microbiota to addition of plant substrate aremoderated by soil Cu levels. Biol Fert Soils 46: 333-342.
44. Wakelin SA, Chu GX, Lardner R, Liang YC, McLaughlin MJ. (2010b). A single application of Cu to field soil has long-term effects on bacterial community structure, diversity, and soil processes. Pedobiologica 53: 149-158.
45. White DC, Sutton SD, Ringelberg DB. (1996). The genus Sphingomonas:physiology and ecology. Curr Opin Biotechn 7: 301-306.