Impact of waterlogging and heat stress on rice rhizosphere microbiome assembly and potential function in carbon and nitrogen transformation

References

• Ahn YH. 2006. Sustainable nitrogen elimination biotechnologies: a review. Process Biochem. 41:1709–1721. doi:10.1016/j.procbio.2006.03.033.
   Web of Science ®Google Scholar
• Allison SD, Treseder KK. 2010. Warming and drying suppress microbial activity and carbon cycling in boreal forest soils. Global Change Biol. 14:2898–2909. doi:10.1111/j.1365-2486.2008.01716.x.
   Web of Science ®Google Scholar
• Anesio AM, Hodson AJ, Fritz A, Psenner R, Sattler B. 2009. High microbial activity on glaciers: importance to the global carbon cycle. Global Change Biol. 15:955–960. doi:10.1111/j.1365-2486.2008.01758.x.
   Web of Science ®Google Scholar
• Baetz U, Martinoia E. 2014. Root exudates: the hidden part of plant defense. Trends Plant Sci. 19:90–98. doi:10.1016/j.tplants.2013.11.006.
   PubMed Web of Science ®Google Scholar
• Banerjee S, Walder F, Buchi L, Meyer M, Held AY, Gattinger A, Keller T, Charles R, van der Heijden MGA. 2019. Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots. ISME J. 13(7):1722–1736. doi:10.1038/s41396-019-0383-2.
   PubMed Web of Science ®Google Scholar
• Bhatti AA, Haq S, Bhat RA. 2017. Actinomycetes benefaction role in soil and plant health. Microb Pathogenesis. 111:458–467. doi:10.1016/j.micpath.2017.09.036.
   PubMed Web of Science ®Google Scholar
• Björn B, Judith P, Dumont MG. 2016. Microbial community structure in the rhizosphere of rice plants. Front Microbiol. 6:1537. doi:10.3389/fmicb.2015.01537.
   PubMed Web of Science ®Google Scholar
• Blagodatskaya EV, Blagodatsky SA, Anderson TH, Kuzyakov Y. 2014. Microbial growth and carbon use efficiency in the rhizosphere and root-free soil. PLoS One. 9:e93282. doi:10.1371/journal.pone.0093282.
   PubMed Web of Science ®Google Scholar
• Blaud A, van der Zaan B, Menon M, Lair GJ, Zhang DY, Huber P, Schiefer J, Blum WEH, Kitzler B, Huang WE. 2018. The abundance of nitrogen cycle genes and potential greenhouse gas fluxes depends on land use type and little on soil aggregate size. Appl Soil Ecol. 125:1–11. doi:10.1016/j.apsoil.2017.11.026.
   Web of Science ®Google Scholar
• Bonanomi G, De Filippis F, Cesarano G, La Storia A, Ercolini D, Scala F. 2016. Organic farming induces changes in soil microbiota that affect agro-ecosystem functions. Soil Biol Biochem. 103:327–336. doi:10.1016/j.soilbio.2016.09.005.
   Web of Science ®Google Scholar
• Bradford MA, McCulley RL, Crowther TW, Oldfield EE, Wood SA, Fierer N. 2019. Cross-biome patterns in soil microbial respiration predictable from evolutionary theory on thermal adaptation. Nat Ecol Evol. 3:223–231. doi:10.1038/s41559-018-0771-4.
   PubMed Web of Science ®Google Scholar
• Brimecombe MJ, De Leij FAAM, Lynch JM. 2007. Rhizodeposition and microbial populations. In: Pinton R, Veranini Z, Nannipieri P, editors. The rhizosphere biochemistry and organic substances at the soil–plant interface. New York (USA): Taylor & Francis Group; p. 73–98.
   Google Scholar
• Bru D, Ramette A, Saby NPA, Dequiedt S, Ranjard L, Jolivet C, Arrouays D, Philippot L. 2011. Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale. ISME J. 5:532–542. doi:10.1038/ismej.2010.130.
   PubMed Web of Science ®Google Scholar
• Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 7:335–336. doi:10.1038/nmeth.f.303.
   PubMed Web of Science ®Google Scholar
• Cheng Y, Zhou WG, Gao CF, Lan K, Gao Y, Wu QY. 2009. Biodiesel production from Jerusalem artichoke (Helianthus Tuberosus L.) tuber by heterotrophic microalgae Chlorella protothecoides. J Chem Technol Biot. 84:777–781.
   Web of Science ®Google Scholar
• Collins MD, Lawson PA, Willems A, Cordoba JJ, Fernandez-Garayzabal J, Garcia P, Cai J, Hippe H, Farrow JAE. 1994. The phylogeny of the genus clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol. 44:812–826. doi:10.1099/00207713-44-4-812.
   PubMedGoogle Scholar
• Colloff MJ, Wakelin SA, Gomez D, Rogers SL. 2008. Detection of nitrogen cycle genes in soils for measuring the effects of changes in land use and management. Soil Biol Biochem. 40:1637–1645. doi:10.1016/j.soilbio.2008.01.019.
   Web of Science ®Google Scholar
• Cozzolino V, Di Meo V, Monda H, Spaccini R, Piccolo A. 2016. The molecular characteristics of compost affect plant growth, arbuscular mycorrhizal fungi, and soil microbial community composition. Biol Fert Soils. 52:15–29. doi:10.1007/s00374-015-1046-8.
   Web of Science ®Google Scholar
• Craine JM, Gelderman TM. 2016. Soil moisture controls on temperature sensitivity of soil organic carbon decomposition for a mesic grassland. Soil Biol Biochem. 43:455–457. doi:10.1016/j.soilbio.2010.10.011.
   Google Scholar
• de Boer W, Folman LB, Summerbell RC, Boddy L. 2005. Living in a fungal world: impact of fungi on soil bacterial niche development. FEMS Microbiol Rev. 29:795–811. doi:10.1016/j.femsre.2004.11.005.
   PubMed Web of Science ®Google Scholar
• Drenovsky RE, Vo D, Graham KJ. 2004. Soil water content and organic carbon availability are major determinants of soil microbial community composition. Microb Ecol. 48:424–430. doi:10.1007/s00248-003-1063-2.
   PubMed Web of Science ®Google Scholar
• Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 26:2460–2461. doi:10.1093/bioinformatics/btq461.
   PubMed Web of Science ®Google Scholar
• Fontaine S, Mariotti A, Abbadie L. 2003. The priming effect of organic matter: a question of microbial competition. Soil Biol Biochem. 35:837–843. doi:10.1016/S0038-0717(03)00123-8.
   Web of Science ®Google Scholar
• Galloway JN, Dentener FJ, Capone DG, Boyer EW, Howarth RW, Seitzinger SP, Asner GP, Cleveland CC, Green PA, Holland EA. 2004. Nitrogen cycles: past, present, and future. Biogeochemistry. 70:153–226. doi:10.1007/s10533-004-0370-0.
   Web of Science ®Google Scholar
• Gavira M, Roldan MD, Castillo F, Moreno-Vivian C. 2002. Regulation of nap gene expression and periplasmic nitrate reductase activity in the phototrophic bacterium Rhodobacter sphaeroides DSM158. J Bacteriol. 184:1693–1702. doi:10.1128/JB.184.6.1693-1702.2002.
   PubMed Web of Science ®Google Scholar
• Grisi B, Grace C, Brookes PC, Benedetti A, Dell’abate MT. 1998. Temperature effects on organic matter and microbial biomass dynamics in temperate and tropical soils. Soil Biol Biochem. 30:1309–1315. doi:10.1016/S0038-0717(98)00016-9.
   Web of Science ®Google Scholar
• Hayden EL, Mele PM, Bougoure DS, Allan CY, Norng S, Piceno YM, Brodie EL, DeSantis TZ, Andersen GL, Williams AL. 2012. Changes in the microbial community structure of bacteria: archaea and fungi in response to elevated CO2 and warming in an Australian native grassland soil. Environ Microbiol. 14:3081–3096. doi:10.1111/j.1462-2920.2012.02855.x.
   PubMed Web of Science ®Google Scholar
• Huws SA, Edwards JE, Kim EJ, Scollan ND. 2007. Specificity and sensitivity of eubacterial primers utilized for molecular profiling of bacteria within complex microbial ecosystems. J Microbiol Meth. 70:565–569. doi:10.1016/j.mimet.2007.06.013.
   PubMed Web of Science ®Google Scholar
• Kandeler E, Brune T, Enowashi E, Dörr N, Guggenberger G, Lamersdorf N, Philippot L. 2009. Response of total and nitrate-dissimilating bacteria to reduced N deposition in a spruce forest soil profile. FEMS Microbiol Ecol. 67:444–454. doi:10.1111/j.1574-6941.2008.00632.x.
   PubMed Web of Science ®Google Scholar
• Kennedy AC. 1999. Bacterial diversity in agroecosystems. Agr Ecosyst Environ. 74:65–76. doi:10.1016/S0167-8809(99)00030-4.
   Web of Science ®Google Scholar
• Kuanar SR, Ray A, Sethi SK, Chattopadhyay K, Sarkar RK. 2017. Physiological basis of stagnant flooding tolerance in rice. Rice Sci. 24:73–84. doi:10.1016/j.rsci.2016.08.008.
   Web of Science ®Google Scholar
• Kuzyakov Y, Domanski G. 2020. Carbon input by plants into the soil. J Plant Nutr Soil Sc. 163:421–431. doi:10.1002/1522-2624(200008)163:4<421::AID-JPLN421>3.0.CO;2-R.
   Google Scholar
• Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Thurber RLV, Knight R. 2013. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 31:814–821. doi:10.1038/nbt.2676.
   PubMed Web of Science ®Google Scholar
• Levy-Booth DJ, Prescott CE, Grayston SJ. 2014. Microbial functional genes involved in nitrogen fixation, nitrification and denitrification in forest ecosystems. Soil Biol Biochem. 75:11–25. doi:10.1016/j.soilbio.2014.03.021.
   Web of Science ®Google Scholar
• Li MY, Ren LH, Zhang JC, Luo L, Qin PF, Zhou YY, Huang C, Tang JY, Huang HL, Chen AW. 2019. Population characteristics and influential factors of nitrogen cycling functional genes in heavy metal contaminated soil remediated by biochar and compost. Sci Total Environ. 651:2166–2174. doi:10.1016/j.scitotenv.2018.10.152.
   PubMed Web of Science ®Google Scholar
• Liu D, Keiblinger KM, Schindlbacher A, Wegner U, Sun H, Fuchs S, Lassek C, Riedel K, Zechmeister-Boltenstern S. 2017. Microbial functionality as affected by experimental warming of a temperate mountain forest soil—A metaproteomics survey. Applied Soil Ecol. 117–118:196–202. doi:10.1016/j.apsoil.2017.04.021.
   Web of Science ®Google Scholar
• McSpadden Gardener BB, Driks A. 2004. Overview of the nature and application of biocontrol microbes: bacillus spp. Phytopathology. 94:1244. doi:10.1094/PHYTO.2004.94.11.1244.
   PubMed Web of Science ®Google Scholar
• Mickan B, Abbott L, Fan J, Hart M, Siddique K, Solaiman Z, Jenkins SN. 2018. Application of compost and clay under water-stressed conditions influences functional diversity of rhizosphere bacteria. Biol Fert Soils. 54:55–70. doi:10.1007/s00374-017-1238-5.
   Web of Science ®Google Scholar
• Mille-Lindblom C, Fischer H, Tranvik LJ. 2006. Antagonism between bacteria and fungi: substrate competition and a possible tradeoff between fungal growth and tolerance towards bacteria. OIKOS. 113:233–242. doi:10.1111/j.2006.0030-1299.14337.x.
   Web of Science ®Google Scholar
• Ng EL, Patti AF, Rose MT, Schefe CR, Wilkinson K, Smernik RJ, Cavagnaro TR. 2014. Does the chemical nature of soil carbon drive the structure and functioning of soil microbial communities? Soil Biol Biochem. 70:54–61. doi:10.1016/j.soilbio.2013.12.004.
   Web of Science ®Google Scholar
• Paranychianakis NV, Tsiknia M, Giannakis G, Nikolaidis NP, Kalogerakis N. 2013. Nitrogen cycling and relationships between ammonia oxidizers and denitrifiers in a clay-loam soil. Appl Microbiol Biot. 97:5507–5515. doi:10.1007/s00253-013-4765-5.
   PubMed Web of Science ®Google Scholar
• Pérez-Jaramillo JE, Mendes R, Raaijmakers JM. 2016. Impact of plant domestication on rhizosphere microbiome assembly and functions. Plant Mol Biol. 90:635–644. doi:10.1007/s11103-015-0337-7.
   PubMed Web of Science ®Google Scholar
• Pettersson M, Bååth E. 2003. Temperature-dependent changes in the soil bacterial community in limed and unlimed soil. FEMS Microbiol Ecol. 45:13–21. doi:10.1016/S0168-6496(03)00106-5.
   PubMed Web of Science ®Google Scholar
• Qiu H, Ge T, Liu J, Chen X, Hu Y, Wu J, Su Y, Kuzyakov Y. 2018. Effects of biotic and abiotic factors on soil organic matter mineralization: experiments and structural modeling analysis. Eur J Soil Biol. 84:27–34. doi:10.1016/j.ejsobi.2017.12.003.
   Web of Science ®Google Scholar
• Reed SC, Townsend AR, Cleveland CC, Nemergut DR. 2010. Microbial community shifts influence patterns in tropical forest nitrogen fixation. Oecologia. 164:521–531. doi:10.1007/s00442-010-1649-6.
   PubMed Web of Science ®Google Scholar
• Ren M, Zhang Z, Wang X, Zhou Z, Chen D, Zeng H, Zhao S, Chen L, Hu T, Zhang C. 2018. Diversity and contributions to nitrogen cycling and carbon fixation of soil salinity shaped microbial communities in Tarim basin. Front Microbiol. 9:431. doi:10.3389/fmicb.2018.00431.
   PubMed Web of Science ®Google Scholar
• Riah-Anglet W, Trinsoutrot-Gattin I, Martin-Laurent F, Laroche-Ajzenberg E, Norini MP, Latour X, Laval K. 2009. Temperature adaptation of soil bacterial communities along an Antarctic climate gradient: predicting responses to climate warming. Global Change Biol. 15:2615–2625. doi:10.1111/j.1365-2486.2009.01959.x.
   Web of Science ®Google Scholar
• Riah-Anglet W, Trinsoutrot-Gattin I, Martin-Laurent F, Laroche-Ajzenberg E, Norini MP, Latour X, Laval K. 2015. Soil microbial community structure and function relationships: a heat stress experiment. Appl Soil Ecol. 86:121–130. doi:10.1016/j.apsoil.2014.10.001.
   Web of Science ®Google Scholar
• Sánchez-García M, Sánchez-Monedero MA, Roig A, López-Cano I, Moreno B, Benitez E, Cayuela ML. 2016. Compost vs biochar amendment: a two-year field study evaluating soil C build-up and N dynamics in an organically managed olive crop. Plant Soil. 401:1–14. doi:10.1007/s11104-016-2794-4.
   Google Scholar
• Schindlbacher A, Rodler A, Kuffner M, Kitzler B, Sessitsch A, Zechmeister-Boltenstern S. 2011. Experimental warming effects on the microbial community of a temperate mountain forest soil. Soil Biol Biochem. 43:1417–1425. doi:10.1016/j.soilbio.2011.03.005.
   PubMed Web of Science ®Google Scholar
• Sharmin F, Wakelin S, Huygens F, Hargreaves M. 2013. Firmicutes dominate the bacterial taxa within sugar-cane processing plants. Sci Rep. 3:3107.
   PubMed Web of Science ®Google Scholar
• Strickland MS, Rousk J. 2010. Considering fungal: bacterial dominance in soils – methods, controls, and ecosystem implications. Soil Biol Biochem. 42:1385–1395. doi:10.1016/j.soilbio.2010.05.007.
   Web of Science ®Google Scholar
• Tanaka N, Yutani K, Aye T, Jinadasa KBSN. 2007. Effect of broken dead culms of Phragmites australis on radial oxygen loss in relation to radiation and temperature. Hydrobiologia. 583:165–172. doi:10.1007/s10750-006-0483-7.
   Web of Science ®Google Scholar
• Tsujimoto R, Kotani H, Yokomizo K, Yamakawa H, Nonaka A, Fujita Y. 2018. Functional expression of an oxygen-labile nitrogenase in an oxygenic photosynthetic organism. Sci Rep. 8(1):7380. doi:10.1038/s41598-018-25396-7.
   PubMedGoogle Scholar
• Visser EJW, Colmer TD, Blom CWPM, Voesenek LACJ. 2010. Changes in growth, porosity, and radial oxygen loss from adventitious roots of selected mono‐and dicotyledonous wetland species with contrasting types of aerenchyma. Plant Cell Environ. 23:1237–1245. doi:10.1046/j.1365-3040.2000.00628.x.
   Google Scholar
• Xiong JB, Sun HB, Peng F, Zhang HY, Xue X, Gibbons SM, Gilbert JA, Chu HY. 2014. Characterizing changes in soil bacterial community structure in response to short-term warming. FEMS Microbiol Ecol. 89:281–292.
   PubMed Web of Science ®Google Scholar
• Yadav S, Kaushik R, Saxena AK, Arora DK. 2011. Diversity and phylogeny of plant growth-promoting bacilli from moderately acidic soil. J Basic Microb. 51:98–106.
   PubMed Web of Science ®Google Scholar
• Zehr JP, Jenkins BD, Short SM, Steward GF. 2003. Nitrogenase gene diversity and microbial community structure: a cross-system comparison. Environ Microbiol. 5:539–554.
   PubMed Web of Science ®Google Scholar
• Zhalnina K, Louie KB, Hao Z, Mansoori N, da Rocha UN, Shi SJ, Cho HJ, Karaoz U, Loque D, Bowen BP. 2018. Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nat Microbiol. 3:470–480.
   PubMed Web of Science ®Google Scholar
• Zhang NL, Wan SQ, Guo JX, Han GD, Gutknecht J, Schmid B, Yu L, Liu WX, Bi J, Wang Z, et al. 2015. Precipitation modifies the effects of warming and nitrogen addition on soil microbial communities in northern Chinese grasslands. Soil Biol Biochem. 89:12–23.
   Web of Science ®Google Scholar
• Zheng W, Zhao ZY, Gong QL, Zhai BN, Li ZY. 2018. Effects of cover crop in an apple orchard on microbial community composition, networks, and potential genes involved with degradation of crop residues in soil. Biol Fert Soils. 54:743–759.
   Web of Science ®Google Scholar