Long-Term Harvest Residue Retention Could Decrease Soil Bacterial Diversities Probably Due to Favouring Oligotrophic Lineages

  • Yaling Zhang
  • Manyun Zhang
  • Li Tang
  • Rongxiao Che
  • Hong Chen
  • Tim Blumfield
  • Sue Boyd
  • Mone Nouansyvong
  • Zhihong Xu
Soil Microbiology


Harvest residues contain large stores of carbon (C) and nitrogen (N) in forest plantations. Decomposing residues can release labile C and N into soil and thus provide substrates for soil bacterial communities. Previous studies showed that residue retention could increase soil C and N pools and activate bacterial communities in the short term (≤ 10 years). The current study examined the effects of a long-term (19-year) harvest residue retention on soil total and water and hot water extractable C and N pools, as well as bacterial communities via Illumina MiSeq sequencing. The experiment was established in a randomised complete block design with four replications, southeast Queensland of Australia, including no (R0), single (R1, 51 to 74 t ha−1 dry matter) and double quantities (R2, 140 t ha−1 dry matter) of residues retained. Generally, no significant differences existed in total C and N, as well as C and N pools extracted by water and hot water among the three treatments, probably due to negligible amounts of labile C and N released from harvest residues. Soil δ15N significantly decreased from R0 to R1 to R2, probably due to reduced N leaching with residue retention (P < 0.001). Residue retention increased the relative abundances of Actinobacteria (P = 0.016) and Spartobacteria (P < 0.001), whereas decreased Betaproteobacteria (P = 0.050). This favour for the oligotrophic groups probably caused the decrease in the bacterial diversity as revealed by Shannon index (P = 0.025). Hence, our study suggests that residue retention is not an appropriate management practice in the long term.


Forest plantation Residue retention Soil δ15Nuclear magnetic resonance Bacterial composition Bacterial diversity 

Supplementary material

248_2018_1162_MOESM1_ESM.docx (183 kb)
ESM 1 (DOCX 183 kb)
248_2018_1162_MOESM2_ESM.docx (17 kb)
ESM 2 (DOCX 17.2 kb)


  1. 1.
    Paquette A, Messier C (2010) The role of plantations in managing the world’s forests in the Anthropocene. Front Ecol Environ 8:27–34CrossRefGoogle Scholar
  2. 2.
    Hernández J, del Pino A, Salvo L, Arrarte G (2009) Nutrient export and harvest residue decomposition patterns of a Eucalyptus dunnii Maiden plantation in temperate climate of Uruguay. For Ecol Manag 258:92–99CrossRefGoogle Scholar
  3. 3.
    Nave LE, Vance ED, Swanston CW, Curtis PS (2010) Harvest impacts on soil carbon storage in temperate forests. For Ecol Manag 259:857–866CrossRefGoogle Scholar
  4. 4.
    Smaill SJ, Clinton P, Greenfield L (2008) Postharvest organic matter removal effects on FH layer and mineral soil characteristics in four New Zealand Pinus radiata plantations. For Ecol Manag 256:558–563CrossRefGoogle Scholar
  5. 5.
    Jones HS, Garrett LG, Beets PN, Kimberley MO, Oliver GR (2008) Impacts of harvest residue management on soil carbon stocks in a plantation forest. Soil Sci Soc Am J 72:1621–1627CrossRefGoogle Scholar
  6. 6.
    Smolander A, Kitunen V, Tamminen P, Kukkola M (2010) Removal of logging residue in Norway spruce thinning stands: long-term changes in organic layer properties. Soil Biol Biochem 42:1222–1228CrossRefGoogle Scholar
  7. 7.
    Eisenbies MH, Vance ED, Aust WM, Seiler JR (2009) Intensive utilization of harvest residues in southern pine plantations: quantities available and implications for nutrient budgets and sustainable site productivity. Bioenergy Res 2:90–98CrossRefGoogle Scholar
  8. 8.
    Robertson FA, Thorburn PJ (2007) Management of sugarcane harvest residues: consequences for soil carbon and nitrogen. Soil Res 45:13–23CrossRefGoogle Scholar
  9. 9.
    Simpson JA, Xu ZH, Smith T, Keay P, Osborne DO, Podberscek M (2000) Effects of site management in pine plantations on the coastal lowlands of subtropical Queensland, Australia. In: Nambiar EKS, Tiarks, A, Cossalter C, Ranger J (ed) Proceedings of the Workshop on Site Management and Productivity in Tropical Plantation Forests, 7–11 December 1999, Kerala, India. Center for International Forestry Research, Bogor, Indonesia, pp 73–81Google Scholar
  10. 10.
    Chen C, Xu Z (2005) Soil carbon and nitrogen pools and microbial properties in a 6-year-old slash pine plantation of subtropical Australia: impacts of harvest residue management. For Ecol Manag 206:237–247CrossRefGoogle Scholar
  11. 11.
    Butnor JR, Johnsen KH, Sanchez FG (2006) Whole-tree and forest floor removal from a loblolly pine plantation have no effect on forest floor CO2 efflux 10 years after harvest. For Ecol Manag 227:89–95CrossRefGoogle Scholar
  12. 12.
    Versini A, Nouvellon Y, Laclau JP et al (2013) The manipulation of organic residues affects tree growth and heterotrophic CO2 efflux in a tropical Eucalyptus plantation. For Ecol Manag 301:79–88CrossRefGoogle Scholar
  13. 13.
    Huang Z, Clinton PW, Davis MR (2011a) Post-harvest residue management effects on recalcitrant carbon pools and plant biomarkers within the soil heavy fraction in Pinus radiata plantations. Soil Biol Biochem 43:404–412CrossRefGoogle Scholar
  14. 14.
    Huang Z, Clinton PW, Davis MR, Yang Y (2011b) Impacts of plantation forest management on soil organic matter quality. J Soils Sediments 11:1309–1316CrossRefGoogle Scholar
  15. 15.
    Kumaraswamy S, Mendham D, Grove T, O’Connell A, Sankaran K, Rance S (2014) Harvest residue effects on soil organic matter, nutrients and microbial biomass in eucalypt plantations in Kerala, India. For Ecol Manag 328:140–149CrossRefGoogle Scholar
  16. 16.
    Blumfield TJ, Xu Z, Saffigna PG (2004) Carbon and nitrogen dynamics under windrowed residues during the establishment phase of a second-rotation hoop pine plantation in subtropical Australia. For Ecol Manag 200:279–291CrossRefGoogle Scholar
  17. 17.
    Courty PE, Buée M, Diedhiou AG, Frey-Klett P, Le Tacon F, Rineau F, Turpault MP, Uroz S, Garbaye J (2010) The role of ectomycorrhizal communities in forest ecosystem processes: new perspectives and emerging concepts. Soil Biol Biochem 42:679–698CrossRefGoogle Scholar
  18. 18.
    Falkowski PG, Fenchel T, Delong EF (2008) The microbial engines that drive Earth’s biogeochemical cycles. Science 320:1034–1039CrossRefPubMedGoogle Scholar
  19. 19.
    Semenov AV, e Silva MCP, Szturc-Koestsier AE, Schmitt H, Salles JF, van Elsas JD (2012) Impact of incorporated fresh 13C potato tissues on the bacterial and fungal community composition of soil. Soil Biol Biochem 49:88–95CrossRefGoogle Scholar
  20. 20.
    Su P, Lou J, Brookes PC, Luo Y, He Y, Xu J (2015) Taxon-specific responses of soil microbial communities to different soil priming effects induced by addition of plant residues and their biochars. J Soils Sediments 17:1–11Google Scholar
  21. 21.
    Fernandez AL, Sheaffer CC, Wyse DL, Staley C, Gould TJ, Sadowsky MJ (2016) Structure of bacterial communities in soil following cover crop and organic fertilizer incorporation. Appl Microbiol Biotechnol 100:9331–9341CrossRefPubMedGoogle Scholar
  22. 22.
    Wang J, Li X, Zhu A, Zhang X, Zhang H, Liang W (2012) Effects of tillage and residue management on soil microbial communities in North China. Plant Soil Environ 58:28–33CrossRefGoogle Scholar
  23. 23.
    Ceja-Navarro JA, Rivera FN, Patiño-Zúñiga L, Govaerts B, Marsch R, Vila-Sanjurjo A, Dendooven L (2010) Molecular characterization of soil bacterial communities in contrasting zero tillage systems. Plant Soil 329:127–137CrossRefGoogle Scholar
  24. 24.
    De la Cruz-Barrón M, Cruz-Mendoza A, Navarro-Noya YE, Ruiz-Valdiviezo VM, Ortíz-Gutiérrez D, Ramírez-Villanueva DA, Luna-Guido M, Thierfelder C, Wall PC, Verhulst N (2017) The bacterial community structure and dynamics of carbon and nitrogen when maize (Zea mays L.) and its neutral detergent fibre were added to soil from Zimbabwe with contrasting management practices. Microb Ecol 73:135–152CrossRefPubMedGoogle Scholar
  25. 25.
    Navarro-Noya YE, Gómez-Acata S, Montoya-Ciriaco N, Rojas-Valdez A, Suárez-Arriaga MC, Valenzuela-Encinas C, Jiménez-Bueno N, Verhulst N, Govaerts B, Dendooven L (2013) Relative impacts of tillage, residue management and crop-rotation on soil bacterial communities in a semi-arid agroecosystem. Soil Biol Biochem 65:86–95CrossRefGoogle Scholar
  26. 26.
    Negassa WC, Guber AK, Kravchenko AN, Marsh TL, Hildebrandt B, Rivers ML (2015) Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria. PLoS One 10:e0123999CrossRefPubMedPubMedCentralGoogle Scholar
  27. 27.
    Mathers NJ, Xu Z (2003) Solid-state 13C NMR spectroscopy: characterization of soil organic matter under two contrasting residue management regimes in a 2-year-old pine plantation of subtropical Australia. Geoderma 114:19–31CrossRefGoogle Scholar
  28. 28.
    Mathers NJ, Mendham DS, O’Connell AM, Grove TS, Xu Z, Saffigna PG (2003) How does residue management impact soil organic matter composition and quality under Eucalyptus globulus plantations in southwestern Australia? For Ecol Manag 179:253–267CrossRefGoogle Scholar
  29. 29.
    Simpson JA, Smith TE, Keay PT, Osborne DO, Xu ZH, Podberscek MI (2004) Impacts of inter-rotation site management on tree growth and soil properties in the first 6.4 years of a hybrid pine plantation in subtropical Australia. In: Nambiar EKS, Ranger J, Tiarks A, Toma T (ed) Site management and productivity in tropical plantation forests: Proceedings of workshops in Congo July 2001 and China February 2003, pp 139–149Google Scholar
  30. 30.
    Simpson JA (1998) Site specific fertilizer requirements of tropical pine plantations. In: Schulte A, Ruhiyat D (eds) Soils of tropical forest ecosystems. Springer Verlag, HeidelbergGoogle Scholar
  31. 31.
    Skjemstad J, Clarke P, Taylor J, Oades J, Newman R (1994) The removal of magnetic materials from surface soils—a solid state 13C CP/MAS NMR study. Soil Res 32:1215–1229CrossRefGoogle Scholar
  32. 32.
    Giovannoni SJ (1991) The polymerase chain reaction. In: Stackebrandt E, Goodfellow MD (eds) Nucleic acid techniques in bacterial systematics1st edn. Wiley, New York, pp 177–203Google Scholar
  33. 33.
    Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow MD (eds) Nucleic acid techniques in bacterial systematics1st edn. Wiley, New York, pp 115–175Google Scholar
  34. 34.
    Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6:1621–1624CrossRefPubMedPubMedCentralGoogle Scholar
  35. 35.
    Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461CrossRefPubMedGoogle Scholar
  36. 36.
    Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10:996–998CrossRefPubMedGoogle Scholar
  37. 37.
    Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336CrossRefPubMedPubMedCentralGoogle Scholar
  38. 38.
    DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodi EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72:5069–5072CrossRefPubMedPubMedCentralGoogle Scholar
  39. 39.
    Tutua SS (2009) Residue management and carbon and nutrient cycling in exotic pine plantations of Southeast Queensland. Dissertation, Giffith UniversityGoogle Scholar
  40. 40.
    Blumfield TJ, Xu Z, Prasolova NV, Mathers NJ (2006) Effect of overlying windrowed harvest residues on soil carbon and nitrogen in hoop pine plantations of subtropical Australia. J Soils Sediments 6:243–248CrossRefGoogle Scholar
  41. 41.
    Olsson BA, Staaf H, Lundkvist H, Bengtsson J, Kaj R (1996) Carbon and nitrogen in coniferous forest soils after clear-felling and harvests of different intensity. For Ecol Manag:19–32Google Scholar
  42. 42.
    Mendham D, O’connell A, Grove T, Rance S (2003) Residue management effects on soil carbon and nutrient contents and growth of second rotation eucalypts. For Ecol Manag 181:357–372CrossRefGoogle Scholar
  43. 43.
    Hyvönen R, Olsson BA, Lundkvist H, Staaf H (2000) Decomposition and nutrient release from Picea abies (L.) Karst. and Pinus sylvestris L. logging residues. For Ecol Manag 126:97–112CrossRefGoogle Scholar
  44. 44.
    Krankina ON, Harmon ME, Griazkin AV (1999) Nutrient stores and dynamics of woody detritus in a boreal forest: modeling potential implications at the stand level. Can J For Res 29:20–32CrossRefGoogle Scholar
  45. 45.
    Bai SH, Reverchon F, Xu CY, Xu Z, Blumfield TJ, Zhao H, Van Zwieten L, Wallace HM (2015) Wood biochar increases nitrogen retention in field settings mainly through abiotic processes. Soil Biol Biochem 90:232–240CrossRefGoogle Scholar
  46. 46.
    Ibell PT, Xu Z, Blumfield TJ (2010) Effects of weed control and fertilization on soil carbon and nutrient pools in an exotic pine plantation of subtropical Australia. J Soils Sediments 10:1027–1038CrossRefGoogle Scholar
  47. 47.
    Ibell PT, Xu Z, Blumfield TJ (2013) The influence of weed control on foliar δ15N, δ13C and tree growth in an 8 year-old exotic pine plantation of subtropical Australia. Plant Soil 369:199–217CrossRefGoogle Scholar
  48. 48.
    Wang Y, Xu Z, Zheng J, Abdullah KM, Zhou Q (2015) δ15N of soil nitrogen pools and their dynamics under decomposing leaf litters in a suburban native forest subject to repeated prescribed burning in southeast Queensland, Australia. J Soils Sediments 15:1063–1074CrossRefGoogle Scholar
  49. 49.
    Palviainen M, Finér L, Laiho R, Shorohova E, Kapitsa E, Vanha-Majamaa I (2010) Carbon and nitrogen release from decomposing Scots pine, Norway spruce and silver birch stumps. For Ecol Manag 259:390–398CrossRefGoogle Scholar
  50. 50.
    Nierop KG, Verstraten JM, Tietema A, Westerveld JW, Wartenbergh PE (2006) Short-and long-term tannin induced carbon, nitrogen and phosphorus dynamics in Corsican pine litter. Biogeochemistry 79:275–296CrossRefGoogle Scholar
  51. 51.
    de Gannes V, Eudoxie G, Hickey WJ (2013) Prokaryotic successions and diversity in composts as revealed by 454-pyrosequencing. Bioresour Technol 133:573–580CrossRefPubMedGoogle Scholar
  52. 52.
    Ramirez-Villanueva DA, Bello-López JM, Navarro-Noya YE, Luna-Guido M, Verhulst N, Govaerts B, Dendooven L (2015) Bacterial community structure in maize residue amended soil with contrasting management practices. Appl Soil Ecol 90:49–59CrossRefGoogle Scholar
  53. 53.
    Wallenstein MD, McMahon S, Schimel J (2007) Bacterial and fungal community structure in Arctic tundra tussock and shrub soils. FEMS Microbiol Ecol 59:428–435CrossRefPubMedGoogle Scholar
  54. 54.
    Bernard L, Mougel C, Maron PA, Nowak V, Lévêque J, Henault C, Haichar FZ, Berge O, Marol C, Balesdent J (2007) Dynamics and identification of soil microbial populations actively assimilating carbon from 13C-labelled wheat residue as estimated by DNA-and RNA-SIP techniques. Environ Microbiol 9:752–764CrossRefPubMedGoogle Scholar
  55. 55.
    Fierer N, Bradford MA, Jackson RB (2007) Toward an ecological classification of soil bacteria. Ecology 88:1354–1364CrossRefPubMedGoogle Scholar
  56. 56.
    Book AJ, Lewin GR, McDonald BR, Takasuka TE, Doering DT, Adams AS, Blodgett JA, Clardy J, Raffa KF, Fox BG (2014) Cellulolytic Streptomyces strains associated with herbivorous insects share a phylogenetically linked capacity to degrade lignocellulose. Appl Environ Microbiol 80:4692–4701CrossRefPubMedPubMedCentralGoogle Scholar
  57. 57.
    Hartmann M, Howes CG, VanInsberghe D, Yu H, Bachar D, Christen R, Nilsson RH, Hallam SJ, Mohn WW (2012) Significant and persistent impact of timber harvesting on soil microbial communities in northern coniferous forests. ISME J 6:2199–2218CrossRefPubMedPubMedCentralGoogle Scholar
  58. 58.
    Jenkins SN, Rushton SP, Lanyon CV, Whiteley AS, Waite IS, Brookes PC, Kemmitt S, Evershed RP, O’Donnell AG (2010) Taxon-specific responses of soil bacteria to the addition of low level C inputs. Soil Biol Biochem 42:1624–1631CrossRefGoogle Scholar
  59. 59.
    Khodadad CL, Zimmerman AR, Green SJ, Uthandi S, Foster JS (2011) Taxa-specific changes in soil microbial community composition induced by pyrogenic carbon amendments. Soil Biol Biochem 43:385–392CrossRefGoogle Scholar
  60. 60.
    Fierer N, Ladau J, Clemente JC, Leff JW, Owens SM, Pollard KS, Knight R, Gilbert JA, McCulley RL (2013) Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science 342:621–624CrossRefPubMedGoogle Scholar
  61. 61.
    Che R, Wang W, Zhang J, Nguyen TT, Tao J, Wang F, Wang Y, Xu Z, Cui X (2016) Assessing soil microbial respiration capacity using rDNA-or rRNA-based indices: a review. J Soils Sediments 16:2698–2708CrossRefGoogle Scholar
  62. 62.
    Kuffner M, Hai B, Rattei T, Melodelima C, Schloter M, Zechmeister-Boltenstern S, Jandl R, Schindlbacher A, Sessitsch A (2012) Effects of season and experimental warming on the bacterial community in a temperate mountain forest soil assessed by 16S rRNA gene pyrosequencing. FEMS Microbiol Ecol 82:551–562CrossRefPubMedPubMedCentralGoogle Scholar
  63. 63.
    Da Rocha UN, Andreote FD, de Azevedo JL, van Elsas JD, van Overbeek LS (2010) Cultivation of hitherto-uncultured bacteria belonging to the Verrucomicrobia subdivision 1 from the potato (Solanum tuberosum L.) rhizosphere. J Soils Sediments 10:326–339CrossRefGoogle Scholar
  64. 64.
    Lin YT, Huang YJ, Tang SL, Whitman WB, Coleman DC, Chiu CY (2010) Bacterial community diversity in undisturbed perhumid montane forest soils in Taiwan. Microb Ecol 59:369–378CrossRefPubMedGoogle Scholar
  65. 65.
    Meng H, Li K, Nie M, Wan JR, Quan ZX, Fang CM, Chen JK, Gu JD, Li B (2013) Responses of bacterial and fungal communities to an elevation gradient in a subtropical montane forest of China. Appl Microbiol Biotechnol 97:2219–2230CrossRefPubMedGoogle Scholar
  66. 66.
    Helfrich M, Ludwig B, Buurman P, Flessa H (2006) Effect of landuse on the composition of soil organic matter in density and aggregate fractions as revealed by solid-state 13C NMR spectroscopy. Geoderma 136:331–341CrossRefGoogle Scholar
  67. 67.
    Fernandez A (2015) Effects of cover crop and fertilizer incorporation on the structure and function of microbial communities in soils under long-term organic management. Dissertation, University of Minnesota.Google Scholar
  68. 68.
    Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, Knight R (2012) Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J 6:1007–1017CrossRefPubMedGoogle Scholar

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Authors and Affiliations

  1. 1.Environmental Futures Research Institute, School of Natural SciencesGriffith UniversityBrisbaneAustralia
  2. 2.University of Chinese Academy of SciencesBeijingChina
  3. 3.Soil and Environment Analysis Centre, Institute of Soil ScienceChinese Academy of SciencesNanjingChina
  4. 4.Centre for Forestry and Horticultural ResearchGriffith UniversityNathanAustralia
  5. 5.School of Biomolecular and Physical SciencesGriffith UniversityNathanAustralia

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