Limits...
Fungal endophyte Phomopsis liquidambari affects nitrogen transformation processes and related microorganisms in the rice rhizosphere.

Yang B, Wang XM, Ma HY, Yang T, Jia Y, Zhou J, Dai CC - Front Microbiol (2015)

Bottom Line: A significant increase in the available nitrate and ammonium contents was found in the rhizosphere soil of endophyte-infected rice under low N conditions.Moreover, P. liquidambari significantly increased the potential nitrification rates, affected the abundance and community structure of AOA, AOB, and diazotrophs under low N conditions in the S1 and S2 stages.Plant-soil feedback mechanisms may be mediated by the rice-endophyte interaction, especially in nutrient-limited soil.

View Article: PubMed Central - PubMed

Affiliation: Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing China ; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing China.

ABSTRACT
The endophytic fungus Phomopsis liquidambari performs an important ecosystem service by assisting its host with acquiring soil nitrogen (N), but little is known regarding how this fungus influences soil N nutrient properties and microbial communities. In this study, we investigated the impact of P. liquidambari on N dynamics, the abundance and composition of N cycling genes in rhizosphere soil treated with three levels of N (urea). Ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and diazotrophs were assayed using quantitative real-time polymerase chain reaction and denaturing gradient gel electrophoresis at four rice growing stages (S0: before planting, S1: tillering stage, S2: grain filling stage, and S3: ripening stage). A significant increase in the available nitrate and ammonium contents was found in the rhizosphere soil of endophyte-infected rice under low N conditions. Moreover, P. liquidambari significantly increased the potential nitrification rates, affected the abundance and community structure of AOA, AOB, and diazotrophs under low N conditions in the S1 and S2 stages. The root exudates were determined due to their important role in rhizosphere interactions. P. liquidambari colonization altered the exudation of organic compounds by rice roots and P. liquidambari increased the concentration of soluble saccharides, total free amino acids and organic acids in root exudates. Plant-soil feedback mechanisms may be mediated by the rice-endophyte interaction, especially in nutrient-limited soil.

No MeSH data available.


Denaturing gradient gel electrophoresis (DGGE) profile and analysis of soil ammonium-oxidizing archaeal communities. (A–D) Canonical correspondence analysis (CCA) of AOA communities generated by the AOA DGGE patterns of four different stages of rice (A) S0, unplanted soil; (B) S1, tillering; (C) S2, grainfilling; (D) S3, ripening. E+, endophyte infected; E-, endophyte uninfected; LN, low N; MN, medium N; HN, high N.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4585018&req=5

Figure 3: Denaturing gradient gel electrophoresis (DGGE) profile and analysis of soil ammonium-oxidizing archaeal communities. (A–D) Canonical correspondence analysis (CCA) of AOA communities generated by the AOA DGGE patterns of four different stages of rice (A) S0, unplanted soil; (B) S1, tillering; (C) S2, grainfilling; (D) S3, ripening. E+, endophyte infected; E-, endophyte uninfected; LN, low N; MN, medium N; HN, high N.

Mentions: The community structure of the AOA, AOB, and diazotrophs in rhizosphere soils were characterized by PCR-DGGE in duplicate for all treatments. N-fertilization levels obviously altered the compositions of AOA, AOB, and diazotroph communities in some of the growing stages (Figures 3–5). Cluster analysis of PCR-DGGE band patterns of AOA amoA genes indicated that P. liquidambari symbiosis treatments (E+) showed low similarity with groups in the control (E-) treatments under low N conditions at both the S1 and S2 stages (less than 45% similarity), whereas high similarity was observed between E- and E+ treatments at other N levels during all stages (more than 60% similarity; Supplementary Figure S2). The CCA analysis also produced similar results, with the E+ treatments occupying an independent region separate from the E- treatments under low N conditions at both the S1 and S2 stages (Figures 3A–D). However, there was a relatively high similarity between the E+ and E- treatments under all three N conditions at the S3 stage, which might indicate that the effects caused by P. liquidambari did not lead to the AOA community being unrecoverable in the long term. Similarly, the community structures of the AOB and diazotrophs displayed similar temporal dynamics as AOA (Figures 4 and 5). There were no distinct differences between the E- and E+ treatments at all N levels during all stages except for under low N conditions at the S1 and S2 stages. The similarity between E+ and E- treatments under low N conditions at the S1 and S2 stages was less than 30 and 50% for AOB (Supplementary Figure S3) and was less than 40 and 15% for diazotrophs (Supplementary Figure S4), respectively. It is noteworthy that the obvious differences in the AOB and diazotroph community structure caused by P. liquidambari also nearly disappeared at the S3 stage (higher than 75% similarity), although different clusters were formed between the E+ and E- treatments under low N conditions. Moreover, CCA analysis showed that N contents (NH4+, NO3-, and total N) and PNR had strong effects on composition of AOA, AOB, and diazotrophs community (Figures 3–5). ANOSIM analysis showed that there were significant differences (R = 0.31, P = 0.043; R = 0.58, P = 0.004, respectively) of AOA and AOB communities between E- and E+ treatments at S1 stage, regardless of N levels. These results implied that the endophyte’s effects on the N-related microbial groups in rice rhizosphere were significant during S1 stage.


Fungal endophyte Phomopsis liquidambari affects nitrogen transformation processes and related microorganisms in the rice rhizosphere.

Yang B, Wang XM, Ma HY, Yang T, Jia Y, Zhou J, Dai CC - Front Microbiol (2015)

Denaturing gradient gel electrophoresis (DGGE) profile and analysis of soil ammonium-oxidizing archaeal communities. (A–D) Canonical correspondence analysis (CCA) of AOA communities generated by the AOA DGGE patterns of four different stages of rice (A) S0, unplanted soil; (B) S1, tillering; (C) S2, grainfilling; (D) S3, ripening. E+, endophyte infected; E-, endophyte uninfected; LN, low N; MN, medium N; HN, high N.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4585018&req=5

Figure 3: Denaturing gradient gel electrophoresis (DGGE) profile and analysis of soil ammonium-oxidizing archaeal communities. (A–D) Canonical correspondence analysis (CCA) of AOA communities generated by the AOA DGGE patterns of four different stages of rice (A) S0, unplanted soil; (B) S1, tillering; (C) S2, grainfilling; (D) S3, ripening. E+, endophyte infected; E-, endophyte uninfected; LN, low N; MN, medium N; HN, high N.
Mentions: The community structure of the AOA, AOB, and diazotrophs in rhizosphere soils were characterized by PCR-DGGE in duplicate for all treatments. N-fertilization levels obviously altered the compositions of AOA, AOB, and diazotroph communities in some of the growing stages (Figures 3–5). Cluster analysis of PCR-DGGE band patterns of AOA amoA genes indicated that P. liquidambari symbiosis treatments (E+) showed low similarity with groups in the control (E-) treatments under low N conditions at both the S1 and S2 stages (less than 45% similarity), whereas high similarity was observed between E- and E+ treatments at other N levels during all stages (more than 60% similarity; Supplementary Figure S2). The CCA analysis also produced similar results, with the E+ treatments occupying an independent region separate from the E- treatments under low N conditions at both the S1 and S2 stages (Figures 3A–D). However, there was a relatively high similarity between the E+ and E- treatments under all three N conditions at the S3 stage, which might indicate that the effects caused by P. liquidambari did not lead to the AOA community being unrecoverable in the long term. Similarly, the community structures of the AOB and diazotrophs displayed similar temporal dynamics as AOA (Figures 4 and 5). There were no distinct differences between the E- and E+ treatments at all N levels during all stages except for under low N conditions at the S1 and S2 stages. The similarity between E+ and E- treatments under low N conditions at the S1 and S2 stages was less than 30 and 50% for AOB (Supplementary Figure S3) and was less than 40 and 15% for diazotrophs (Supplementary Figure S4), respectively. It is noteworthy that the obvious differences in the AOB and diazotroph community structure caused by P. liquidambari also nearly disappeared at the S3 stage (higher than 75% similarity), although different clusters were formed between the E+ and E- treatments under low N conditions. Moreover, CCA analysis showed that N contents (NH4+, NO3-, and total N) and PNR had strong effects on composition of AOA, AOB, and diazotrophs community (Figures 3–5). ANOSIM analysis showed that there were significant differences (R = 0.31, P = 0.043; R = 0.58, P = 0.004, respectively) of AOA and AOB communities between E- and E+ treatments at S1 stage, regardless of N levels. These results implied that the endophyte’s effects on the N-related microbial groups in rice rhizosphere were significant during S1 stage.

Bottom Line: A significant increase in the available nitrate and ammonium contents was found in the rhizosphere soil of endophyte-infected rice under low N conditions.Moreover, P. liquidambari significantly increased the potential nitrification rates, affected the abundance and community structure of AOA, AOB, and diazotrophs under low N conditions in the S1 and S2 stages.Plant-soil feedback mechanisms may be mediated by the rice-endophyte interaction, especially in nutrient-limited soil.

View Article: PubMed Central - PubMed

Affiliation: Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing China ; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing China.

ABSTRACT
The endophytic fungus Phomopsis liquidambari performs an important ecosystem service by assisting its host with acquiring soil nitrogen (N), but little is known regarding how this fungus influences soil N nutrient properties and microbial communities. In this study, we investigated the impact of P. liquidambari on N dynamics, the abundance and composition of N cycling genes in rhizosphere soil treated with three levels of N (urea). Ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and diazotrophs were assayed using quantitative real-time polymerase chain reaction and denaturing gradient gel electrophoresis at four rice growing stages (S0: before planting, S1: tillering stage, S2: grain filling stage, and S3: ripening stage). A significant increase in the available nitrate and ammonium contents was found in the rhizosphere soil of endophyte-infected rice under low N conditions. Moreover, P. liquidambari significantly increased the potential nitrification rates, affected the abundance and community structure of AOA, AOB, and diazotrophs under low N conditions in the S1 and S2 stages. The root exudates were determined due to their important role in rhizosphere interactions. P. liquidambari colonization altered the exudation of organic compounds by rice roots and P. liquidambari increased the concentration of soluble saccharides, total free amino acids and organic acids in root exudates. Plant-soil feedback mechanisms may be mediated by the rice-endophyte interaction, especially in nutrient-limited soil.

No MeSH data available.