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Carbon/nitrogen ratio as a major factor for predicting the effects of organic wastes on soil bacterial communities assessed by DNA-based molecular techniques

Environmental Science and Pollution Research volume 17, pages 807–815 (2010)Cite this article

Abstract

Background, aim, and scope

Current Australian legislation permits the beneficial application of grease trap waste (GTW) to agricultural soil, viewing it as a beneficial source of organic matter and soil conditioner containing no/low amounts of metals or pathogenic organisms. However, little is known about the influence of GTW on soil bacterial community. A field experiment was established at Menangle in south western Sydney in Australia to quantitatively assess the impacts of different types (GTW CO and GTW CL) and amounts of GTW application on the soil bacterial community and diversity. Furthermore, a municipal solid waste (MSW) compost was simultaneously examined to compare against the other organic wastes. Knowledge about the shifts in microbial community structure and diversity following the applications of organic wastes could help to evaluate the ecological consequences on the soil and thus to develop sound regulatory guidelines for the beneficial reuse of organic wastes in agricultural lands.

Materials and methods

Soil samples were collected from recycled organics plots treated with different types and quantity of organic wastes. The field experimental treatments included control (CK, without application of any organic wastes), low amount of GTW CO (COL), GTW CL (CLL), and MSW (ML), and high amounts of GTW CO (COH), GTW CL (CLH), and MSW compost (MH). Microbial DNA was extracted from soil samples and the 16S rRNA genes were polymerase chain reaction (PCR)-amplified. The PCR products were analyzed by denaturing gradient gel electrophoresis (DGGE), cloning, and sequencing. The bacterial community structures and diversity were assessed using the DGGE profiles and clone libraries constructed from the excised DGGE bands.

Results

DGGE-based analyses showed that application of the GTW CO, regardless of the amount applied, had significant negative effects on soil bacterial genotypic diversity and community structure compared with the control, while the applications of other organic wastes including the GTW CL and MSW had no clear effects. The effects of the rate of organic waste application on soil bacterial community characteristics varied with the types of organic wastes applied. Sequence-based analyses of 126 clones indicated that Proteobacteria (53.2%) was the dominant taxa at the experimental site, followed by Actinobacteria (9.5%), Bacteroidetes (7.9%), Firmicutes (7.9%), Gemmatimonadetes (5.6%), Chloroflexi (2.4%), Acidobacteria (1.6%) and the unclassified group (11.9%). In the COH treatment, Acidobacteria, Bacteroidetes, and Gemmatimonadetes were not detected; the percentages of Firmicutes, Proteobacteria, and Actinobacteria in the COH treatment were significantly different from those in CK. There is a significant positive correlation (r = 0.71, p = 0.002) between the C/N ratio of organic wastes and the bacterial genotypic communities.

Discussion

Both the type and the amount of GTW applied affected soil bacterial genotypic diversity and community structure. The different effects of various types of organic wastes on soil bacterial characteristics may be predicted by the differences in specific properties of organic wastes such as C/N ratio, as evidenced by the strong and significant positive relationship between the bacterial community distance and the environmental distance of C/N ratio. This also indicates that the C/N ratio of GTW applied can be a major driver for the shift in the soil bacterial community.

Conclusions

Our results revealed that the effects of organic wastes on soil bacterial communities varied with the types of organic wastes, and depending on the rate of application. Application of the GTW CO led to significant shifts in soil bacterial community diversity and structure. The effects of different types of organic wastes on the soil bacterial characteristics can be predicted by the differences of specific properties of organic wastes, such as the C/N ratio. Sequence-based analyses of 126 clones indicated that Proteobacteria was the dominant taxa at the experimental site.

Recommendations and perspectives

Our results have important implications for developing sound regulatory guidelines for the beneficial reuse of organic wastes, indicating that GTW CO and similar organic waste treatments may not be suitable for application in agricultural soils due to its significant negative effect on soil bacterial community.

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References

  • American Public Health Association (APHA), American Water Works Association, Water Environment Federation (2005) Standard Methods for the Examination of Water and Wastewater. 21st edition. American Public Health Association, Washington DC. Pp1368

    Google Scholar 

  • Bååth E, Díaz-Raviña M, Frostegård Å, Campbell CD (1998) Effect of metal-rich sludge amendments on the soil microbial community. Appl Environ Microbiol 64:238–245

    Google Scholar 

  • Bardgett RD, Freeman C, Ostle NJ (2008) Microbial contributions to climate change through carbon cycle feedbacks. ISME J 2:805–814

    Article  CAS  Google Scholar 

  • Bell T, Ager D, Song J-I, Newman JA, Thompson IP, Lilley AK, van der Gast CJ (2005a) Larger islands house more bacterial taxa. Science 308:1884

    Article  CAS  Google Scholar 

  • Bell T, Newman JA, Silverman BW, Turner SL, Lilley AK (2005b) The contribution of species richness and composition to bacterial services. Nature 436:1157–1160

    Article  CAS  Google Scholar 

  • Bundy JG, Paton GI, Campbell CD (2002) Microbial communities in different soil types do not converge after diesel contamination. J Appl Microbiol 92:276–288

    Article  CAS  Google Scholar 

  • Cardinale BJ, Srivastava DS, Duffy JE, Wright JP, Downing AL, Sankaran M, Jouseau C (2006) Effects of biodiversity on the functioning of trophic groups and ecosystems. Nature 443:989–992

    Article  CAS  Google Scholar 

  • Daniel R (2005) The metagenomics of soil. Nat Rev Micro 3:470–478

    Article  CAS  Google Scholar 

  • Enwall K, Nyberg K, Bertilsson S, Cederlund H, Stenstrom J, Hallin S (2007) Long-term impact of fertilization on activity and composition of bacterial communities and metabolic guilds in agricultural soil. Soil Biol Biochem 39:106–115

    Article  CAS  Google Scholar 

  • Gans J, Wolinsky M, Dunbar J (2005) Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309:1387–1390

    Article  CAS  Google Scholar 

  • Ge Y, He J-Z, Zhu Y-G, Zhang J-B, Xu Z, Zhang L-M, Zheng Y-M (2008a) Differences in soil bacterial diversity: driven by contemporary disturbances or historical contingencies? ISME J 2:254–264

    Article  CAS  Google Scholar 

  • Ge Y, Zhang J-B, Zhang L-M, Yang M, He J-Z (2008b) Long-term fertilization regimes affect bacterial community structure and diversity of an agricultural soil in northern China. J Soils Sediments 8:43–50

    Article  CAS  Google Scholar 

  • Girvan MS, Bullimore J, Pretty JN, Osborn AM, Ball AS (2003) Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Appl Environ Microbiol 69:1800–1809

    Article  CAS  Google Scholar 

  • He JZ, Xu ZH, Hughes J (2005) Analyses of soil fungal communities in adjacent natural forest and hoop pine plantation ecosystems of subtropical Australia using molecular approaches based on 18S rRNA genes. FEMS Microbiol Lett 247:91–100

    Article  CAS  Google Scholar 

  • He JZ, Xu ZH, Hughes J (2006) Molecular bacterial diversity of a forest soil under residue management regimes in subtropical Australia. FEMS Microbiol Ecol 55:38–47

    Article  CAS  Google Scholar 

  • Huber T, Faulkner G, Hugenholtz P (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20:2317–2319

    Article  CAS  Google Scholar 

  • Janssen PH (2006) Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 72:1719–1728

    Article  CAS  Google Scholar 

  • Naeem S, Li S (1997) Biodiversity enhances ecosystem reliability. Nature 390:507–509

    Article  CAS  Google Scholar 

  • Peacock AD, Mullen MD, Ringelberg DB, Tyler DD, Hedrick DB, Gale PM, White DC (2001) Soil microbial community responses to dairy manure or ammonium nitrate applications. Soil Biol Biochem 33:1011–1019

    Article  CAS  Google Scholar 

  • Ramette A (2007) Multivariate analyses in microbial ecology. FEMS Microbiol Ecol 62:142–160

    Article  CAS  Google Scholar 

  • Rashid MT, Voroney RP (2004) Land application of oily food waste and corn production on amended soils. Agron J 96:997–1004

    Article  Google Scholar 

  • Reche I, Pulido-Villena E, Morales-Baquero R, Casamayor EO (2005) Does ecosystem size determine aquatic bacterial richness? Ecology 86:1715–1722

    Article  Google Scholar 

  • Roesch LFW, Fulthorpe RR, Riva A, Casella G, Hadwin AKM, Kent AD, Daroub SH, Camargo FAO, Farmerie WG, Triplett EW (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1:283–290

    CAS  Google Scholar 

  • Ros M, Pascual JA, Garcia C, Hernandez MT, Insam H (2006) Hydrolase activities, microbial biomass and bacterial community in a soil after long-term amendment with different composts. Soil Biol Biochem 38:3443–3452

    Article  CAS  Google Scholar 

  • Saison C, Degrange V, Oliver R, Millard P, Commeaux C, Montange D, Le Roux X (2006) Alteration and resilience of the soil microbial community following compost amendment: effects of compost level and compost-borne microbial community. Environ Microbiol 8:247–257

    Article  CAS  Google Scholar 

  • Smit E, Leeflang P, Gommans S, van den Broek J, van Mil S, Wernars K (2001) Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Appl Environ Microbiol 67:2284–2291

    Article  CAS  Google Scholar 

  • Sun HY, Deng SP, Raun WR (2004) Bacterial community structure and diversity in a century-old manure-treated agroecosystem. Appl Environ Microbiol 70:5868–5874

    Article  CAS  Google Scholar 

  • Torsvik V, Salte K, Sørheim R, Goksøyr J (1990) Comparison of phenotypic diversity and DNA heterogeneity in a population of soil bacteria. Appl Environ Microbiol 56:776–781

    CAS  Google Scholar 

  • Torsvik V, Daae FL, Sandaa R-A, Øvreås L (1998) Novel techniques for analysing microbial diversity in natural and perturbed environments. J Biotechnol 64:53–62

    Article  CAS  Google Scholar 

  • Venables WN, Ripley BD (2002) Modern applied statistics with S. Springer, Berlin

    Google Scholar 

  • Witter E, Gong P, Bååth E, Marstorp H (2000) A study of the structure and metal tolerance of the soil microbiual community six years after cessation of sewage sludge. Environ Toxicol Chem 19:1983–1991

    Article  CAS  Google Scholar 

  • Xu Z, Chen CR (2006) Fingerprinting global climate change and forest management within rhizosphere carbon and nutrient cycling processes. Environ Sci Pollut Res 13:293–298

    Article  Google Scholar 

  • Yu Z, Morrison M (2004) Comparisons of different hypervariable regions of rrs genes for use in fingerprinting of microbial communities by PCR-denaturing gradient gel electrophoresis. Appl Environ Microbiol 70:4800–4806

    Article  CAS  Google Scholar 

  • Zhang L, Xu Z (2008) Assessing bacterial diversity in soil. J Soils Sediments 8:379–388

    Article  CAS  Google Scholar 

  • Zheng Y, Zhang L-M, Zheng Y-M, Di H, He J-Z (2008) Abundance and community composition of methanotrophs in a Chinese paddy soil under long-term fertilization practices. J Soils Sediments 8:406–414

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This research was jointly supported by the Australian Research Council, the Natural Science Foundation of China, the Chinese Academy of Sciences, and a New South Wales Government Treasury Enhancement Grant. The assistances of staff for soil sampling and data collecting from both Chinese and Australian sides are sincerely appreciated. The authors would also like to thank Ms. Marijke Heenan for her lab assistance and proofreading of this manuscript.

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Affiliations

  1. Centre for Forestry and Horticultural Research and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland, 4111, Australia

    Yuan Ge, Chengrong Chen, Zhihong Xu & Yan He

  2. Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China

    Yuan Ge & Ji-Zheng He

  3. Centre for Recycled Organics in Agriculture, NSW Department of Primary Industries, Richmond, NSW, 2753, Australia

    Simon M. Eldridge & Kwong Yin Chan

  4. College of Environmental and Natural Resource Sciences, Zhejiang University, Hangzhou, 310029, China

    Yan He

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  1. Yuan Ge
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  2. Chengrong Chen
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  3. Zhihong Xu
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  5. Kwong Yin Chan
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  6. Yan He
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Correspondence to Chengrong Chen or Ji-Zheng He.

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Ge, Y., Chen, C., Xu, Z. et al. Carbon/nitrogen ratio as a major factor for predicting the effects of organic wastes on soil bacterial communities assessed by DNA-based molecular techniques. Environ Sci Pollut Res 17, 807–815 (2010). https://doi.org/10.1007/s11356-009-0185-6

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  • DOI: https://doi.org/10.1007/s11356-009-0185-6

Keywords

  • Bacterial community
  • Bacterial diversity
  • Cloning and sequencing
  • Denaturing gradient gel electrophoresis
  • Organic waste
  • Soil