R E F E R E N C E S
Abarenkov, K., Nilsson, R. H., Larsson, K. H., Alexander, I. J., Eberhardt, U., Erland, S., Pennanen, T. (2010). The UNITE database for molecular identification of fungi–recent updates and future perspectives.New Phytologist , 186 (2), 281-285. https://10.1111/j.1469-8137.2009.03160.x
Andrews, S. S., Karlen, D. L., & Mitchell, J. P. (2002). A comparison of soil quality indexing methods for vegetable production systems in Northern California. Agriculture Ecosystem & Environment ,90 (1), 25-45. https://10.1016/S0167-8809(01)00174-8
Armenise, E., Redmile-Gordon, M. A., Stellacci, A. M., Ciccarese, A., & Rubino, P. (2013). Developing a soil quality index to compare soil fitness for agricultural use under different managements in the Mediterranean environment. Soil & Tillage Research , 130 , 91-98. https://10.1016/j.still.2013.02.013
Baldrian, P. (2017). Microbial activity and the dynamics of ecosystem processes in forest soils. Current Opinion In Microbiology , 37 , 128-134. https://10.1016/j.mib.2017.06.008
Bastida, F., Luis Moreno, J., Hernández, T., & García, C. (2006). Microbiological degradation index of soils in a semiarid climate.Soil biology & biochemistry , 38 (12), 3463-3473. https://10.1016/j.soilbio.2006.06.001
Berhe, A. A., Harte, J., Harden, J. W., & Torn, M. S. (2007). The Significance of the Erosion-induced Terrestrial Carbon Sink. Bioscience ,57 (4). https://10.1641/B570408
Bernhard Flury, & Riedwyl, H. (1988). Multivariate Statistics. A Practical Approach . London: Chapman and Hall.
Bünemann, E. K., Bongiorno, G., Bai, Z., Creamer, R. E., De Deyn, G., de Goede, R., Brussaard, L. (2018). Soil quality–A critical review. Soil Biology and Biochemistry , 120 , 105-125. https://10.1016/j.soilbio.2018.01.030
Byrne, B. M., & Erlbaums, L. (2009). Structural equation modeling with AMOS: basic concepts, applications, and programming . London: Routledge.
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., & Costello, E. E. A. (2010). QIIME allows analysis of high-throughput community sequencing data. Nature Methods , 7 , 335-336. https://10.1038/nmeth0510-335
Carrino-Kyker, S. R., Kluber, L. A., Petersen, S. M., Coyle, K. P., Hewins, C. R., Deforest, J. L., Anderson, I. (2016). Mycorrhizal fungal communities respond to experimental elevation of soil pH and P availability in temperate hardwood forests. FEMS microbiology ecology ,92 (3), w24. https://10.1093/femsec/fiw024
Chagnon, P., Bradley, R. L., Maherali, H., & Klironomos, J. N. (2013). A trait-based framework to understand life history of mycorrhizal fungi.Trends in Plant Science , 18 (9), 484-491. https://10.1016/j.tplants.2013.05.001
Cooke, R. C., & Rayner, A. (1984). Ecology of saprotrophic fungi . London: Longman.
Coughlan, A. P., Dalpé, Y., Lapointe, L., & Piché, Y. (2000). Soil pH-induced changes in root colonization, diversity, and reproduction of symbiotic arbuscular mycorrhizal fungi from healthy and declining maple forests.Canadian Journal of Forest Research , 30 (10), 1543-1554. https://10.1139/cjfr-30-10-1543
Deacon, J. (2006). Fungal biology. Mycological Research , 110 (1), 121-122. https://10.1016/j.mycres.2005.11.002
Delgado-Baquerizo, M., Maestre, F. T., Reich, P. B., Jeffries, T. C., Gaitan, J. J., Encinar, D., Singh, B. K. (2016). Microbial diversity drives multifunctionality in terrestrial ecosystems. Nature Communications , 7 (1), 1-8. https://10.1038/ncomms10541
Doran, J. W., & Parkin, T. B. (1996). Quantitative indicators of soil quality: a minimum data set. Soil Science Society of America , 25-37. https://10.2136/sssaspecpub49.c2
Duhamel, M., Wan, J., Bogar, L. M., Segnitz, R. M., Duncritts, N. C., & Peay, K. G. (2019). Plant selection initiates alternative successional trajectories in the soil microbial community after disturbance.Ecological Monographs , 89 (3), e1367. https://10.1002/ecm.1367
Edgar, R. C. (2013). UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods , 10 (10), 996-998. https://10.1038/nmeth.2604
FAO (2015). Global Forest Resources Assessment 2015: how are the world’s forests changing? In: Food and Agriculture Organization of the United Nations.
Frankenberger, W., & Tabatabai, M. A. (1991). L-glutaminase activity of soil.Soil Biology and Biochemistry , 23 (9), 869-874. https://10.1016/0038-0717(91)90099-6
Fraser, F. C., Hallett, P. D., Wookey, P. A., Hartley, I. P., & Hopkins, D. W. (2013). How do enzymes catalysing soil nitrogen transformations respond to changing temperatures? Biology and Fertility of Soils ,49 (1), 99-103. https://10.1007/s00374-012-0722-1
Grayston, S. J., Vaughan, D., & Jones, D. (1997). Rhizosphere carbon flow in trees, in comparison with annual plants: the importance of root exudation and its impact on microbial activity and nutrient availability. Applied Soil Ecology , 5 (1), 29-56. https://10.1016/S0929-1393(96)00126-6
Grime, J. P. (1979). Plant strategies and vegetation processes. Biologia Plantarum , 23 (4), 254. https://10.1007/BF02895358
Guillaume, T., Damris, M., & Kuzyakov, Y. (2015). Losses of soil carbon by converting tropical forest to plantations: erosion and decomposition estimated by δ13C. Global Change Biology , 21 (9), 3548-3560. https://10.1111/gcb.12907
Gunina, A., Smith, A. R., Godbold, D. L., Jones, D. L., & Kuzyakov, Y. (2017). Response of soil microbial community to afforestation with pure and mixed species. Plant and Soil , 412 (1-2), 357-368. https://10.1007/s11104-016-3073-0
Hepper, C. M. (1984). Regulation of spore germination of the vesicular-arbuscular mycorrhizal fungus Acaulospora laevis by soil pH.Transactions of the British Mycological Society , 83 (1), 154-156. https://10.1016/S0007-1536(84)80258-2
Johnson, N. C., Rowland, D. L., Corkidi, L., & Allen, E. B. (2008). Plant winners and losers during grassland N-eutrophication differ in biomass allocation and mycorrhizas. Ecology , 89 (10), 2868-2878. https://10.1890/07-1394.1
Jones, D. L., Hodge, A., & Kuzyakov, Y. (2004). Plant and mycorrhizal regulation of rhizodeposition. New Phytologist , 163 (3), 459-480. https://10.1111/j.1469-8137.2004.01130.x
Kamaa, M., Mburu, H., Blanchart, E., Chibole, L., Chotte, J., Kibunja, C., & Lesueur, D. (2011). Effects of organic and inorganic fertilization on soil bacterial and fungal microbial diversity in the Kabete long-term trial, Kenya. Biology and Fertility of Soils , 47 (3), 315-321. https://10.1007/s00374-011-0539-3
Kanazawa, S., & Kiyota, H. (2000). Effect of fertilizer and manure application on L-glutaminase and L-asparaginase activities in soils.Soil science and plant nutrition , 46 (3), 741-744. https://10.1080/00380768.2000.10409139
Kerfahi, D., Tripathi, B. M., Dong, K., Go, R., & Adams, J. M. (2016). Rainforest conversion to rubber plantation may not result in lower soil diversity of bacteria, fungi, and nematodes. Microbial ecology ,72 (2), 359-371. https://10.1007/s00248-016-0790-0
Krashevska, V., Klarner, B., Widyastuti, R., Maraun, M., & Scheu, S. (2015). Impact of tropical lowland rainforest conversion into rubber and oil palm plantations on soil microbial communities. Biology and fertility of soils , 51 (6), 697-705. https://10.1007/s00374-015-1021-4
Lan, G., Wu, Z., Yang, C., Sun, R., Chen, B., & Zhang, X. (2021). Forest conversion alters the structure and functional processes of tropical forest soil microbial communities. Land Degradation & Development , 32 (2), 613-627. https://10.1002/ldr.3757
Lauber, C. L., Strickland, M. S., Bradford, M. A., & Fierer, N. (2008). The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biology and Biochemistry ,40 (9), 2407-2415. https://10.1016/j.soilbio.2008.05.021
Liu, T., Wu, X., Li, H., Alharbi, H., Wang, J., Dang, P., Yan, W. (2020). Soil organic matter, nitrogen and pH driven change in bacterial community following forest conversion. Forest Ecology and Management , 477 , 118473. https://10.1016/j.foreco.2020.118473
Lundell, T. K., Makela, M. R., & Hilden, K. (2010). Lignin-modifying enzymes in filamentous basidiomycetes–ecological, functional and phylogenetic review. Journal of basic microbiology , 50 (1), 5-20. https://10.1002/jobm.200900338
Mcguire, K. L., D Angelo, H., Brearley, F. Q., Gedallovich, S. M., Babar, N., Yang, N., Fierer, N. (2015). Responses of soil fungi to logging and oil palm agriculture in Southeast Asian tropical forests. Microbial Ecology , 69 (4), 733-747. https://10.1007/s00248-014-0468-4
Nakayama, M., Imamura, S., Taniguchi, T., & Tateno, R. (2019). Does conversion from natural forest to plantation affect fungal and bacterial biodiversity, community structure, and co-occurrence networks in the organic horizon and mineral soil? Forest Ecology and Management ,446 , 238-250. https://10.1016/j.foreco.2019.05.042
Nguyen, N. H., Song, Z., Bates, S. T., Branco, S., Tedersoo, L., Menke, J., Kennedy, P. G. (2016). FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecology ,20 , 241-248. https://10.1016/j.funeco.2015.06.006
Osono, T. (2006). Role of phyllosphere fungi of forest trees in the development of decomposer fungal communities and decomposition processes of leaf litter. Canadian Journal of Microbiology , 52 (8), 701-716. https://10.1139/w06-023
Peay, K. G., Baraloto, C., & Fine, P. V. A. (2013). Strong coupling of plant and fungal community structure across western Amazonian rainforests.The ISME Journal , 7 (9), 1852-1861. https://10.1038/ismej.2013.66
Põlme, S., Bahram, M., Yamanaka, T., Nara, K., Dai, Y. C., Grebenc, T., Tedersoo, L. (2013). Biogeography of ectomycorrhizal fungi associated with alders (Alnus spp.) in relation to biotic and abiotic variables at the global scale. New phytologist , 198 (4), 1239-1249. https://10.1111/nph.12170
Prescott, C. E., & Grayston, S. J. (2013). Tree species influence on microbial communities in litter and soil: Current knowledge and research needs.Forest Ecology and Management , 309 , 19-27. https://10.1016/j.foreco.2013.02.034
Raiesi, F. (2017). A minimum data set and soil quality index to quantify the effect of land use conversion on soil quality and degradation in native rangelands of upland arid and semiarid regions. Ecological Indicators , 75 , 307-320. https://10.1016/j.ecolind.2016.12.049
Steidinger, B. S., Crowther, T. W., Liang, J., Van Nuland, M. E., Werner, G. D. A., Reich, P. B., Peay, K. G. (2019). Climatic controls of decomposition drive the global biogeography of forest-tree symbioses. Nature ,569 (7756), 404-408. https://10.1038/s41586-019-1128-0
Sterkenburg, E., Bahr, A., Brandstrom, D. M., Clemmensen, K. E., & Lindahl, B. D. (2015). Changes in fungal communities along a boreal forest soil fertility gradient. New phytologist , 207 (4), 1145-1158. https://10.1111/nph.13426
Stursova, M., Zifcakova, L., Leigh, M. B., Burgess, R., & Baldrian, P. (2012). Cellulose utilization in forest litter and soil: identification of bacterial and fungal decomposers. FEMS microbiology ecology ,80 (3), 735-746. https://10.1111/j.1574-6941.2012.01343.x
Sun, R., Dsouza, M., Gilbert, J. A., Guo, X., Wang, D., Guo, Z., Chu, H. (2016). Fungal community composition in soils subjected to long-term chemical fertilization is most influenced by the type of organic matter.Environmental Microbiology , 18 (12), 5137-5150. https://10.1111/1462-2920.13512
Tripathi, B. M., Edwards, D. P., Mendes, L. W., Kim, M., Dong, K., Kim, H., & Adams, J. M. (2016). The impact of tropical forest logging and oil palm agriculture on the soil microbiome. Molecular Ecology ,25 (10), 2244-2257. https://10.1111/mec.13620
Uroz, S., Buée, M., Deveau, A., Mieszkin, S., & Martin, F. (2016). Ecology of the forest microbiome: Highlights of temperate and boreal ecosystems.Soil Biology and Biochemistry , 103 , 471-488. https://10.1016/j.soilbio.2016.09.006
Vailaya, A., Cline, M. S., Workman, C., Bader, G. D., Isserlin, R., Creech, M., Ideker, T. (2007). Integration of biological networks and gene expression data using Cytoscape. Nature protocols , 2 (10), 2366-2382. https://10.1038/nprot.2007.324
Van der Linde, S., Suz, L. M., Orme, C. D. L., Cox, F., Andreae, H., Asi, E., Bidartondo, M. I. (2018). Environment and host as large-scale controls of ectomycorrhizal fungi. Nature , 558 (7709), 243-248. https://10.1038/s41586-018-0189-9
Wang, X., Zhang, W., Liu, Y., Jia, Z., Li, H., Yang, Y., Zhang, X. (2021). Identification of microbial strategies for labile substrate utilization at phylogenetic classification using a microcosm approach. Soil Biology and Biochemistry , 153 , 107970. https://10.1016/j.soilbio.2020.107970
Watanabe, K. (2010). Detection of protease genes in field soil applied with liquid livestock feces and speculation on their function and origin. Soil Science & Plant Nutrition , 55 (1), 42-52. https://10.1111/j.1747-0765.2008.00323.x
White, T. J., Bruns, T., Lee, S., & Taylor, J. (1990). 38-Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis, M. A., Gelfand, D. H., Sninsky, J. J., & White, T. J. (Eds.),PCR Protocols (pp. 315-322). San Diego: Academic Press.
Wu, H., Xiang, W., Ouyang, S., Forrester, D. I., Zhou, B., Chen, L., Peng, C. (2019). Linkage between tree species richness and soil microbial diversity improves phosphorus bioavailability. Functional Ecology , 33 (8), 1549-1560. https://10.1111/1365-2435.13355
Yakov, Kuzyakov, A., Gunina, K., Zamanian, J., Tian, Y., X, L., Alharbi, L. (2020). New approaches for evaluation of soil health, sensitivity and resistance to degradation. Frontiers of Agricultural Science and Engineering , v.7 (03), 56-62. https://10.15302/J-FASE-2020338
Yang, K., Zhu, J., Xu, S., & Zheng, X. (2018). Conversion from temperate secondary forests into plantations (Larix spp.): Impact on belowground carbon and nutrient pools in northeastern China. Land Degradation & Development , 29 (11), 4129-4139. https://10.1002/ldr.3169
Yang, M., Yang, D., & Yu, X. (2018). Soil microbial communities and enzyme activities in sea-buckthorn (Hippophae rhamnoides) plantation at different ages. PLoS One , 13 (1), e190959. https://10.1371/journal.pone.0190959
Zarafshar, M., Bazot, S., Matinizadeh, M., Bordbar, S. K., Rousta, M. J., Kooch, Y., Negahdarsaber, M. (2020). Do tree plantations or cultivated fields have the same ability to maintain soil quality as natural forests?Applied Soil Ecology , 151 , 103536. https://10.1016/j.apsoil.2020.103536
Zhang, Y., Xu, X., Li, Z., Liu, M., Xu, C., Zhang, R., & Luo, W. (2019). Effects of vegetation restoration on soil quality in degraded karst landscapes of southwest China. Science of The Total Environment ,650 , 2657-2665. https://10.1016/j.scitotenv.2018.09.372