Wetlands provide essential functions to the ecosphere that range from water filtration to flood control. Current methods of evaluating the quality of wetlands include assessing vegetation, soil type, and period of inundation. With recent advances in molecular and bioinformatic techniques, measurement of the structure and composition of soil bacterial communities have become an alternative to traditional methods of ecological assessment. The objective of the current study was to determine whether soil bacterial community composition and structure changed along a single transect in Macon County, AL. Proteobacteria were the most abundant phyla throughout the soils in the study (ranging from 42.1% to 49.9% of total sequences). Phyla Acidobacteria (37.4%) and Verrucomicrobia (7.0%) were highest in wetland soils, Actinobacteria (14.6%) was highest in the transition area, and Chloroflexi (1.6%) was highest in upland soils. Principle Components Analysis (relative abundance) and Principle Coordinates Analysis (PCoA) (Unifrac weighted metric) plots were generated, showing distinction amongst the ecosystem types through clustering by taxonomic abundance and Unifrac scores at 3% dissimilarity, respectively. Selected soil properties (soil organic carbon and phosphatase enzyme activity) also differed significantly in transition soil ecosystem types, while showing predominance in the wetland area. This study suggests that with further study the structure and composition of soil bacterial communities may eventually be an important indicator of ecological impact in wetland ecosystems.
References
[1]
Costanza, R.; d’Arge, R.; de Groot, R.; Farber, S.; Grasso, M.; Hannon, B.; Limburg, K.; Naeem, S.; O’Neill, R.V.; Paruelo, J.; et al. The value of the world’s ecosystem services and natural capital. Nature 1997, 387, 253–260, doi:10.1038/387253a0.
[2]
Dahl, T.E. Wetlands Losses in the United States 1780’S to 1980’s; Fish and Wildlife Service: Washington, DC, USA, 1990; p. 13.
[3]
Dahl, T.E. Status and Trends of Wetlands in the Conterminous United States 1998 to 2004; Fish and Wildlife Service: Washington, DC, USA, 2006; p. 112.
[4]
Lilly, J.P. Soil Facts Wetland Issues. Available online: http://www.soil.ncsu.edu/publications/Soilfacts/AG-439-26/AG-439-26.pdf (accessed on 15 April 2013).
[5]
Whittecar, G.R.; Daniels, W.L. Use of hydrogeomorphic concepts to design created wetlands in southeaster Virginia. Geomorphology 1999, 31, 355–371, doi:10.1016/S0169-555X(99)00081-1.
[6]
Faulkner, S.P.; Patrick, W.H., Jr.; Gambrell, R.P. Field techniques for measuring wetland soil parameters. Soil Sci. Soc. Am. J. 1989, 53, 883–890, doi:10.2136/sssaj1989.03615995005300030042x.
[7]
Stolt, M.H.; Genthner, M.H.; Daniels, W.L.; Groover, V.A.; Nagle, S.; Haering, K.C. Comparison of soil and other environmental conditions in constructed and adjacent palustrine reference wetlands. Wetlands 2000, 20, 671–683.
[8]
Campbell, D.A.; Cole, C.A.; Brooks, R.P. A comparison of created and natural wetlands in Pennsylvania, USA. Wetl. Ecol. Manag. 2002, 10, 41–49.
[9]
Bruland, G.L.; Richardson, C.J. Comparison of soil organic matter in created, restored and paired natural wetlands in North Carolina. Wetl. Ecol. Manag. 2006, 14, 245–251, doi:10.1007/s11273-005-1116-z.
[10]
Acosta-Martinez, V.; Dowd, S.; Yung, S.; Allen, V. Tag encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biol. Biochem. 2008, 40, 2762–2770.
[11]
Shange, R.S.; Ankumah, R.O.; Ibekwe, A.M.; Zabawa, R.; Dowd, S.E. Distinct soil bacterial communities revealed under a diversely managed agroecosystem. PLoS One 2012, 7, e40338.
[12]
Dick, W.A.; Ali Tabatabai, M. Significance and Potential Uses of Soil Enzymes. In Soil Microbial Ecology: Applications in Agricultural and Environmental Management; Metting, F.B., Ed.; Marcel Dekker, Inc.: New York, NY, USA, 1992; pp. 95–127.
[13]
Acosta-Martínez, V.; Cruz, L.; Sotomayor-Ramirez, D.; Pérez-Alegría, L. Enzyme activities as affected by soil properties and land use in a tropical watershed. Appl. Soil Ecol. 2007, 35, 35–45, doi:10.1016/j.apsoil.2006.05.012.
[14]
Shange, R.S.; Ankumah, R.O.; Githinji, L.; Zabawa, R. Spatial assessment of selected soil properties within an industrial poultry production site. Air Soil Water Res. 2012, 5, 59–68.
[15]
Davidson, E.A.; Ackerman, I.L. Changes in soil carbon inventories following cultivation of previously untilled soils. Biogeochemistry 1993, 20, 161–193.
[16]
Mann, L.K. Changes in soil carbon after cultivation. Soil Sci. 1986, 142, 279–288, doi:10.1097/00010694-198611000-00006.
[17]
Schlesinger, W.H. Changes in Soil Carbon Storage and Associated Properties with Disturbance and Recovery. In The Changing Carbon Cycle: A Global Analysis; Trabalka, J.R., Reichle, D.E., Eds.; Springer-Verlag: Berlin, Germany, 1985; pp. 194–220.
[18]
Post, W.M.; Mann, L.K. Changes in Soil Organic Carbon and Nitrogen as a Result of Cultivation. In Soils and the Greenhouse Effect; Bouwman, A.F., Ed.; John Wiley & Sons: New York, NY, USA, 1990; pp. 401–406.
[19]
Mankolo, R.; Reddy, C.; Senwo, Z.; Nyakatawa, E.; Sajjala, S. Soil biochemical changes induced by poultry litter application and conservation tillage under cotton production systems. Agronomy 2012, 2, 187–198, doi:10.3390/agronomy2030187.
[20]
Song, Y.; Song, C.; Yang, G.; Miao, Y.; Wang, J.; Guo, Y. Changes in labile organic carbon fractions and soil enzyme activities after marshland reclamation and restoration in the Sanjiang Plain in Northeast China. Environ. Manag. 2012, 50, 418–426, doi:10.1007/s00267-012-9890-x.
[21]
McArthur, J.V. Bacteria as Biomonitors. In Bioassessment and Management of North American Fresh Water Wetlands; Rader, R.B., Batzer, D.P., Wissinger, S.A., Eds.; John Wiley & Sons: New York, NY, USA, 2001; pp. 249–261.
[22]
Van der Heijden, M.G.; Bardgett, R.D.; van Straalen, N.M. The unseen majority: Soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol. Lett. 2008, 3, 296–310, doi:10.1111/j.1461-0248.2007.01139.x.
[23]
Wright, A.L.; Reddy, K.R. Phosphorus lading effects on extracellular enzyme activity in Everglades wetland soils. Soil Sci. Soc. Am. J. 2001, 65, 588–595, doi:10.2136/sssaj2001.652588x.
[24]
Soil Survey of Macon County Alabama. Available online: http://soildatamart.nrcs.usda.gov/Manuscripts/AL087/0/Macon.pdf (accessed on 15 April 2013).
[25]
Tabatabai, M.A. Enzymes. In Methods of Soil Analysis, Part 2: Microbiological and Biochemical properties; Weaver, R.W., Augle, S., Bottomly, P.J., Bezdicek, D., Smith, S., Tabatabai, M.A., Wollum, A., Eds.; Soil Science Society of America: Madison, WI, USA, 1994; pp. 775–833.
[26]
Bandick, A.K.; Dick, R.P. Field management effects on soil enzyme activities. Soil Biol. Biochem. 1999, 31, 1471–1479, doi:10.1016/S0038-0717(99)00051-6.
[27]
Elsgaard, L.; Anderson, G.H.; Eriksen, J. Measurement of arylsulphatase activity in agricultural soils using a simplified assay. Soil Biol. Biochem. 2002, 34, 79–82, doi:10.1016/S0038-0717(01)00157-2.
[28]
Dowd, S.E.; Sun, Y.; Secor, P.R.; Rhoads, D.D.; Wolcott, B.M.; James, G.A.; Wolcott, R.D. Survey of bacterial diversity in chronic wounds using pyrosequencing, DGGE, and full ribosome shotgun sequencing. BMC Microbiol. 2008, 8, 43, doi:10.1186/1471-2180-8-43.
[29]
Dowd, S.E.; Sun, Y.; Wolcott, R.D.; Carroll, J.A. Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies: Bacterial diversity in the ileum of newly weaned Salmonella-infected pigs. Foodborne Pathog. Dis. 2008, 5, 459–472, doi:10.1089/fpd.2008.0107.
[30]
Gontcharova, V.; Youn, E.; Wolcott, R.D.; Hollister, E.B.; Gentry, T.J.; Dowd, S.E. Black Box Chimera Check (B2C2): A windows-based software for batch depletion of chimeras from bacterial 16S rRNA gene datasets. Open Microbiol. J. 2010, 4, 47–52, doi:10.2174/1874285801004010047.
[31]
Schloss, P.D.; Westcott, S.L.; Ryabin, T.; Hall, J.R.; Hartmann, M.; Hollister, E.B.; Lesniewski, R.A.; Oakley, B.B.; Parks, D.H.; Robinson, C.J.; et al. Introducing mothur: open source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 2009, 75, 7537–7541, doi:10.1128/AEM.01541-09.
Cole, J.R.; Chai, B.; Farris, R.J.; Wang, Q.; Kulam-Syed-Mohideen, A.S.; McGarrell, D.M.; Bandela, A.M.; Cardenas, E.; Garrity, G.M.; Tiedje, J.M. The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res. 2007, 35, D169–D172, doi:10.1093/nar/gkl889.
[34]
Chao, A.; Ma, M.C.; Yang, M.C.K. Stopping rules and estimation for recapture debugging with unequal failure rates. Biometrika 1993, 80, 193–201, doi:10.1093/biomet/80.1.193.
[35]
Chao, A. Nonparametric estimation of the number of classes in a population. Scand. J. Stat. 1984, 11, 265–270.
[36]
Clymo, R.S.; Reddaway, E.J.F. Productivity of Sphagnum (bog-moss) and peat accumulation. Hydrobiologia 1971, 12, 181–192.
[37]
Mausbach, M.J.; Richardson, J.L. Biogeochemical processes in hydric soil formation. Curr. T. Wetl. Biogeochem. 1994, 1, 68–127.
[38]
Pimentel, D.; Harvey, C.; Resosudarmo, P.; Sinclair, K.; Kunz, D.; McNair, M.; Crist, S.; Shpritz, L.; Fitton, L.; Sa.ouri, R.; et al. Environmental and economic costs soil erosion and conservation benefts. Science 1995, 267, 1117–1123, doi:10.1126/science.267.5201.1117.
[39]
Hartanto, H.; Prabhu, R.; Widayat, A.S.E.; Asdak, C. Factors affecting runoff and soil erosion: Plot-Level soil loss monitoring for assessing sustainability of forest management. For. Ecol. Manage 2003, 180, 361–374, doi:10.1016/S0378-1127(02)00656-4.
[40]
Gardner, T.; Acosta-Martinez, V.; Calderón, F.; Zobeck, T.; Baddock, M.; Van Pelt, R.; Senwo, Z.; Dowd, S.; Cox, S. Pyrosequencing reveals bacteria carried in different wind-eroded sediments. J. Environ. Qual 2011, 41, 744–53.
[41]
Spain, A.M.; Krumholz, L.R.; Elshahed, M.S. Abundance, composition, diversity and novelty of soil Proteobacteria. ISME J. 2009, 3, 992–1000, doi:10.1038/ismej.2009.43.
[42]
Kersters, K.; de Vos, P.; Gillis, M.; Swings, J.; Vandamme, P.; Stackebrandt, E. Introduction to the Proteobacteria. In The Prokaryotes: A Handbook on the Biology of Bacteria; Dwarkin, M., Falkow, S., Rosenberg, E., Schleifer, K.H., Stackebrandt, E., Eds.; Springer: New York, NY, USA, 2006; pp. 3–37.
[43]
Gardner, T.G.; Acosta-Martínez, V.; Senwo, Z.; Dowd, S.E. Soil rhizosphere microbial communities and enzyme activities under organic farming in Alabama. Diversity 2011, 3, 308–328.
[44]
Fierer, N.; Bradford, M.A.; Jackson, R.B. Toward an ecological classification of soil bacteria. Ecology 2007, 88, 1354–1364, doi:10.1890/05-1839.
[45]
Jangid, K.; Williams, M.A.; Franzluebbers, A.J.; Sanderlin, J.S.; Reeves, J.H.; Jenkins, M.B.; Endale, D.M.; Coleman, D.C.; Whitman, W.B. Relative impacts of land-use, management intensity and fertilization upon soil microbial community structure in agricultural systems. Soil Biol. Biochem. 2008, 40, 2843–2853, doi:10.1016/j.soilbio.2008.07.030.
[46]
Nacke, H.; Thurmer, A.; Wollherr, A.; Will, C.; Hodac, L.; Herold, N.; Sch？ning, I.; Schrumpf, M.; Daniel, R. Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils. PLoS One 2011, 6, e17000, doi:10.1371/journal.pone.0017000.
[47]
Acosta-Martínez, V.; Dowd, S.E.; Sun, Y.; Webster, D.; Allen, V.G. Pyrosequencing analysis for characterization of soil bacterial populations as affected by an integrated livestock-cotton production system. Appl. Soil Ecol. 2010, 45, 13–25, doi:10.1016/j.apsoil.2010.01.005.
[48]
Empadinhas, N.; da Costa, M.S. Diversity, biological roles and biosynthetic pathways for sugar-glycerate containing compatible solutes in bacteria and Archaea. Environ. Microbiol. 2011, 13, 2056–2077, doi:10.1111/j.1462-2920.2010.02390.x.
[49]
Bergmann, G.; Bates, S.; Eilers, K.; Lauber, C.; Caporaso, J.; Walters, W.; Knight, R.; Fierer, N. The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biol. Biochem. 2011, 43, 1450–1455, doi:10.1016/j.soilbio.2011.03.012.
Dedysh, S.N. Cultivating uncultured bacteria from northern wetlands: Knowledge gained and remaining gaps. Front. Microbiol. 2011, 2, 184, doi:10.3389/fmicb.2011.00184.
[52]
Janssen, P.H. Identifying the dominant soil bacteria taxa in libraries of 16S rRNA and 16S rRNA genes. Appl. Environ. Microbiol. 2006, 72, 1719–1728, doi:10.1128/AEM.72.3.1719-1728.2006.
[53]
Mendes, R.; Kruijt, M.; de Bruijn, I.; Dekkers, E.; van der Voort, M.; Schneider, J.M.; Piceno, Y.M.; DeSantis, F.Z.; Andersen, G.L.; Bakker, P.; et al. Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 2011, 332, 1097–1100, doi:10.1126/science.1203980.
[54]
Bardhan, S.; Jose, S.; Jenkins, M.A.; Webster, C.R.; Udawatta, R.P.; Stehn, S.E. Microbial community diversity and composition across a gradient of soil acidity in spruce–fir forests of the southern Appalachian Mountains. Appl. Soil Ecol. 2012, 61, 60–68, doi:10.1016/j.apsoil.2012.04.010.
[55]
Burke, R.A.; Molina, M.; Cox, J.E.; Osher, L.J.; Piccolo, M.C. Stable carbon isotope ratio and composition of microbial fatty acids in tropical soils. J. Environ. Qual. 2003, 32, 198–206.
[56]
Waldrop, M.P.; Balser, T.C.; Firestone, M.K. Linking microbial community composition to function in a tropical soil. Soil Biol. Biochem. 2000, 32, 1837–1846, doi:10.1016/S0038-0717(00)00157-7.
[57]
Hill, P.; Kristufek, V.; Dijfkhuizen, L.; Boddy, C.; Kroetsch, D.; van Elsas, J.D. Land use intensity controls actinobacterial community structure. Microb. Ecol. 2011, 61, 286–302, doi:10.1007/s00248-010-9752-0.
[58]
Hartman, W.H.; Richardson, C.J.; Vilgalys, R.; Bruland, G.L. Environmental and anthropogenic controls of bacterial communities in wetland soils. Proc. Natl. Acad. Sci. USA 2008, 105, 17842–17847, doi:10.1073/pnas.0808254105.
[59]
Lazzarini, A.; Cavaletti, L.; Toppo, G.; Marinelli, F. Rare genera of actinomycetes as potential producers of new antibiotics. Antonie van Leeuwenhoek 2000, 78, 399–405, doi:10.1023/A:1010287600557.
[60]
Lee, J.P.; Hwang, B.Y. Diversity of antifungal actinomycetes in various vegetative soils of Korea. Can. J. Microbiol. 2002, 48, 407–417, doi:10.1139/w02-025.
[61]
Bouizgarne, B.; El Hadrami, I.; Ouhdouch, Y. Novel production of isochainin by a strain of Streptomyces sp. isolated from rhizosphere soil of the indigenous Moroccan plant Argania. spinosa L.. World J. Microbiol. Biotechnol. 2006, 22, 423–429, doi:10.1007/s11274-005-9051-y.
[62]
Nurjasmi, R.; Widada, J. Diversity of actinomycetes at several forest types in Wanagama I Yogyakarta and their potency as a producer of antifungal compound. Indo J. Biotech. 2009, 14, 1196–1205.
[63]
Fierer, N.; Schimel, J.; Holden, P. Variations in microbial community composition through two soil depth profiles. Soil Biol. Biochem. 2003, 35, 167–176, doi:10.1016/S0038-0717(02)00251-1.
