Abstract
Soil microbial communities play a vital role in biogeochemical cycling and ecosystem functions at the aggregate scale. Soil fractionation methods can affect the interpretation of microbial spatial distribution and ecological processes in aggregates. However, there is a lack of comparative studies illustrating the differences between wet sieving and settling fractionation on soil aggregate microbial communities. In this study, we compared bacterial and fungal community composition and diversity within three soil aggregates sizes separated by wet sieving and settling tube apparatus. Settling fractionation increased the relative abundance of Verrucomicrobia and Planctomycetes by 80.1%-93.6% and 54.5%-100%, respectively, but reduced that of Actinobacteria and Firmicutes by 16.7%-36.9% and 41.4%-95.7% respectively, in the three aggregate size fractions in comparison with wet sieving. However, the relative abundance of major genus (relative abundance > 0.2%) rather than phylum of fungal communities were significantly different for the two fractionation methods (P < 0.05). Compared with wet sieving, settling fractionation resulted in the detection of significantly less bacterial diversity (decreased by 14.2-18.7% for OTU richness and 6.8-6.9% for Shannon index) but more fungal diversity (increased by 12.3-51.3% for OTU richness and 13.8-35.1% for Shannon index) in finest soil aggregates. Distinct aggregate-disrupting energy from settling fractionation and wet sieving resulted in different size distributions and soil physicochemical and biological properties, leading to the differentiation of microhabitats and microbial communities. Settling fractionation and wet sieving both revealed significant differences in microbial communities among aggregate size fractions (P < 0.05). Here, our findings highlight that wet sieving should be favored in numerous studies, while settling fractionation may prove particularly suitable for research within the context of erosion.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Almajmaie A, Hardie M, Acuna T, Birch C (2017) Evaluation of methods for determining soil aggregate stability. Soil Tillage Res 167:39–45. https://doi.org/10.1016/j.still.2016.11.003
Bach EM, Hofmockel KS (2014) Soil aggregate isolation method affects measures of intra-aggregate extracellular enzyme activity. Soil Biol Biochem 69:54–62. https://doi.org/10.1016/j.soilbio.2013.10.033
Bach EM, Williams RJ, Hargreaves SK, Yang F, Hofmockel KS (2018) Greatest soil microbial diversity found in micro-habitats. Soil Biol Biochem 118:217–226. https://doi.org/10.1016/j.soilbio.2017.12.018
Blaud A, Menon M, van der Zaan B, Lair GJ, Banwart SA (2017) Effects of Dry and Wet Sieving of Soil on Identification and Interpretation of Microbial Community Composition, in: advances in Agronomy. Academic Press Inc., pp 119–142. https://doi.org/10.1016/bs.agron.2016.10.006
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, bin Kang K, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu Y-X, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik Av, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson AD, Xu ZZ Zaneveld, J.R., Zhang, Y., Zhu, Q., Knight, R., Caporaso, J.G., 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 37, 852–857
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R (2011) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci 108(supplement1):4516–4522. https://doi.org/10.1073/pnas.1000080107
Clarke K, Green R (1988) Statistical design and analysis for a biological effects study. Mar Ecol Prog Ser 46:213–226. https://doi.org/10.3354/meps046213
R Core Team (2022) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/
Davinic M, Fultz LM, Acosta-Martinez V, Calderón FJ, Cox SB, Dowd SE, Allen VG, Zak JC, Moore-Kucera J (2012) Pyrosequencing and mid-infrared spectroscopy reveal distinct aggregate stratification of soil bacterial communities and organic matter composition. Soil Biol Biochem 46:63–72. https://doi.org/10.1016/j.soilbio.2011.11.012
Ducret A, Grangeasse C (2021) Recent progress in our understanding of peptidoglycan assembly in Firmicutes. Curr Opin Microbiol 60:44–50. https://doi.org/10.1016/J.MIB.2021.01.011
Edgar RC (2013) Highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10:996–998. https://doi.org/10.1038/nmeth.2604
Elliott ET (1986) Aggregate structure and Carbon, Nitrogen, and Phosphorus in native and cultivated soils. Soil Sci Soc Am J 50:627–633. https://doi.org/10.2136/sssaj1986.03615995005000030017x
Felde VJMNL, Schweizer SA, Biesgen D, Ulbrich A, Uteau D, Knief C, Graf-Rosenfellner M, Kögel-Knabner I, Peth S (2021) Wet sieving versus dry crushing: soil microaggregates reveal different physical structure, bacterial diversity and organic matter composition in a clay gradient. Eur J Soil Sci 72:810–828. https://doi.org/10.1111/ejss.13014
Gao X, Xie Y, Liu G, Liu B, Duan X (2015) Effects of soil erosion on soybean yield as estimated by simulating gradually eroded soil profiles. Soil Tillage Res 145:126–134. https://doi.org/10.1016/J.STILL.2014.09.004
Gao X, Hu Y, Sun Q, Du L, Duan P, Yao L, Guo S (2018) Erosion-induced carbon losses and CO2 emissions from Loess and Black soil in China. CATENA 171:533–540. https://doi.org/10.1016/j.catena.2018.08.001
Gao X, Li W, Salman A, Wang R, Du L, Yao L, Hu Y, Guo S (2020) Impact of topsoil removal on soil CO2 emission and temperature sensitivity in Chinese Loess Plateau. Sci Total Environ 708:135102. https://doi.org/10.1016/j.scitotenv.2019.135102
Gao X, Berhe AA, Hu Y, et al. (2023) Role of soil organic matter composition and microbial communities on SOC stability: insights from particle-size aggregates. J Soils Sediments 23:2878–2891. https://doi.org/10.1007/s11368-023-03528-5
Hawley N (1982) Settling velocity distribution of natural aggregates. J Geophys Res 87:9489–9498. https://doi.org/10.1029/JC087iC12p09489
He Y, Hu Y, Gao X, Wang R, Guo S, Li X (2020) Minor topography governing erosional distribution of SOC and temperature sensitivity of CO2 emissions: comparisons between concave and convex toposequence. J Soils Sediments 20:1906–1919. https://doi.org/10.1007/s11368-020-02575-6
Hu Y, Kuhn NJ (2016) Erosion-induced exposure of SOC to mineralization in aggregated sediment. CATENA 137:517–525. https://doi.org/10.1016/j.catena.2015.10.024
Hu Y, Fister W, Rüegg H-R, Kinnell PA, Kuhn NJ (2013) The use of equivalent quarz size and settling tube apparatus to fractionate soil aggregates by settling velocity. Geomorphology Techniques (Online Edition), British Society for Geomorphology 1, section, 1–9
Hu Y, Berhe AA, Fogel ML, Heckrath GJ, Kuhn NJ (2016) Transport-distance specific SOC distribution: does it skew erosion induced C fluxes? Biogeochemistry 128:339–351. https://doi.org/10.1007/s10533-016-0211-y
Jiang J, Guo S, Zhang Y, Liu Q, Wang R, Wang Z, Li N, Li R (2015) Changes in temperature sensitivity of soil respiration in the phases of a three-year crop rotation system. Soil Tillage Res 150:139–146. https://doi.org/10.1016/J.STILL.2015.02.002
Jiao S, Chen W, Wang J, Du N, Li Q, Wei G (2018) Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems. Microbiome 6:13. https://doi.org/10.1186/s40168-018-0526-0
Jiao P, Li Z, Yang L, He J, Chang X, Xiao H, Nie X, Tong D (2021) Bacteria are more sensitive than fungi to moisture in eroded soil by natural grass vegetation restoration on the Loess Plateau. Sci Total Environ 756:143899. https://doi.org/10.1016/j.scitotenv.2020.143899
Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M, Bates ST, Bruns TD, Bengtsson-Palme J, Callaghan TM (2013) Towards a unified paradigm for sequence‐based identification of fungi. Mol Ecol 22:5271–5277. https://doi.org/10.1111/mec.12481
Liao H, Gao S, Hao X, Qin F, Ma S, Chen W, Huang Q (2021) Soil aggregate isolation method affects interpretation of protistan community. Soil Biol Biochem 161:108388. https://doi.org/10.1016/j.soilbio.2021.108388
Lin Y, Ye G, Kuzyakov Y, Liu D, Fan J, Ding W (2019) Long-term manure application increases soil organic matter and aggregation, and alters microbial community structure and keystone taxa. Soil Biol Biochem 134:187–196. https://doi.org/10.1016/j.soilbio.2019.03.030
Loch RJ (2001) Settling velocity - a new approach to assessing soil and sediment properties. Comput Electron Agric 31:305–316. https://doi.org/10.1016/S0168-1699(00)00189-7
Lu G, Tian H, Tan X, Megharaj M, He Y, He W (2020) Distribution of soil nutrients and enzyme activities in different aggregates under two sieving methods. Soil Sci Soc Am J 84:331–344. https://doi.org/10.1002/saj2.20011
Magoč T, Salzberg SL (2011) Fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27:2957–2963. https://doi.org/10.1093/bioinformatics/btr507
Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17:10–12. https://doi.org/10.14806/EJ.17.1.200
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies JJ, Glockner FO, Gloeckner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590–D596. https://doi.org/10.1093/nar/gks1219
Rabbi SMF, Minasny B, McBratney AB, Young IM (2020) Microbial processing of organic matter drives stability and pore geometry of soil aggregates. Geoderma 360:114033. https://doi.org/10.1016/j.geoderma.2019.114033
Reichert JM, Norton LD, Favaretto N, Huang C, Blume E (2009) Settling velocity, Aggregate Stability, and Interrill Erodibility of soils varying in Clay Mineralogy. Soil Sci Soc Am J 73:1369–1377. https://doi.org/10.2136/sssaj2007.0067
Sainju UM (2006) Carbon and nitrogen pools in soil aggregates separated by dry and wet sieving methods. Soil Sci 171:937–949. https://doi.org/10.1097/01.ss0000228062.30958.5a
Seaton FM, George PBL, Lebron I, Jones DL, Creer S, Robinson DA (2020) Soil textural heterogeneity impacts bacterial but not fungal diversity. Soil Biol Biochem 144:107766. https://doi.org/10.1016/j.soilbio.2020.107766
Smith DP, Peay KG (2014) Sequence depth, not PCR replication, improves ecological inference from next generation DNA sequencing. PLoS One 9:e90234. https://doi.org/10.1371/journal.pone.0090234
Six J, Elliott ET, Paustian K (2000) Soil macroaggregate turnover and microaggregate formation: a mechanism for C sequestration under no-tillage agriculture. Soil Biol Biochem 32:2099–2103. https://doi.org/10.1016/S0038-0717(00)00179-6
Starr GC, Lal R, Malone R, Hothem D, Owens L, Kimble J (2000) Modeling soil carbon transported by water erosion processes. Land Degrad and Dev 11:83–91. https://doi.org/10.1002/(SICI)1099-145X(200001/02)11:1<83::AID-LDR370>3.0.CO;2-W
Trivedi P, Rochester IJ, Trivedi C, van Nostrand JD, Zhou J, Karunaratne S, Anderson IC, Singh BK (2015) Soil aggregate size mediates the impacts of cropping regimes on soil carbon and microbial communities. Soil Biol Biochem 91:169–181. https://doi.org/10.1016/j.soilbio.2015.08.034
Upton RN, Bach EM, Hofmockel KS (2019) Spatio-temporal microbial community dynamics within soil aggregates. Soil Biol Biochem 132:58–68. https://doi.org/10.1016/j.soilbio.2019.01.016
Wang R, Hu Y, Khan A, Du L, Wang Y, Hou F, Guo S (2021) Soil prokaryotic community structure and co-occurrence patterns on the fragmented Chinese Loess Plateau: effects of topographic units of a soil eroding catena. CATENA 198:105035. https://doi.org/10.1016/J.CATENA.2020.105035
Xiao L, Hu Y, Greenwood P, Kuhn NJ (2015) A combined Raindrop Aggregate Destruction Test-Settling Tube (RADT-ST) approach to identify the settling velocity of sediment. Hydrology 2:176–192. https://doi.org/10.3390/hydrology2040176
Acknowledgements
This work was supported by the National Natural Sciences Foundation of China (Nos. 42107360 and 42207408), the West Light Foundation of the Chinese Academy of Sciences (XAB2020YN03) and the Chinese Scholarship Council (No. 201906300021). The contributions of Yao He and Xihui Wu to soil physicochemical properties determination are also gratefully acknowledged. The authors are also greatly thankful to the two anonymous reviewers for their constructive comments.
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Conflict of interest
The authors declare no conflicts of interest.
Additional information
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic Supplementary Material
Below is the link to the electronic supplementary material.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Gao, X., Wang, R., Hu, Y. et al. Effects of Fractionation Methods on Soil Aggregate Microbial Community Composition: Settling vs. Wet Sieving. J Soil Sci Plant Nutr 24, 1160–1171 (2024). https://doi.org/10.1007/s42729-024-01618-y
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s42729-024-01618-y