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Influence of land use on bacterial and archaeal diversity and community structures in three natural ecosystems and one agricultural soil

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Abstract

Studying shifts in microbial communities under different land use can help in determining the impact of land use on microbial diversity. In this study, we analyzed four different land-use types to determine their bacterial and archaeal diversity and abundance. Three natural ecosystems, that is, wetland (WL), grassland (GL), and forest (FR) soils, and one agricultural soil, that is, tea plantation (TP) soil, were investigated to determine how land use shapes bacterial and archaeal diversity. For this purpose, molecular analyses, such as quantitative polymerase chain reaction (Q-PCR), 16S rRNA gene sequencing, and terminal restriction fragment length polymorphism (T-RFLP), were used. Soil physicochemical properties were determined, and statistical analyses were performed to identify the key factors affecting microbial diversity in these soils. Phylogenetic affiliations determined using the Ribosomal Database Project (RDP) database and T-RFLP revealed that the soils had differing bacterial diversity. WL soil was rich in only Proteobacteria, whereas GR soil was rich in Proteobacteria, followed by Actinobacteria. FR soil had higher abundance of Chloroflexi species than these soils. TP soil was rich in Actinobacteria, followed by Chloroflexi, Acidobacteria, Proteobacteria, and Firmicutes. The archaeal diversity of GL and FR soils was similar in that most of their sequences were closely related to Nitrososphaerales (Thaumarchaeota phylum). In contrast, WL soil, followed by TP soil, had greater archaeal diversity than other soils. Eight different archaeal classes were found in WL soil, and Pacearchaeota class was the richest one. The abundance of bacterial and archaeal 16S rRNA gene copies in WL and GL soils was significantly higher than that in FR and TP soils. Redundancy analysis showed that bacterial diversity was influenced by abiotic factors, e.g., total organic carbon and pH, whereas total nitrogen, pH, and cation exchange capacity (CEC) significantly affected archaeal community composition. Pearson correlation analysis showed that bacterial and archaeal 16S rRNA gene abundance had the highest correlation with clay content (r > 0.905, P < 0.01), followed by total-P, CEC, pH, and silt (%). These results will lead to more comprehensive understanding of how land use affects microbial distribution.

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References

  • Acosta-Martı´nez V, Dowd S, Sun Y, Allen VG (2008) Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biol Biochem 40:2762–2770

    Article  Google Scholar 

  • Acosta-Martı´nez V, Dowd SE, Sun Y, Wester D, Allen V (2010) Pyrosequencing analysis for characterization of soil bacterial populations as affected by an integrated livestock-cotton production system. Appl Soil Ecol 45:13–25

    Article  Google Scholar 

  • Aschenbach K, Conrad R, Rˇeháková K, Doležal J, Janatková K, Roey Angel R (2013) Methanogens at the top of the world: occurrence and potential activity of methanogens in newly deglaciated soils in high-altitude cold deserts in the Western Himalayas. Front Microbiol 4:359. doi:10.3389/fmicb.2013.00359

    Article  PubMed  PubMed Central  Google Scholar 

  • Bach L, Grytnes J, Halvorsen R, Ohlson M (2010) Tree influence on soil microbial community structure. Soil Biol Biochem 42:1934–1943

    Article  CAS  Google Scholar 

  • Balser TC, Wixon D, Moritz LK, Lipps L (2010) The microbiology of natural soils. In: Dixon GR TE (ed) Soil microbiology and sustainable crop production. Springer, Heidelberg, pp 27–58

    Chapter  Google Scholar 

  • Bates ST, Berg-Lyons D, Caporaso JG, Walters WA, Knight R, Fierer N (2011) Examining the global distribution of dominant archaeal populations in soil. ISME J 5:908–917

    Article  CAS  PubMed  Google Scholar 

  • Bjo’rnssona L, Hugenholtz P, Tyson GW, Blackall LL (2002) Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal. Microbiology 148:2309–2318

    Article  Google Scholar 

  • Butterly CR, McNeill AM, Baldock JA, Marschner P (2011) Rapid changes in carbon and phosphorus after rewetting of dry soil. Biol Fertil Soils 47:41–50

    Article  CAS  Google Scholar 

  • Çakmakç R, Dönmez MF, Ertürk Y, Erat M, Haznedar A, Sekban R (2010) Diversity and metabolic potential of culturable bacteria from the rhizosphere of Turkish tea grown in acidic soils. Plant Soil 332:299–318. doi:10.1007/s11104-010-0295-4

    Article  Google Scholar 

  • Cunliffe M, Schafer H, Harrison E, Cleave S, Upstill-Goddard R, Murrell JC (2008) Phylogenetic and functional gene analysis of the bacterial and archaeal communities associated with the surface microlayer of an estuary. ISME J 2:776–789

    Article  CAS  PubMed  Google Scholar 

  • Deng Y, Cui X, Herna´ndez M, Dumont MG (2014) Microbial diversity in Hummock and Hollow soils of three wetlands on the Qinghai-Tibetan plateau revealed by 16S rRNA pyrosequencing. PLoS One 9:e103115. doi:10.1371/journal.pone.0103115

    Article  PubMed  PubMed Central  Google Scholar 

  • Faoro H et al (2010) Influence of soil characteristics on the diversity of bacteria in the southern Brazilian Atlantic forest. Appl Environ Microbiol 76:4744–4749

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 103:626–631

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Goldfarb KC et al (2011) Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance. Front Microbiol 22:1–10

    Google Scholar 

  • Hackl E, Zechmeister-Boltenstern S, Bodrossy L, Sessitsch A (2004) Comparison of diversities and compositions of bacterial populations inhabiting natural forest soils. Appl Environ Microbiol 70:5057–5065

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kan J et al (2011) Archaea in Yellowstone Lake. ISME J 5:1784–1795

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kemnitz D, Kolb S, Conrad R (2007) High abundance of Crenarchaeota in a temperate acidic forest soil. FEMS Microbiol Ecol 60:442–448

    Article  CAS  PubMed  Google Scholar 

  • Keshri J, Mishra A, Jha B (2013) Microbial population index and community structure in saline–alkaline soil using gene targeted metagenomics. Microbiol Res 168:165–173

    Article  CAS  PubMed  Google Scholar 

  • Kim HM et al (2014) Bacterial community structure and soil properties of a subarctic tundra soil in Council, Alaska. FEMS Microbiol Ecol 89:465–475

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Konopka A (2009) What is microbial community ecology? ISME J 3:1223–1230

    Article  PubMed  Google Scholar 

  • Long XE, Yao HY, Wang J, Huang Y, Singh B, Zhu YG (2015) Community structure and soil pH determine chemoautotrophic carbon dioxide fixation in drained paddy soils. Environ Sci Technol 49:7152–7160

    Article  CAS  PubMed  Google Scholar 

  • Lu J, Idris U, Harmon B, Hofacre C, Maurer JJ, Lee MD (2003) Diversity and succession of the intestinal bacterial community of the maturing broiler chicken. Appl Environ Microbiol 69:6816–6824

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lupatini M, Jacques RJS, Antoniolli ZI, Suleiman AKA, Fulthorpe RR, Roesch LFW (2013) Land-use change and soil type are drivers of fungal and archaeal communities in the Pampa biome. World J Microbiol Biotechnol 29:223–233

    Article  CAS  PubMed  Google Scholar 

  • Lynch JM, Bragg E (1985) Microorganisms and soil aggregate stability. Adv Soil Sci 2:133–171

    Article  Google Scholar 

  • Müller T, Höper H (2004) Soil organic matter turnover as a function of the soil clay content: consequences for model applications. Soil Biol Biochem 36:877–888. doi:10.1016/j.soilbio.2003.12.015

    Article  Google Scholar 

  • Nacke H, Thu¨rmer A, Wollherr A, Will C, Hodac L et al (2011) Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils. PLos One. 6:e17000

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nannipieri R, Ascher J, Ceccherini MT, Landi L, Pietramellara G, Renella G (2003) Microbial diversity and soil functions. Euro. J Soil Sci 54:655–670

    Article  Google Scholar 

  • Olsen SR, Somers LE (1982) Phosphorus. In: K De Page AL (ed) Methods of soil analysis, vol 2. Soil Science Society of America, Madison, pp 403–448

    Google Scholar 

  • Pacchioni RG, Carvalho FM, Thompson CE et al (2014) Taxonomic and functional profiles of soil samples from Atlantic forest and Caatinga biomes in northeastern Brazil. Microbiol Open. 3:299–315

    Article  CAS  Google Scholar 

  • Pachiadaki MG, Kallionaki A, Dählmann A, De Lange GJ, Kormas KA (2011) Diversity and spatial distribution of prokaryotic communities along a sediment vertical profile of a deep-sea mud volcano. Microb Ecol 62:655–668

    Article  PubMed  Google Scholar 

  • Page A, Miller R, Keeney D (1982) Total carbon, organic carbon, and organic matter. In: K De Page AL (ed) Methods of soil analysis, vol 2. Soil Science Society of America, Madison, pp 539–579

    Google Scholar 

  • Rhoades JD (1982) Cation exchangeable capacity. In: M. R. In Pace AL KD (ed) Methods of soil analysis, part 2: chemical and microbiological properties, 2nd edn. American Society of Agronomy, Inc., Soil Science Society of America, Madison, pp 149–165

    Google Scholar 

  • Roesch LFW et al (2007) Pyrose-quencing enumerates and contrasts soil microbial diversity. ISME J 1:283–290

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rousk J et al (2010) Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J 4:1340–1351

    Article  PubMed  Google Scholar 

  • Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor

  • Scharpenseel HW (1993) Major carbon reservoirs of the pedosphere; source-sink relations; potential of D14C and δ13C as supporting methodologies. Water Air Soil Pollut 70:431–442

    Article  CAS  Google Scholar 

  • Shen JP, Cao P, Hu HW, He JZ (2013) Differential response of archaeal groups to land use change in an acidic red soil. Sci Total Environ 461:742–749

    Article  PubMed  Google Scholar 

  • Steenwerth KL, Jackson LE, Caldero´n FJ, Stromberg MR, Scow KM (2003) Soil microbial community composition and land use history in cultivated and grassland ecosystems in coastal California. Soil Biol Biochem 35:489–500

    Article  Google Scholar 

  • Stieglmeier M et al (2014) Nitrososphaera viennensis gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon from soil and a member of the archaeal phylum Thaumarchaeota. Int J Syst Evol Microbiol 64:2738–2752

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Suna H, Terhonena E, Koskinenb K, Paulinb L, Kasanena R, Asiegbua FO (2014) Bacterial diversity and community structure along different peat soilsin boreal forest. Appl Soil Ecol 74:37–45

    Article  Google Scholar 

  • Tupinambá DD et al (2016) Archaeal community changes associated with cultivation of Amazon Forest soil with oil palm. Archae 2016:1–14

    Article  Google Scholar 

  • Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naïve bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ward NL et al (2009) Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Appl Environ Microbiol 75:2046–2056

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ye G et al (2009) Distribution and diversity of bacteria and archaea in marine sediments affected by gas hydrates at Mississippi canyon in the Gulf of Mexico. Geomicrobiol J 26:370–381

    Article  CAS  Google Scholar 

  • Ying JY, Zhang LM, He JZ (2010) Putative ammonia-oxidizing bacteria and archaea in an acidic red soil with different land utilization patterns. Environ Microbiol Rep 2(2):304–312

    Article  CAS  PubMed  Google Scholar 

  • Yuan HZ, Ge T, Chen CY, O’Donnell AG, Wu JS (2012) Significant role for microbial autotrophy in the sequestration of soil carbon. Appl Environ Microbiol 78:2328–2336

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yuan HZ et al (2013) Effect of land use on the abundance and diversity of autotrophic bacteria as measured by ribulose-1,5-biphosphate carboxylase/oxygenase (RubisCO) large subunit gene abundance in soils. Biol Fertil Soils 49:609–616

    Article  CAS  Google Scholar 

  • Zhang L, Xu ZH (2008) Assessing bacterial diversity in soil. J Soil Sediment 8:379–388

    Article  CAS  Google Scholar 

  • Zhang Y et al (2014) Community structure and elevational diversity patterns of soil Acidobacteria. J Environ Sci 26:1717–1724. doi:10.1016/j.jes. 2014.06.012

    Article  Google Scholar 

Download references

Acknowledgements

This study was financially supported by the National Natural Science Foundation of China (41522107; 41503081), National Key Research and Development Program (2016YFE0101100), the CHINA-ASEAN Talented Young Scientist Visiting Program (2014–2015), and NSFC Research Fund for International Young Scientists (41450110432). We thank Public Service Technology Center, Institute of Subtropical Agriculture, Chinese Academy of Sciences for technical assistance and Biotechnology Research Department, Myanmar.

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Authors and Affiliations

  1. Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, Hunan, China

    Tin Mar Lynn, Qiong Liu, Yajun Hu, Hongzhao Yuan, Xiaohong Wu, Jinshui Wu & Tida Ge

  2. Changsha Observation and Research Station for Agricultural environment, Chinese Academy of Sciences, Changsha, 410125, China

    Tin Mar Lynn, Qiong Liu, Yajun Hu, Hongzhao Yuan, Jinshui Wu & Tida Ge

  3. University of Chinese Academy of Sciences, Beijing, China

    Qiong Liu

  4. Biotechnology Research Department, Ministry of Education, Kyaukse, 100301, Myanmar

    Aye Aye Khai

  5. Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, 410004, China

    Xiaohong Wu

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  1. Tin Mar Lynn
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Correspondence to Yajun Hu.

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Communicated by Erko Stackebrandt.

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Lynn, T.M., Liu, Q., Hu, Y. et al. Influence of land use on bacterial and archaeal diversity and community structures in three natural ecosystems and one agricultural soil. Arch Microbiol 199, 711–721 (2017). https://doi.org/10.1007/s00203-017-1347-4

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  • DOI: https://doi.org/10.1007/s00203-017-1347-4

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