80
S. Ambreetha et al.
6. Berendsen, R.L., Pieterse, C.M.J., Bakker, P.A.H.M.: The rhizosphere microbiome and plant
health. Trends Plant Sci. 17, 478–486 (2012). https://doi.org/10.1016/j.tplants.2012.04.001
7. Bhattacharyya, P., et al.: Elucidation of rice rhizosphere metagenome in relation to methane
and nitrogen metabolism under elevated carbon dioxide and temperature using whole genome
metagenomic approach. Sci. Total Environ. 542, 886–898 (2016). https://doi.org/10.1016/j.
scitotenv.2015.10.154
8. Bodelier, P., Dedysh, S.: Microbiology of wetlands. Front. Microbiol. 4 (2013). https://doi.
org/10.3389/fmicb.2013.00079
9. Braker, G., Zhou, J., Wu, L., Devol, A.H., Tiedje, J.M.: Nitrite Reductase Genes nirK and
nirS as functional markers to investigate diversity of denitrifying bacteria in Pacific Northwest
Marine sediment communities. Appl. Environ. Microbiol. 66, 2096–2104 (2000). https://doi.
org/10.1128/aem.66.5.2096-2104
10. Buresh, R.J., Casselman, M.E., Patrick, W.H.: Nitrogen fixation in flooded soil systems, a
review. In: Brady, N.C. (ed.), Advances in Agronomy, vol 33, pp. 149–192. Academic Press
(1980). https://doi.org/10.1016/S0065-2113(08)60166-2
11. Buresh, R.J., Reddy, K.R., Van Kessel, C.: Nitrogen Transformations in Submerged Soils
Nitrogen in Agricultural Systems, pp. 401–436 (2008)
12. Cai, Y., Zheng, Y., Bodelier, P.L.E., Conrad, R., Jia, Z.: Conventional methanotrophs are
responsible for atmospheric methane oxidation in paddy soils . Nat. Commun. 7, 11728
(2016). https://doi.org/10.1038/ncomms11728
13. Cao, Y., Sun, H., Zhang, J., Chen, G., Zhu, H., Zhou, S., Xiao, H.: Effects of wheat straw
addition on dynamics and fate of nitrogen applied to paddy soils. Soil Till Res. 178, 92–98
(2018). https://doi.org/10.1016/j.still.2017.12.023
14. Che, S. -g, et al.: Review grain yield and nitrogen use efficiency in rice production regions in
China . J. Integr. Agric. 14, 2456–2466 (2015). https://doi.org/10.1016/S2095-3119(15)612
28-X
15. Chen, Z., Luo, X., Hu, R., Wu, M., Wu, J., Wei, W.: Impact of long-term fertilization on the
composition of denitrifier communities based on nitrite reductase analyses in a paddy soil.
Microbial. Ecol. 60, 850–861 (2010). https://doi.org/10.1007/s00248-010-9700-z
16. Choudhury, A.T.M.A., Kennedy, I.R.: Prospects and potentials for systems of biological
nitrogen fixation in sustainable rice production. Biol. Fert. Soils 39, 219–227 (2004). https://
doi.org/10.1007/s00374-003-0706-2
17. Costa, E., Pérez, J., Kreft, J.U.: Why is metabolic labour divided in nitrification? Trends
Microbiol. 14, 213–219 (2006). https://doi.org/10.1016/j.tim.2006.03.006
18. Cucu, M.A., Said-Pullicino, D., Maurino, V., Bonifacio, E., Romani, M., Celi, L.: Influence
of redox conditions and rice straw incorporation on nitrogen availability in fertilized paddy
soils. Biol. Fert. Soils 50, 755–764 (2014). https://doi.org/10.1007/s00374-013-0893-4
19. Cui, H.-L., Duan, G.-L., Zhang, H., Cheng, W., Zhu, Y.-G.: Microbiota in non-flooded and
flooded rice culms. FEMS Microbiol. Ecol. 95 (2019). https://doi.org/10.1093/femsec/fiz036
20. Daims, H., et al.: Complete nitrification by Nitrospira bacteria. Nature 528, 504 (2015). https://
doi.org/10.1038/nature16461
21. Daims, H., Lücker, S., Wagner, M.: A New Perspective on Microbes Formerly Known as
Nitrite-Oxidizing Bacteria. Trends Microbiol. 24, 699–712 (2016). https://doi.org/10.1016/j.
tim.2016.05.004
22. Delgado-Baquerizo, M., et al.: Microbial diversity drives multifunctionality in terrestrial
ecosystems. Nat. Commun. 7, 10541 (2016). 10.1038/ncomms10541
23. Devêvre, O.C., Horwáth, W.R.: Stabilization of fertilizer nitrogen-15 into humic substances in
aerobic vs waterlogged soil following straw incorporation. Soil Sci. Soc. Am. J. 65, 499–510
(2001). 10.2136/sssaj2001.652499x
24. Dharmappa, P.M., et al.: Introgression of root and water use efficiency traits enhances water
productivity: an evidence for physiological breeding in rice (Oryza sativa L.) Rice 12(14)
(2019) https://doi.org/10.1186/s12284-019-0268-z
25. Ding, L.J., An, X.L., Li, S., Zhang, G.L., Zhu, Y.G.: Nitrogen loss through anaerobic ammonium oxidation coupled to iron reduction from paddy soils in a chronosequence. Environ. Sci.
Technol. 48, 10641–10647 (2014). https://doi.org/10.1021/es503113s
S. Ambreetha et al.
6. Berendsen, R.L., Pieterse, C.M.J., Bakker, P.A.H.M.: The rhizosphere microbiome and plant
health. Trends Plant Sci. 17, 478–486 (2012). https://doi.org/10.1016/j.tplants.2012.04.001
7. Bhattacharyya, P., et al.: Elucidation of rice rhizosphere metagenome in relation to methane
and nitrogen metabolism under elevated carbon dioxide and temperature using whole genome
metagenomic approach. Sci. Total Environ. 542, 886–898 (2016). https://doi.org/10.1016/j.
scitotenv.2015.10.154
8. Bodelier, P., Dedysh, S.: Microbiology of wetlands. Front. Microbiol. 4 (2013). https://doi.
org/10.3389/fmicb.2013.00079
9. Braker, G., Zhou, J., Wu, L., Devol, A.H., Tiedje, J.M.: Nitrite Reductase Genes nirK and
nirS as functional markers to investigate diversity of denitrifying bacteria in Pacific Northwest
Marine sediment communities. Appl. Environ. Microbiol. 66, 2096–2104 (2000). https://doi.
org/10.1128/aem.66.5.2096-2104
10. Buresh, R.J., Casselman, M.E., Patrick, W.H.: Nitrogen fixation in flooded soil systems, a
review. In: Brady, N.C. (ed.), Advances in Agronomy, vol 33, pp. 149–192. Academic Press
(1980). https://doi.org/10.1016/S0065-2113(08)60166-2
11. Buresh, R.J., Reddy, K.R., Van Kessel, C.: Nitrogen Transformations in Submerged Soils
Nitrogen in Agricultural Systems, pp. 401–436 (2008)
12. Cai, Y., Zheng, Y., Bodelier, P.L.E., Conrad, R., Jia, Z.: Conventional methanotrophs are
responsible for atmospheric methane oxidation in paddy soils . Nat. Commun. 7, 11728
(2016). https://doi.org/10.1038/ncomms11728
13. Cao, Y., Sun, H., Zhang, J., Chen, G., Zhu, H., Zhou, S., Xiao, H.: Effects of wheat straw
addition on dynamics and fate of nitrogen applied to paddy soils. Soil Till Res. 178, 92–98
(2018). https://doi.org/10.1016/j.still.2017.12.023
14. Che, S. -g, et al.: Review grain yield and nitrogen use efficiency in rice production regions in
China . J. Integr. Agric. 14, 2456–2466 (2015). https://doi.org/10.1016/S2095-3119(15)612
28-X
15. Chen, Z., Luo, X., Hu, R., Wu, M., Wu, J., Wei, W.: Impact of long-term fertilization on the
composition of denitrifier communities based on nitrite reductase analyses in a paddy soil.
Microbial. Ecol. 60, 850–861 (2010). https://doi.org/10.1007/s00248-010-9700-z
16. Choudhury, A.T.M.A., Kennedy, I.R.: Prospects and potentials for systems of biological
nitrogen fixation in sustainable rice production. Biol. Fert. Soils 39, 219–227 (2004). https://
doi.org/10.1007/s00374-003-0706-2
17. Costa, E., Pérez, J., Kreft, J.U.: Why is metabolic labour divided in nitrification? Trends
Microbiol. 14, 213–219 (2006). https://doi.org/10.1016/j.tim.2006.03.006
18. Cucu, M.A., Said-Pullicino, D., Maurino, V., Bonifacio, E., Romani, M., Celi, L.: Influence
of redox conditions and rice straw incorporation on nitrogen availability in fertilized paddy
soils. Biol. Fert. Soils 50, 755–764 (2014). https://doi.org/10.1007/s00374-013-0893-4
19. Cui, H.-L., Duan, G.-L., Zhang, H., Cheng, W., Zhu, Y.-G.: Microbiota in non-flooded and
flooded rice culms. FEMS Microbiol. Ecol. 95 (2019). https://doi.org/10.1093/femsec/fiz036
20. Daims, H., et al.: Complete nitrification by Nitrospira bacteria. Nature 528, 504 (2015). https://
doi.org/10.1038/nature16461
21. Daims, H., Lücker, S., Wagner, M.: A New Perspective on Microbes Formerly Known as
Nitrite-Oxidizing Bacteria. Trends Microbiol. 24, 699–712 (2016). https://doi.org/10.1016/j.
tim.2016.05.004
22. Delgado-Baquerizo, M., et al.: Microbial diversity drives multifunctionality in terrestrial
ecosystems. Nat. Commun. 7, 10541 (2016). 10.1038/ncomms10541
23. Devêvre, O.C., Horwáth, W.R.: Stabilization of fertilizer nitrogen-15 into humic substances in
aerobic vs waterlogged soil following straw incorporation. Soil Sci. Soc. Am. J. 65, 499–510
(2001). 10.2136/sssaj2001.652499x
24. Dharmappa, P.M., et al.: Introgression of root and water use efficiency traits enhances water
productivity: an evidence for physiological breeding in rice (Oryza sativa L.) Rice 12(14)
(2019) https://doi.org/10.1186/s12284-019-0268-z
25. Ding, L.J., An, X.L., Li, S., Zhang, G.L., Zhu, Y.G.: Nitrogen loss through anaerobic ammonium oxidation coupled to iron reduction from paddy soils in a chronosequence. Environ. Sci.
Technol. 48, 10641–10647 (2014). https://doi.org/10.1021/es503113s