Niche and metabolic principles explain patterns of diversity and distribution: Theory and a case study with soil bacterial communities

Proceedings of the Royal Society B: Biological Sciences

Volumn 282, Issue 1809, 2015, Pages

  Okie, Jordan G ^a,b   Van Horn, David J ^c   Storch, David ^d,e   Barrett, John E ^e   Gooseff, Michael N ^f   Kopsova, Lenka ^d   Takacs Vesbach, Cristina D ^c  

^a ARIZONA STATE UNIVERSITY   (United States)

^b ARIZONA STATE UNIVERSITY   (United States)

^c UNIVERSITY OF NEW MEXICO   (United States)

^d CHARLES UNIVERSITY   (Czech Republic)

^e VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

^f Department of Mechanical Engineering   (United States)

Author keywords

Elevational gradient; Macroecology; Metabolic theory; Microbial biogeography; Microbial communities; Species richness patterns

Indexed keywords

BACTERIUM; BIOGEOGRAPHY; CLIMATE VARIATION; COMMUNITY STRUCTURE; GROWTH RATE; LOW TEMPERATURE; MACROECOLOGY; METABOLISM; MICROBIAL COMMUNITY; NICHE; POPULATION DISTRIBUTION; PREDICTION; SALINITY; SOIL MICROORGANISM; SPECIES DIVERSITY; SPECIES RICHNESS; TAXONOMY; TEMPERATURE EFFECT;

ANTARCTICA;

BACTERIA (MICROORGANISMS);

ANTARCTICA; BACTERIUM; ECOSYSTEM; METABOLISM; MICROBIOLOGY; MICROFLORA;

ANTARCTIC REGIONS; BACTERIA; ECOSYSTEM; MICROBIOTA; SOIL MICROBIOLOGY;

EID: 84931292256     PISSN: 09628452     EISSN: 14712954     Source Type: Journal    
DOI: 10.1098/rspb.2014.2630     Document Type: Article

References (48)

1. Hutchinson GE. 1957 Concluding remarks. Cold Springs Harbor Symp. Quant. Biol. 22, 415–427. (doi:10.1101/SQB.1957.022.01.039)
2. Brown JH, Gillooly JF, Allen AP, Savage VM, West GB. 2004 Toward a metabolic theory of ecology. Ecology 85, 1771–1789. (doi:10.1890/03-9000)
3. Rohde K. 1992 Latitudinal gradients in species diversity: the search for the primary cause. Oikos 65, 514–527. (doi:10.2307/3545569)
4. Allen AP, Brown JH, Gillooly JF. 2002 Global biodiversity, biochemical kinetics, and the energeticequivalence rule. Science 297, 1545–1548. (doi:10.1126/science.1072380)
5. Storch D. 2012 Biodiversity and its energetic and thermal controls. In Metabolic ecology: a scaling approach (eds RM Sibly, JH Brown, A Kodric-Brown), pp. 120–131. Oxford, UK: Wiley & Sons.
6. Sanders NJ, Lessard J-P, Fitzpatrick MC, Dunn RR. 2007 Temperature, but not productivity or geometry, predicts elevational diversity gradients in ants across spatial grains. Glob. Ecol. Biogeogr. 16, 640–649. (doi:10.1111/j.1466-8238.2007.00316.x)
7. Tittensor DP, Mora C, Jetz W, Lotze HK, Ricard D, Berghe EV, Worm B. 2010 Global patterns and predictors of marine biodiversity across taxa. Nature 466, 1098–1101. (doi:10.1038/nature09329)
8. Bryant JA, Lamanna C, Morlon H, Kerkhoff AJ, Enquist BJ, Green JL. 2008 Microbes on mountainsides: contrasting elevational patterns of bacterial and plant diversity. Proc. Natl Acad. Sci. USA 105, 11 505–11 511. (doi:10.1073/pnas.0801920105)
9. Fierer N, McCain CM, Meir P, Zimmermann M, Rapp JM, Silman MR, Knight R. 2011 Microbes do not follow the elevational diversity patterns of plants and animals. Ecology 92, 797–804. (doi:10.1890/10-1170.1)
10. Wang J, Soininen J, Zhang Y, Wang B, Yang X, Shen J. 2011 Contrasting patterns in elevational diversity between microorganisms and macroorganisms. J. Biogeogr. 38, 595–603. (doi:10.1111/j.1365-2699.2010.02423.x)
11. Shen C, Xiong J, Zhang H, Feng Y, Lin X, Li X, Liang W, Chu H. 2013 Soil pH drives the spatial distribution of bacterial communities along elevation on Changbai Mountain. Soil Biol. Biochem. 57, 204–211. (doi:10.1016/j.soilbio.2012.07.013)
12. Singh D, Takahashi K, Kim M, Chun J, Adams JM. 2012 A hump-backed trend in bacterial diversity with elevation on Mount Fuji, Japan. Microb. Ecol. 63, 429–437. (doi:10.1007/s00248-011-9900-1)
13. Treonis A et al. 2012 Soil nematodes and their prokaryotic prey along an elevation gradient in the Mojave Desert (Death Valley National Park, California, USA). Diversity 4, 363–374. (doi:10.3390/d4040363)
14. Fierer N, Jackson RB. 2006 The diversity and biogeography of soil bacterial communities. Proc. Natl Acad. Sci. USA 103, 626–631. (doi:10.1073/pnas.0507535103)
15. Fuhrman JA, Steele JA, Hewson I, Schwalbach MS, Brown MV, Green JL, Brown JH. 2008 A latitudinal diversity gradient in planktonic marine bacteria. Proc. Natl Acad. Sci. 105, 7774–7778. (doi:10.1073/pnas.0803070105)
16. Wang J, Soininen J, Zhang Y, Wang B, Yang X, Shen J. 2012 Patterns of elevational beta diversity in micro- and macroorganisms. Glob. Ecol. Biogeogr. 21, 743–750. (doi:10.1111/j.1466-8238.2011.00718.x)
17. Lozupone CA, Knight R. 2007 Global patterns in bacterial diversity. Proc. Natl Acad. Sci. USA 104, 11 436–11 440. (doi:10.1073/pnas.0611525104)
18. Lauber CL, Hamady M, Knight R, Fierer N. 2009 Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl. Environ. Microbiol. 75, 5111–5120. (doi:10.1128/AEM.00335-09)
19. Savage VM, Gillooly JF, Brown JH, West GB, Charnov EL. 2004 Effects of body size and temperature on population growth. Am. Nat. 163, 429–441. (doi:10.1086/381872)
20. Corkrey R, Olley J, Ratkowsky D, McMeekin T, Ross T. 2012 Universality of thermodynamic constants governing biological growth rates. PLoS ONE 7, e32003. (doi:10.1371/journal.pone.0032003)
21. Eppley RW. 1972 Temperature and phytoplankton growth in the sea. Fish Bull. 70, 1063–1085.
22. Price PB, Sowers T. 2004 Temperature dependence of metabolic rates for microbial growth, maintenance, and survival. Proc. Natl Acad. Sci. USA 101, 4631–4636. (doi:10.1073/pnas.0400522101)
23. Angilletta Jr MJ, Huey RB, Frazier MR. 2009 Thermodynamic effects on organismal performance: is hotter better? Physiol. Biochem. Zool. 83, 197–206. (doi:10.1086/648567)
24. Okie JG. 2012 Microorganisms. In Metabolic ecology: a scaling approach (eds RM Sibly, JH Brown, A Kodric-Brown), pp. 133–153. Oxford, UK: Wiley & Sons.
25. Frank SA. 2009 The common patterns of nature. J. Evol. Biol. 22, 1563–1585. (doi:10.1111/j.1420-9101.2009.01775.x)
26. Harte J. 2011 Maximum entropy and ecology: a theory of abundance, distribution, and energetics. Oxford, UK: Oxford University Press.
27. Harte J, Newman EA. 2014 Maximum information entropy: a foundation for ecological theory. Trends Ecol. Evol. 29, 384–389. (doi:10.1016/j.tree.2014.04.009)
28. Doran PT, McKay CP, Clow GD, Dana GL, Fountain AG, Nylen T, Lyons WB. 2002 Valley floor climate observations from the McMurdo Dry Valleys, Antarctica, 1986–2000. J. Geophys. Res. 107, 4772. (doi:10.1029/2001JD002045)
29. Fountain AG, Nylen TH, Monaghan A, Basagic HJ, Bromwich D. 2010 Snow in the McMurdo Dry Valleys, Antarctica. Int. J. Climatol. 30, 633–642. (doi:10.1002/joc.1933)
30. Barrett JE, Virginia RA, Wall DH, Parsons AN, Powers LE, Burkins MB. 2004 Variation in biogeochemistry and soil biodiversity across spatial scales in a polar desert ecosystem. Ecology 85, 3105–3118. (doi:10.1890/03-0213)
31. Van Horn DJ, Van Horn ML, Barrett JE, Gooseff MN, Altrichter AE, Geyer KM, Zeglin LH, Takacs-Vesbach CD. 2013 Factors controlling soil microbial biomass and bacterial diversity and community composition in a cold desert ecosystem: role of geographic scale. PLoS ONE 8, e66103. (doi:10.1371/journal.pone.0066103)
32. Fountain A, Levy J, Van Horn D, Gooseff MA. 2014 The McMurdo Dry Valleys: a landscape on the threshold of change. Geomorphology 225, 25–35. (doi:10.1016/j.geomorph.2014.03.044)
33. Dowd SF, Sun Y, Wolcott RD, Domingo A, Carroll JA. 2008 Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies: bacterial diversity in the ileum of newly weaned Salmonella-infected pigs. Foodborne Pathog. Dis. 5, 459–472. (doi:10.1089/fpd.2008.0107)
34. Chao A. 1984 Nonparametric estimation of the number of classes in a population. Scand. J. Stat. 11, 265–270.
35. Ter Braak C, Šmilauer P. 2012 Canoco reference manual and user’s guide: software for ordination (v. 5.0). Microcomput. Power.
36. R Development Core Team. 2011 R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing.
37. Witherow RA, Lyons WB, Bertler NA, Welch KA, Mayewski PA, Sneed SB, Nylen T, Handley MJ, Fountain A. 2006 The aeolian flux of calcium, chloride and nitrate to the McMurdo Dry Valleys landscape: evidence from snow pit analysis. Antarct. Sci. 18, 497–505. (doi:10.1017/S095410200600054X)
38. Wang Z, Brown JH, Tang Z, Fang J. 2009 Temperature dependence, spatial scale, and tree species diversity in eastern Asia and North America. Proc. Natl Acad. Sci. USA 106, 13388–13392. (doi:10.1073/pnas.0905030106)
39. Gaston KJ. 2000 Global patterns in biodiversity. Nature 405, 220–227. (doi:10.1038/35012228)
40. Wright DH. 1983 Species-energy theory: an extension of species-area theory. Oikos 41, 496–506. (doi:10.2307/3544109)
41. Kraft NJ et al. 2011 Disentangling the drivers of b diversity along latitudinal and elevational gradients. Science 333, 1755–1758. (doi:10.1126/science.1208584)
42. Stevens GC. 1989 The latitudinal gradient in geographical range: how so many species coexist in the tropics. Am. Nat. 133, 240–256. (doi:10.1086/284913)
43. Telford RJ, Vandvik V, Birks HJB. 2006 Dispersal limitations matter for microbial morphospecies. Science 312, 1015. (doi:10.1126/science.1125669)
44. Burkins MB, Virginia RA, Chamberlain CP, Wall DH. 2000 Origin and distribution of soil organic matter in Taylor Valley, Antarctica. Ecology 81, 2377–2391. (doi:10.1890/0012-9658(2000)081[2377:OADOSO]2.0.CO;2)
45. Sokol ER, Herbold CW, Lee CK, Cary SC, Barrett J. 2013 Local and regional influences over soil microbial metacommunities in the Transantarctic Mountains. Ecosphere 4, art136. (doi:10.1890/ES13-00136.1)
46. Burnside WR, Erhardt EB, Hammond ST, Brown JH. 2014 Rates of biotic interactions scale predictably with temperature despite variation. Oikos 123, 1449–1456. (doi:10.1111/oik.01199)
47. Bonn A, Storch D, Gaston KJ. 2004 Structure of the species-energy relationship. Proc. R. Soc. Lond. B 271, 1685–1691. (doi:10.1098/rspb.2004.2745)
48. Colwell RK, Rangel TF. 2009 Hutchinson’s duality: the once and future niche. Proc. Natl Acad. Sci. USA 106, 19651–19658. (doi:10.1073/pnas.0901650106)