References
Abell, G.C.J., Robert, S.S., Frampton, D.M.F., Volkman, J.K., Rizwi, F., Csontos, J. et al. (2012). High-Throughput Analysis of Ammonia Oxidiser Community Composition via a Novel, amoA-Based Functional Gene Array. Plos One , 7.
Allan, E., Manning, P., Alt, F., Binkenstein, J., Blaser, S., Bluthgen, N. et al. (2015). Land use intensification alters ecosystem multifunctionality via loss of biodiversity and changes to functional composition. Ecol. Lett. , 18, 834-843.
Banerjee, S., Kirkby, C.A., Schmutter, D., Bissett, A., Kirkegaard, J.A. & Richardson, A.E. (2016). Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil. Soil. Biol. Biochem. , 97, 188-198.
Banerjee, S., Schlaeppi, K. & van der Heijden, M.G.A. (2018). Keystone taxa as drivers of microbiome structure and functioning. Nat. Rev. Microbiol. , 16, 567-576.
Banerjee, S., Walder, F., Buchi, L., Meyer, M., Held, A.Y., Gattinger, A. et al. (2019). Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots.ISME J. , 13, 1722-1736.
Bardgett, R.D. & van der Putten, W.H. (2014). Belowground biodiversity and ecosystem functioning. Nature , 515, 505-511.
Bell, T., Newman, J.A., Silverman, B.W., Turner, S.L. & Lilley, A.K. (2005). The contribution of species richness and composition to bacterial services. Nature , 436, 1157-1160.
Bender, S.F., Wagg, C. & van der Heijden, M.G.A. (2016). An Underground Revolution: Biodiversity and Soil Ecological Engineering for Agricultural Sustainability. Trends Ecol. Evol. , 31, 440-452.
Benjamini, Y., Krieger, A.M. & Yekutieli, D. (2006). Adaptive linear step-up procedures that control the false discovery rate.Biometrika , 93, 491-507.
Berry, D. & Widder, S. (2014). Deciphering microbial interactions and detecting keystone species with co-occurrence networks. Front. Microbiol. , 5, 219.
Bossio, D.A. & Scow, K.M. (1998). Impacts of Carbon and Flooding on Soil Microbial Communities: Phospholipid Fatty Acid Profiles and Substrate Utilization Patterns. Microb. Ecol. , 35, 265-278.
Brose, U. & Hillebrand, H. (2016). Biodiversity and ecosystem functioning in dynamic landscapes. Philos. Trans. R. Soc. Lond. B Biol. Sci. , 371, 20150267.
Campbell, C.D., Chapman, S.J., Cameron, C.M., Davidson, M.S. & Potts, J.M. (2003). A rapid microtiter plate method to measure carbon dioxide evolved from carbon substrate amendments so as to determine the physiological profiles of soil microbial communities by using whole soil. Appl. Environ. Microbiol. , 69, 3593-3599.
Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K. et al. (2010). QIIME allows analysis of high-throughput community sequencing data. Nat Methods , 7, 335-336.
Cardinale, B.J., Duffy, J.E., Gonzalez, A., Hooper, D.U., Perrings, C., Venail, P. et al. (2012). Biodiversity loss and its impact on humanity. Nature , 486, 59-67.
Chen, Q.-L., Ding, J., Zhu, D., Hu, H.-W., Delgado-Baquerizo, M., Ma, Y.-B. et al. (2020). Rare microbial taxa as the major drivers of ecosystem multifunctionality in long-term fertilized soils. Soil Biol. Biochem. , 141, 107686.
Cheng, X., Yang, Y., Li, M., Dou, X. & Zhang, Q. (2013). The impact of agricultural land use changes on soil organic carbon dynamics in the Danjiangkou Reservoir area of China. Plant Soil , 366, 415-424.
Daam, M.A., Teixeira, H., Lillebø, A.I. & Nogueira, A.J.A. (2019). Establishing causal links between aquatic biodiversity and ecosystem functioning: Status and research needs. Sci. Total Environ. , 656, 1145-1156.
Dai, S., Liu, Q., Zhao, J. & Zhang, J. (2018). Ecological niche differentiation of ammonia-oxidising archaea and bacteria in acidic soils due to land use change. Soil Res. , 56, 71–79.
de Vries, F.T. & Shade, A. (2013). Controls on soil microbial community stability under climate change. Front. Microbiol. , 4, 265.
Delgado-Baquerizo, M., Eldridge, D.J., Ochoa, V., Gozalo, B., Singh, B.K. & Maestre, F.T. (2017). Soil microbial communities drive the resistance of ecosystem multifunctionality to global change in drylands across the globe. Ecol. Lett. , 20, 1295-1305.
Delgado-Baquerizo, M., Giaramida, L., Reich, P.B., Khachane, A.N., Hamonts, K., Edwards, C. et al. (2016a). Lack of functional redundancy in the relationship between microbial diversity and ecosystem functioning. J. Ecol. , 104, 936-946.
Delgado-Baquerizo, M., Maestre, F.T., Reich, P.B., Jeffries, T.C., Gaitan, J.J., Encinar, D. et al. (2016b). Microbial diversity drives multifunctionality in terrestrial ecosystems. Nat. Commun. , 7, 10541.
Deng, Y., Jiang, Y.H., Yang, Y.F., He, Z.L., Luo, F. & Zhou, J.Z. (2012). Molecular ecological network analyses. Bmc Bioinformatics , 13, 113.
Edgar, R.C., Haas, B.J., Clemente, J.C., Quince, C. & Knight, R. (2011). UCHIME improves sensitivity and speed of chimera detection.Bioinformatics , 27, 2194-2200.
Fan, K., Weisenhorn, P., Gilbert, J.A. & Chu, H. (2018). Wheat rhizosphere harbors a less complex and more stable microbial co-occurrence pattern than bulk soil. Soil Biol. Biochem. , 125, 251-260.
Feng, J., Wu, J.J., Zhang, Q., Zhang, D.D., Li, Q.X., Long, C.Y.et al. (2018). Stimulation of nitrogen-hydrolyzing enzymes in soil aggregates mitigates nitrogen constraint for carbon sequestration following afforestation in subtropical China. Soil. Biol. Biochem. , 123, 136-144.
Fierer, N. (2017). Embracing the unknown: disentangling the complexities of the soil microbiome. Nat. Rev. Microbiol. , 15, 579-590.
Francis, C.A., Roberts, K.J., Beman, J.M., Santoro, A.E. & Oakley, B.B. (2005). Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc. Natl. Acad. Sci. U S A , 102, 14683-14688.
Gao, S.J., Cao, W.D., Zou, C.Q., Gao, J.S., Huang, J., Bai, J.S.et al. (2018). Ammonia-oxidizing archaea are more sensitive than ammonia-oxidizing bacteria to long-term application of green manure in red paddy soil. Appl Soil Ecol , 124, 185-193.
Hatzenpichler, R. (2012). Diversity, Physiology, and Niche Differentiation of Ammonia-Oxidizing Archaea. Appl. Environ. Microbiol. , 78, 7501-7510.
Hink, L., Gubry-Rangin, C., Nicol, G.W. & Prosser, J.I. (2018). The consequences of niche and physiological differentiation of archaeal and bacterial ammonia oxidisers for nitrous oxide emissions. ISME J. , 12, 1084-1093.
Hooper, D.U., Chapin, F.S., Ewel, J.J., Hector, A., Inchausti, P., Lavorel, S. et al. (2005). Effects of biodiversity on ecosystem functioning: a consensus of current knowledge. Ecol. Monogr. , 75, 3-35.
Hu, A.Y., Ju, F., Hou, L.Y., Li, J.W., Yang, X.Y., Wang, H.J. et al. (2017). Strong impact of anthropogenic contamination on the co-occurrence patterns of a riverine microbial community. Environ. Microbiol. , 19, 4993-5009.
Isbell, F., Craven, D., Connolly, J., Loreau, M., Schmid, B., Beierkuhnlein, C. et al. (2015). Biodiversity increases the resistance of ecosystem productivity to climate extremes. Nature , 526, 574-U263.
Jia, Z., Zhou, X., Xia, W., Fornara, D., Wang, B., Wasson, E.A. et al. (2020). Evidence for niche differentiation of nitrifying communities in grassland soils after 44 years of different field fertilization scenarios. Pedosphere , 30, 87-97.
Kaiser, K., Wemheuer, B., Korolkow, V., Wemheuer, F., Nacke, H., Schoning, I. et al. (2016). Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests. Sci. Rep-Uk , 6, 33696.
Ke, X.B., Angel, R., Lu, Y.H. & Conrad, R. (2013). Niche differentiation of ammonia oxidizers and nitrite oxidizers in rice paddy soil. Environ. Microbiol. , 15, 2275-2292.
Li, Z., Zeng, Z., Tian, D., Wang, J., Fu, Z., Zhang, F. et al.(2020). Global patterns and controlling factors of soil nitrification rate. Glob. Change Biol. , 26, 4147-4157.
Liu, J., Yu, Z., Yao, Q., Sui, Y., Shi, Y., Chu, H. et al.(2018). Ammonia-Oxidizing Archaea Show More Distinct Biogeographic Distribution Patterns than Ammonia-Oxidizing Bacteria across the Black Soil Zone of Northeast China. Front. Microbiol. , 9.
Liu, J.J., Yu, Z.H., Yao, Q., Sui, Y.Y., Shi, Y., Chu, H.Y. et al. (2019). Biogeographic Distribution Patterns of the Archaeal Communities Across the Black Soil Zone of Northeast China. Front. Microbiol. , 10, 23.
Louca, S., Parfrey, L.W. & Doebeli, M. (2016). Decoupling function and taxonomy in the global ocean microbiome. Science , 353, 1272-1277.
Manning, P., van der Plas, F., Soliveres, S., Allan, E., Maestre, F.T., Mace, G. et al. (2018). Redefining ecosystem multifunctionality.Nat. Ecol. Evol. , 2, 427-436.
Meyer, S.T., Ptacnik, R., Hillebrand, H., Bessler, H., Buchmann, N., Ebeling, A. et al. (2018). Biodiversity–multifunctionality relationships depend on identity and number of measured functions.Nat. Ecol. Evol. , 2, 44-49.
Nie, M., Pendall, E., Bell, C., Gasch, C.K., Raut, S., Tamang, S.et al. (2013). Positive climate feedbacks of soil microbial communities in a semi-arid grassland. Ecol. Lett. , 16, 234-241.
Pester, M., Rattei, T., Flechl, S., Grongroft, A., Richter, A., Overmann, J. et al. (2012). amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions. Environ Microbiol , 14, 525-539.
Peters, M.K., Hemp, A., Appelhans, T., Becker, J.N., Behler, C., Classen, A. et al. (2019). Climate-land-use interactions shape tropical mountain biodiversity and ecosystem functions. Nature , 568, 88-92.
Qiao, N., Schaefer, D., Blagodatskaya, E., Zou, X.M., Xu, X.L. & Kuzyakov, Y. (2014). Labile carbon retention compensates for CO2 released by priming in forest soils. Glob. Change Biol. , 20, 1943-1954.
Rivett, D.W. & Bell, T. (2018). Abundance determines the functional role of bacterial phylotypes in complex communities. Nat. Microbiol. , 3, 767-772.
Rotthauwe, J.H., Witzel, K.P. & Liesack, W. (1997). The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations.Appl. Environ. Microbiol. , 63, 4704-4712.
Schimel, J.P. & Schaeffer, S.M. (2012). Microbial control over carbon cycling in soil. Front. Microbiol. , 3, 348.
Shen, J.-P., Zhang, L.-M., Di, H.J. & He, J.-Z. (2012). A review of ammonia-oxidizing bacteria and archaea in Chinese soils. Front. Microbiol. , 3, 296.
Srivastava, D.S. & Vellend, M. (2005). Biodiversity-Ecosystem Function Research: Is It Relevant to Conservation? Annu. Rev. Ecol. Evol. Syst. , 36, 267-294.
Strong, J.A., Andonegi, E., Bizsel, K.C., Danovaro, R., Elliott, M., Franco, A. et al. (2015). Marine biodiversity and ecosystem function relationships: The potential for practical monitoring applications. Estuar. Coast. Shelf Sci. , 161, 46-64.
Tilman, D., Isbell, F. & Cowles, J.M. (2014). Biodiversity and Ecosystem Functioning. Annu. Rev. Ecol. Evol. Syst. , 45, 471-493.
Tilman, D., Reich, P.B., Knops, J.M.H., Wedin, D.A., Mielke, T. & Lehman, C. (2001). Diversity and Productivity in a Long-Term Grassland Experiment. Science , 294, 843-845.
Torsvik, V. & Øvreås, L. (2002). Microbial diversity and function in soil: from genes to ecosystems. Curr. Opin. Microbiol. , 5, 240-245.
Trivedi, C., Delgado-Baquerizo, M., Hamonts, K., Lai, K.T., Reich, P.B. & Singh, B.K. (2019a). Losses in microbial functional diversity reduce the rate of key soil processes. Soil. Biol. Biochem. , 135, 267-274.
Trivedi, C., Reich, P.B., Maestre, F.T., Hu, H.W., Singh, B.K. & Delgado-Baquerizo, M. (2019b). Plant-driven niche differentiation of ammonia-oxidizing bacteria and archaea in global drylands. ISME J. , 13, 2727-2736.
Trivedi, P., Delgado-Baquerizo, M., Jeffries, T.C., Trivedi, C., Anderson, I.C., Lai, K. et al. (2017a). Soil aggregation and associated microbial communities modify the impact of agricultural management on carbon content. Environ. Microbiol. , 19, 3070-3086.
Trivedi, P., Delgado-Baquerizo, M., Trivedi, C., Hamonts, K., Anderson, I.C. & Singh, B.K. (2017b). Keystone microbial taxa regulate the invasion of a fungal pathogen in agro-ecosystems. Soil. Biol. Biochem. , 111, 10-14.
Trivedi, P., Delgado-Baquerizo, M., Trivedi, C., Hu, H.W., Anderson, I.C., Jeffries, T.C. et al. (2016). Microbial regulation of the soil carbon cycle: evidence from gene-enzyme relationships. ISME J. , 10, 2593-2604.
Turnbull, L.A., Isbell, F., Purves, D.W., Loreau, M. & Hector, A. (2016). Understanding the value of plant diversity for ecosystem functioning through niche theory. Proc. R Soc. B-Biol. Sci. , 283, 20160536.
van der Plas, F. (2019). Biodiversity and ecosystem functioning in naturally assembled communities. Biol Rev , 94, 1220-1245.
Veen, G.F., van der Putten, W.H. & Bezemer, T.M. (2018). Biodiversity-ecosystem functioning relationships in a long-term non-weeded field experiment. Ecology , 99, 1836-1846.
Veum, K.S., Lorenz, T. & Kremer, R.J. (2019). Phospholipid Fatty Acid Profiles of Soils under Variable Handling and Storage Conditions.Agron. J. , 111, 1090-1096.
Wagg, C., Schlaeppi, K., Banerjee, S., Kuramae, E.E. & Van Der Heijden, M.G.A. (2019). Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning. Nat. Commun. , 10, 4841.
Wang, L., Delgado-Baquerizo, M., Wang, D., Isbell, F., Liu, J., Feng, C.et al. (2019). Diversifying livestock promotes multidiversity and multifunctionality in managed grasslands. Proc. Natl. Acad. Sci. U S A , 116, 6187-6192.
Weiss, S., Van Treuren, W., Lozupone, C., Faust, K., Friedman, J., Deng, Y. et al. (2016). Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. ISME J. , 10, 1669-1681.
Yang, F., Wu, J., Zhang, D., Chen, Q., Zhang, Q. & Cheng, X. (2018). Soil bacterial community composition and diversity in relation to edaphic properties and plant traits in grasslands of southern China.Appl. Soil Ecol. , 128, 43-53.
Zhang, Q., Wu, J.J., Yang, F., Lei, Y., Zhang, Q.F. & Cheng, X.L. (2016). Alterations in soil microbial community composition and biomass following agricultural land use change. Sci. Rep-Uk , 6, 36587.
Zhou, Z.-F., Wang, M.-X., Liu, W.-L., Li, Z.-L., Luo, F. & Xie, D.-T. (2015). A comparative study of ammonia-oxidizing archaea and bacteria in acidic and alkaline purple soils. Ann. Microbiol. , 66, 615-623.
Zhou, Z., Wang, C. & Luo, Y. (2020). Meta-analysis of the impacts of global change factors on soil microbial diversity and functionality.Nat. Commun. , 11, 3072.