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Regulating soil bacterial diversity, community structure and enzyme activity using residues from golden apple snails

  • 1.

    Duchene, O., Vian, J.-F. & Celette, F. Intercropping with legume for agroecological cropping systems: complementarity and facilitation processes and the importance of soil microorganisms. A review. Agric. Ecosyst. Environ. 240, 148–161. https://doi.org/10.1016/j.agee.2017.02.019 (2017).

    Article  Google Scholar 

  • 2.

    Tilman, D., Cassman, K. G., Matson, P. A., Naylor, R. & Polasky, S. Agricultural sustainability and intensive production practices. Nature 418, 671. https://doi.org/10.1038/nature01014 (2002).

    ADS  CAS  Article  Google Scholar 

  • 3.

    Duchene, O. et al. Integrating multipurpose perennial grains crops in Western European farming systems. Agric. Ecosyst. Environ. 284, 106591. https://doi.org/10.1016/j.agee.2019.106591 (2019).

    Article  Google Scholar 

  • 4.

    Karamesouti, M. et al. Land-use and land degradation processes affecting soil resources: evidence from a traditional Mediterranean cropland (Greece). CATENA 132, 45–55. https://doi.org/10.1016/j.catena.2015.04.010 (2015).

    Article  Google Scholar 

  • 5.

    Guo, J. H. et al. Significant acidification in major Chinese croplands. Science 327, 1008–1010. https://doi.org/10.1126/science.1182570 (2010).

    ADS  CAS  Article  Google Scholar 

  • 6.

    Brinkmann, N. et al. Intensive tropical land use massively shifts soil fungal communities. Sci. Rep. 9, 3403. https://doi.org/10.1038/s41598-019-39829-4 (2019).

    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 7.

    Muhammed, S. E. et al. Impact of two centuries of intensive agriculture on soil carbon, nitrogen and phosphorus cycling in the UK. Sci. Total Environ. 634, 1486–1504. https://doi.org/10.1016/j.scitotenv.2018.03.378 (2018).

    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 8.

    Galloway, J. N. et al. Transformation of the nitrogen cycling: recent trends, questions, and potential solutions. Science 320, 889–892. https://doi.org/10.1126/science.1136674 (2008).

    ADS  CAS  Article  Google Scholar 

  • 9.

    Zhao, Y. et al. Soil acidification in China: is controlling SO2 emissions enough? Environ. Sci. Technol. 43, 8021–8026. https://doi.org/10.1021/es901430n (2009).

    ADS  CAS  Article  Google Scholar 

  • 10.

    Alonso, F. P., Arias, J. S., Fernández, R. O., Fernández, P. G. & Serrano, R. E. Agronomic implications of the supply of lime and gypsum by-products to palexerults from western Spain. Soil Sci. 171, 65–81. https://doi.org/10.1097/01.ss.0000200557.253069.50 (2006).

    ADS  CAS  Article  Google Scholar 

  • 11.

    Chiu, Y.-W. et al. Alterations of biochemical indicators in hepatopancreas of the golden apple snail, Pomacea canaliculata, from paddy fields in Taiwan. J. Environ. Biol. 35, 667–673 (2014).

    PubMed  PubMed Central  Google Scholar 

  • 12.

    Dong, S., Zheng, G., Yu, X. & Fu, C. Biological control of golden apple snail, Pomacea canaliculata by Chinese soft-shelled turtle, Pelodiscus sinensis in the wild rice, Zizania latifolia field. Sci. Agric. 69, 142–146. https://doi.org/10.1590/S0103-90162012000200009 (2012).

    Article  Google Scholar 

  • 13.

    Guo, J., Zhang, J.-E., Zhao, B., Luo, M. & Zhang, C. The role of spotted green pufferfish Tetraodon nigroviridis in controlling golden apple snail Pomacea canaliculata: an effective biological control approach involving a new agent. Biocontrol Sci. Technol. 26, 1100–1112. https://doi.org/10.1080/09583157.2016.1185511 (2016).

    Article  Google Scholar 

  • 14.

    Olivier, H. M., Jenkins, J. A., Berhow, M. & Carter, J. A pilot study testing a natural and a synthetic molluscicide for controlling invasive apple snails (Pomacea maculata). Bull. Environ. Contam. Toxicol. 96, 289–294. https://doi.org/10.1007/s00128-015-1709-z (2016).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 15.

    Litsinger, J. & Estano, D. B. Management of the golden apple snail Pomacea canaliculata (Lamarck) in rice. Crop Prot. 12, 363–370. https://doi.org/10.1016/0261-2194(93)90079-X (1993).

    Article  Google Scholar 

  • 16.

    Teo, S. S. Evaluation of different duck varieties for the control of the golden apple snail (Pomacea canaliculata) in transplanted and direct seeded rice. Crop Prot. 20, 599–604. https://doi.org/10.1016/S0261-2194(01)00029-1 (2001).

    Article  Google Scholar 

  • 17.

    Halwart, M. The golden apple snail Pomacea canaliculata in Asian rice farming systems: present impact and future threat. Int. J. Pest Manag. 40, 199–206. https://doi.org/10.1080/09670879409371882 (1994).

    Article  Google Scholar 

  • 18.

    Serra, A. The use of golden snail Pomacea Sp. as animal feed in the Philippines. Tropicultura 15, 40–43 (1997).

    Google Scholar 

  • 19.

    Wang, J. et al. Using golden apple snail to mitigate its invasion and improve soil quality: a biocontrol approach. Environ. Sci. Pollut. Res. 27, 14903–14914. https://doi.org/10.1007/s11356-020-07998-9 (2020).

    CAS  Article  Google Scholar 

  • 20.

    Haynes, R. J. & Zhou, Y.-F. Effect of pH and added slag on the extractability of Si in two Si-deficient sugarcane soils. Chemosphere 193, 431–437. https://doi.org/10.1016/j.chemosphere.2017.10.175 (2018).

    ADS  CAS  Article  PubMed  Google Scholar 

  • 21.

    Rousk, J. et al. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 4, 1340–1351. https://doi.org/10.1038/ismej.2010.58 (2010).

    Article  PubMed  Google Scholar 

  • 22.

    Lauber, C. L., Strickland, M. S., Bradford, M. A. & Fierer, N. The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biol. Biochem. 40, 2407–2415. https://doi.org/10.1016/j.soilbio.2008.05.021 (2008).

    CAS  Article  Google Scholar 

  • 23.

    Ramirez, K. S., Craine, J. M. & Fierer, N. Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes. Glob. Change Biol. 18, 1918–1927. https://doi.org/10.1111/j.1365-2486.2012.02639.x (2012).

    ADS  Article  Google Scholar 

  • 24.

    Campbell, B. J., Polson, S. W., Hanson, T. E., Mack, M. C. & Schuur, E. A. The effect of nutrient deposition on bacterial communities in Arctic tundra soil. Environ. Microbiol. 12, 1842–1854. https://doi.org/10.1111/j.1462-2920.2010.02189.x (2010).

    CAS  Article  PubMed  Google Scholar 

  • 25.

    Yu, H. et al. Responses of soil biological traits and bacterial communities to nitrogen fertilization mediate maize yields across three soil types. Soil Till. Res. 185, 61–69. https://doi.org/10.1016/j.still.2018.08.017 (2019).

    Article  Google Scholar 

  • 26.

    Fierer, N. & Jackson, R. B. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. 103, 626–631. https://doi.org/10.1073/pnas.0507535103 (2006).

    ADS  CAS  Article  PubMed  Google Scholar 

  • 27.

    Roesch, L. F. W. et al. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 1, 283–290. https://doi.org/10.1038/ismej.2007.53 (2007).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 28.

    Waring, B. G., Weintraub, S. R. & Sinsabaugh, R. L. Ecoenzymatic stoichiometry of microbial nutrient acquisition in tropical soils. Biogeochemistry 117, 101–113. https://doi.org/10.1007/s10533-013-9849-x (2014).

    CAS  Article  Google Scholar 

  • 29.

    Baldrian, P. Microbial enzyme-catalyzed processes in soils and their analysis. Plant Soil Environ. 55, 370–378 (2009).

    CAS  Article  Google Scholar 

  • 30.

    Jian, S. et al. Soil extracellular enzyme activities, soil carbon and nitrogen storage under nitrogen fertilization: a meta-analysis. Soil Biol. Biochem. 101, 32–43 (2016).

    CAS  Article  Google Scholar 

  • 31.

    Frankenberger, W. & Bingham, F. Influence of salinity on soil enzyme activities 1. Soil Sci. Soc. Am. J. 46, 1173–1177. https://doi.org/10.2136/sssaj1982.03615995004600060011x (1982).

    ADS  CAS  Article  Google Scholar 

  • 32.

    Wang, Y. et al. The influence of soil heavy metals pollution on soil microbial biomass, enzyme activity, and community composition near a copper smelter. Ecotoxicol. Environ. Saf. 67, 75–81. https://doi.org/10.1016/j.ecoenv.2006.03.007 (2007).

    CAS  Article  Google Scholar 

  • 33.

    Camenzind, T., Hättenschwiler, S., Treseder, K. K., Lehmann, A. & Rillig, M. C. Nutrient limitation of soil microbial processes in tropical forests. Ecol. Monogr. 88, 4–21. https://doi.org/10.1002/ecm.1279 (2018).

    Article  Google Scholar 

  • 34.

    Alvarez, G. et al. Catalytic power of enzymes decreases with temperature: New insights for understanding soil C cycling and microbial ecology under warming. Glob. Change Biol. 24, 4238–4250. https://doi.org/10.1111/gcb.14281 (2018).

    ADS  Article  Google Scholar 

  • 35.

    Semer, R. & Reddy, K. R. Evaluation of soil washing process to remove mixed contaminants from a sandy loam. J. Hazard. Mater. 45, 45–57. https://doi.org/10.1016/0304-3894(96)82887-1 (1996).

    CAS  Article  Google Scholar 

  • 36.

    He, Z., Baligar, V., Ritchey, K., Martens, D. & Kemper, W. Factors affecting phosphate rock dissolution in acid soil amended with liming materials and cellulose. Soil Sci. Soc. Am. J. 60, 1596–1601. https://doi.org/10.2136/sssaj1996.03615995006000050045x (1996).

    ADS  CAS  Article  Google Scholar 

  • 37.

    Moreno, J., Hernández, T. & Garcia, C. Effects of a cadmium-contaminated sewage sludge compost on dynamics of organic matter and microbial activity in an arid soil. Biol. Fertil. Soils 28, 230–237. https://doi.org/10.1007/s003740050487 (1999).

    CAS  Article  Google Scholar 

  • 38.

    Lauber, C. L., Zhou, N., Gordon, J. I., Knight, R. & Fierer, N. Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. FEMS Microbiol. Lett. 307, 80–86. https://doi.org/10.1111/j.1574-6968.2010.01965.x (2010).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 39.

    Dong, L. et al. Enhanced nitrate-nitrogen removal by modified attapulgite-supported nanoscale zero-valent iron treating simulated groundwater. J. Environ. Manag. 213, 151–158. https://doi.org/10.1016/j.jenvman.2018.02.073 (2018).

    CAS  Article  Google Scholar 

  • 40.

    Bray, R. H. & Kurtz, L. Determination of total, organic, and available forms of phosphorus in soils. Soil Sci. 59, 39–46 (1945).

    ADS  CAS  Article  Google Scholar 

  • 41.

    Au-Bell, C. W. et al. High-throughput fluorometric measurement of potential soil extracellular enzyme activities. J. Vis. Exp. 81, e50961. https://doi.org/10.3791/50961 (2013).

    CAS  Article  Google Scholar 

  • 42.

    Edgar, R. C. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 10, 996. https://doi.org/10.1038/nmeth.2604 (2013).

    CAS  Article  Google Scholar 

  • 43.

    Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194–2200. https://doi.org/10.1093/bioinformatics/btr381 (2011).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 44.

    Quast, C. et al. 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 (2012).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 45.

    Meenatchi, R. et al. Revealing the impact of global mass bleaching on coral microbiome through 16S rRNA gene-based metagenomic analysis. Microbiol. Res. 233, 126408. https://doi.org/10.1016/j.micres.2019.126408 (2020).

    CAS  Article  Google Scholar 

  • 46.

    Gotelli, N. J. & Colwell, R. K. Estimating species richness. Biol. Divers. Front. Meas. Assess. 12, 39–54 (2011).

    Google Scholar 

  • 47.

    Keenan, S. W., Schaeffer, S. M., Jin, V. L. & DeBruyn, J. M. Mortality hotspots: nitrogen cycling in forest soils during vertebrate decomposition. Soil Biol. Biochem. 121, 165–176. https://doi.org/10.1016/j.soilbio.2018.03.005 (2018).

    CAS  Article  Google Scholar 

  • 48.

    Birla, A., Singh, B., Upadhyay, S. & Sharma, Y. Kinetics studies of synthesis of biodiesel from waste frying oil using a heterogeneous catalyst derived from snail shell. Biores. Technol. 106, 95–100. https://doi.org/10.1016/j.biortech.2011.11.065 (2012).

    CAS  Article  Google Scholar 

  • 49.

    Lauber, C. L., Hamady, M., Knight, R. & Fierer, N. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl. Environ. Microbiol. 75, 5111–5120. https://doi.org/10.1128/AEM.00335-09 (2009).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 50.

    Nicol, G. W., Leininger, S., Schleper, C. & Prosser, J. I. The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environ. Microbiol. 10, 2966–2978. https://doi.org/10.1111/j.1462-2920.2008.01701.x (2008).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 51.

    Delgado-Baquerizo, M. et al. A global atlas of the dominant bacteria found in soil. Science 359, 320–325. https://doi.org/10.1126/science.aap9516 (2018).

    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 52.

    Li, Q. et al. Biochar amendment decreases soil microbial biomass and increases bacterial diversity in Moso bamboo (Phyllostachys edulis) plantations under simulated nitrogen deposition. Environ. Res. Lett. 13, 1–10. https://doi.org/10.1088/1748-9326/aab53a (2018).

    CAS  Article  Google Scholar 

  • 53.

    Xiong, J. et al. Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan Plateau. Environ. Microbiol. 14, 2457–2466. https://doi.org/10.1111/j.1462-2920.2012.02799.x (2012).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 54.

    Leff, J. W. et al. Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. Proc. Natl. Acad. Sci. 112, 10967–10972. https://doi.org/10.1073/pnas.1508382112 (2015).

    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 55.

    Gomez, E., Ferreras, L. & Toresani, S. Soil bacterial functional diversity as influenced by organic amendment application. Biores. Technol. 97, 1484–1489. https://doi.org/10.1016/j.biortech.2005.06.021 (2006).

    CAS  Article  Google Scholar 

  • 56.

    Freitag, T. E., Chang, L., Clegg, C. D. & Prosser, J. I. Influence of inorganic nitrogen management regime on the diversity of nitrite-oxidizing bacteria in agricultural grassland soils. Appl. Environ. Microbiol. 71, 8323–8334. https://doi.org/10.1128/AEM.71.12.8323-8334.2005 (2005).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 57.

    Zhang, Y. et al. Fertilization shapes bacterial community structure by alteration of soil pH. Front. Microbiol. 8, 1325. https://doi.org/10.3389/fmicb.2017.01325 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  • 58.

    Nemergut, D. R. et al. The effects of chronic nitrogen fertilization on alpine tundra soil microbial communities: implications for carbon and nitrogen cycling. Environ. Microbiol. 10, 3093–3105. https://doi.org/10.1111/j.1462-2920.2008.01735.x (2008).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 59.

    Zhang, H. et al. Gemmatimonas aurantiaca gen. nov., sp. nov., a Gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov. Int. J. Syst. Evol. Microbiol. 53, 1155–1163. https://doi.org/10.1099/ijs.0.02520-0 (2003).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 60.

    Sheng, Y. & Zhu, L. Biochar alters microbial community and carbon sequestration potential across different soil pH. Sci. Total Environ. 622, 1391–1399. https://doi.org/10.1016/j.scitotenv.2017.11.337 (2018).

    ADS  CAS  Article  PubMed  Google Scholar 

  • 61.

    Cobo-Díaz, J. F. et al. Metagenomic assessment of the potential microbial nitrogen pathways in the rhizosphere of a Mediterranean forest after a wildfire. Microb. Ecol. 69, 895–904. https://doi.org/10.1007/s00248-015-0586-7 (2015).

    Article  PubMed  Google Scholar 

  • 62.

    Wang, C., Liu, D. & Bai, E. Decreasing soil microbial diversity is associated with decreasing microbial biomass under nitrogen addition. Soil Biol. Biochem. 120, 126–133. https://doi.org/10.1016/j.soilbio.2018.02.003 (2018).

    CAS  Article  Google Scholar 

  • 63.

    Fierer, N., Bradford, M. A. & Jackson, R. B. Toward an ecological classification of soil bacteria. Ecology 88, 1354–1364. https://doi.org/10.1890/05-1839 (2007).

    Article  PubMed  Google Scholar 

  • 64.

    Jones, R. T. et al. A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J. 3, 442–453. https://doi.org/10.1038/ismej.2008.127 (2009).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 65.

    Baker, B. J. et al. Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling. ISME J. 7, 1962–1973. https://doi.org/10.1038/ismej.2013.85 (2013).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 66.

    Xu, N., Tan, G., Wang, H. & Gai, X. Effect of biochar additions to soil on nitrogen leaching, microbial biomass and bacterial community structure. Eur. J. Soil Biol. 74, 1–8. https://doi.org/10.1016/j.ejsobi.2016.02.004 (2016).

    CAS  Article  Google Scholar 

  • 67.

    Prasanna, S. N. R. Soil pH and its role in cyanobacterial abundance and diversity in rice field soils. Appl. Ecol. Environ. Res. 5, 103–113. https://doi.org/10.15666/aeer/0502_103113 (2007).

    Article  Google Scholar 

  • 68.

    Shen, C. et al. Soil pH drives the spatial distribution of bacterial communities along elevation on Changbai Mountain. Soil Biol. Biochem. 57, 204–211. https://doi.org/10.1016/j.soilbio.2012.07.013 (2013).

    CAS  Article  Google Scholar 

  • 69.

    Waldrop, M., Balser, T. & Firestone, M. Linking microbial community composition to function in a tropical soil. Soil Biol. Biochem. 32, 1837–1846. https://doi.org/10.1016/S0038-0717(00)00157-7 (2000).

    CAS  Article  Google Scholar 

  • 70.

    Bombeo-Tuburan, I., Fukumoto, S. & Rodriguez, E. Use of the golden apple snail, cassava, and maize as feeds for the tiger shrimp, Penaeus monodon, in ponds. Aquaculture 131, 91–100 (1995).

    Article  Google Scholar 

  • 71.

    DeForest, J. L., Zak, D. R., Pregitzer, K. S. & Burton, A. J. Atmospheric nitrate deposition, microbial community composition, and enzyme activity in northern hardwood forests. Soil Sci. Soc. Am. J. 68, 132–138. https://doi.org/10.2136/sssaj2004.1320 (2004).

    ADS  CAS  Article  Google Scholar 

  • 72.

    Keeler, B. L., Hobbie, S. E. & Kellogg, L. E. Effects of long-term nitrogen addition on microbial enzyme activity in eight forested and grassland sites: implications for litter and soil organic matter decomposition. Ecosystems 12, 1–15. https://doi.org/10.1007/s10021-008-9199-z (2009).

    CAS  Article  Google Scholar 

  • 73.

    Carreiro, M., Sinsabaugh, R., Repert, D. & Parkhurst, D. Microbial enzyme shifts explain litter decay responses to simulated nitrogen deposition. Ecology 81, 2359–2365. https://doi.org/10.1890/0012-9658(2000)081[2359:MESELD]2.0.CO;2 (2000).

    Article  Google Scholar 

  • 74.

    Demisie, W. & Zhang, M. Effect of biochar application on microbial biomass and enzymatic activities in degraded red soil. Afr. J. Agric. Res. 10, 755–766. https://doi.org/10.5897/AJAR2013.8209 (2015).

    CAS  Article  Google Scholar 

  • 75.

    Zheng, M., Huang, J., Chen, H., Wang, H. & Mo, J. Responses of soil acid phosphatase and beta-glucosidase to nitrogen and phosphorus addition in two subtropical forests in southern China. Eur. J. Soil Biol. 68, 77–84. https://doi.org/10.1016/j.ejsobi.2015.03.010 (2015).

    CAS  Article  Google Scholar 


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