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The Scion/Rootstock Genotypes and Habitats Affect Arbuscular Mycorrhizal Fungal Community in Citrus.

Song F, Pan Z, Bai F, An J, Liu J, Guo W, Bisseling T, Deng X, Xiao S - Front Microbiol (2015)

Bottom Line: However, the AMF community structure of citrus is largely unknown.Over 7,40,000 effective sequences were obtained from 77 citrus root samples.These sequences were assigned to 75 AMF virtual taxa, of which 66 belong to Glomus, highlighting an absolute dominance of this AMF genus in symbiosis with citrus roots.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University Wuhan, China.

ABSTRACT
Citrus roots have rare root hairs and thus heavily depend on arbuscular mycorrhizal fungi (AMF) for mineral nutrient uptake. However, the AMF community structure of citrus is largely unknown. By using 454-pyrosequencing of 18S rRNA gene fragment, we investigated the genetic diversity of AMF colonizing citrus roots, and evaluated the impact of habitats and rootstock and scion genotypes on the AMF community structure. Over 7,40,000 effective sequences were obtained from 77 citrus root samples. These sequences were assigned to 75 AMF virtual taxa, of which 66 belong to Glomus, highlighting an absolute dominance of this AMF genus in symbiosis with citrus roots. The citrus AMF community structure is significantly affected by habitats and host genotypes. Interestingly, our data suggests that the genotype of the scion exerts a greater impact on the AMF community structure than that of the rootstock where the physical root-AMF association occurs. This study not only provides a comprehensive assessment for the community composition of the AMF in citrus roots under different conditions, but also sheds novel insights into how the AMF community might be indirectly influenced by the spatially separated yet metabolically connected partner-the scion-of the grafted citrus tree.

No MeSH data available.


Related in: MedlinePlus

Neighbor-joining phylogenetic tree of AMF species detected in citrus roots. The F84+Gamma nucleotide substitution model was used and bootstrap values of >50 are shown.
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Figure 2: Neighbor-joining phylogenetic tree of AMF species detected in citrus roots. The F84+Gamma nucleotide substitution model was used and bootstrap values of >50 are shown.

Mentions: To further define the AMF sequence diversity, all the effective reads assigned to AMF were aligned against the AMF sequences deposited in MAARJAM database (http://maarjam.botany.ut.ee/), which resulted in 80 AMF virtual taxa (VT). Because five of the 80 VT each has only one effective read, they may be sequence artifacts (Öpik et al., 2009; Hiiesalu et al., 2014) and were excluded from subsequent analyses. Thus, a total of 75 AMF VT (corresponding to 5,27,394 effective reads and 70.92% of total effective reads) were identified from our 77 citrus root samples, indicating a high-level of genetic diversity among the AMF colonizing citrus roots. Based on the neighbor-joining analysis, the 75 VT of Glomeramycota could be assigned to six known AMF families: Glomeraceae (66 VT), Acaulosporaceae (3 VT), Paraglomeraceae (2 VT), Claroideoglomeraceae (2 VT), Paraglomeraceae (1 VT), and Gigasporaceae (1 VT) (Figure 2; Table S3). The 66 Glometaceae VT could be further divided into Glomus group A (31 VT) and Glomus group B (35 VT). Not surprisingly, Glomus, the sole genus of the Glomeraceae family, absolutely dominates the AMF in citrus roots, as is the case with other plant species (Lin et al., 2012; Hiiesalu et al., 2014; Xiang et al., 2014). Specifically, the 66 Glomus VT account for 99.83% (5,26,478) effective sequence reads with the top 10 Glomus VT making up two thirds of the total AMF sequence reads, indicating high heterogeneity in abundance within Glomus in citrus roots (Table S3). To better understand the major AMF species associated with citrus samples, we also performed networks analyses for the AMF species among different habitats and scion/rootstock genotypes. Among all the 75 AMF species we detected, only Glomus. MO-G117_VTX00114 (also known as Rhizophagus irregularis) presented in all of the 23 samples. In addition, the AMF species Glomus.sp._VTX00213 and Glomus. Glo7_VTX00214 presented in 86% (20/23) of the total samples, Glomus.NF13_VTX00419 and Glomus.Glo8_VTX00175 presented in 91% (21/23) of the total samples. Results also showed that 10 VT (13.33% of total VT) were shared among 8 habitats, and 3 VT (4%) were shared among 14 host genotypes (Newhall sweet orange/Zhique, Mandarin/Red tangerine, Ponkan/Citrange, Ponkan/Poncirus, Poncirus, Citrange, Limec × Orange, Poncirus × Tangerine, Orange/Poncirus, Mandarin/Poncirus, Pummelo/Poncirus, Mandarin/Yuzu, Newhall sweet orange/Red tangerine and Newhall sweet orange/Poncirus). Three AMF species Glomus.NF13_VTX00419 (2nd abundance of all the VT, 65,008 effective reads, 12.33% of the 5,27,394 effective reads assigned in MAARJAM database), Glomus.MO-G17_VTX00114 (3rd, 37,932 effective reads, 7.19%) and Glomus.Afrothismia.foertheriana.symbiont_VTX00111 (16th, 9320 effective reads, 1.77%) presented in all the 8 habitats and 14 host genotypes (Figure S3).


The Scion/Rootstock Genotypes and Habitats Affect Arbuscular Mycorrhizal Fungal Community in Citrus.

Song F, Pan Z, Bai F, An J, Liu J, Guo W, Bisseling T, Deng X, Xiao S - Front Microbiol (2015)

Neighbor-joining phylogenetic tree of AMF species detected in citrus roots. The F84+Gamma nucleotide substitution model was used and bootstrap values of >50 are shown.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664953&req=5

Figure 2: Neighbor-joining phylogenetic tree of AMF species detected in citrus roots. The F84+Gamma nucleotide substitution model was used and bootstrap values of >50 are shown.
Mentions: To further define the AMF sequence diversity, all the effective reads assigned to AMF were aligned against the AMF sequences deposited in MAARJAM database (http://maarjam.botany.ut.ee/), which resulted in 80 AMF virtual taxa (VT). Because five of the 80 VT each has only one effective read, they may be sequence artifacts (Öpik et al., 2009; Hiiesalu et al., 2014) and were excluded from subsequent analyses. Thus, a total of 75 AMF VT (corresponding to 5,27,394 effective reads and 70.92% of total effective reads) were identified from our 77 citrus root samples, indicating a high-level of genetic diversity among the AMF colonizing citrus roots. Based on the neighbor-joining analysis, the 75 VT of Glomeramycota could be assigned to six known AMF families: Glomeraceae (66 VT), Acaulosporaceae (3 VT), Paraglomeraceae (2 VT), Claroideoglomeraceae (2 VT), Paraglomeraceae (1 VT), and Gigasporaceae (1 VT) (Figure 2; Table S3). The 66 Glometaceae VT could be further divided into Glomus group A (31 VT) and Glomus group B (35 VT). Not surprisingly, Glomus, the sole genus of the Glomeraceae family, absolutely dominates the AMF in citrus roots, as is the case with other plant species (Lin et al., 2012; Hiiesalu et al., 2014; Xiang et al., 2014). Specifically, the 66 Glomus VT account for 99.83% (5,26,478) effective sequence reads with the top 10 Glomus VT making up two thirds of the total AMF sequence reads, indicating high heterogeneity in abundance within Glomus in citrus roots (Table S3). To better understand the major AMF species associated with citrus samples, we also performed networks analyses for the AMF species among different habitats and scion/rootstock genotypes. Among all the 75 AMF species we detected, only Glomus. MO-G117_VTX00114 (also known as Rhizophagus irregularis) presented in all of the 23 samples. In addition, the AMF species Glomus.sp._VTX00213 and Glomus. Glo7_VTX00214 presented in 86% (20/23) of the total samples, Glomus.NF13_VTX00419 and Glomus.Glo8_VTX00175 presented in 91% (21/23) of the total samples. Results also showed that 10 VT (13.33% of total VT) were shared among 8 habitats, and 3 VT (4%) were shared among 14 host genotypes (Newhall sweet orange/Zhique, Mandarin/Red tangerine, Ponkan/Citrange, Ponkan/Poncirus, Poncirus, Citrange, Limec × Orange, Poncirus × Tangerine, Orange/Poncirus, Mandarin/Poncirus, Pummelo/Poncirus, Mandarin/Yuzu, Newhall sweet orange/Red tangerine and Newhall sweet orange/Poncirus). Three AMF species Glomus.NF13_VTX00419 (2nd abundance of all the VT, 65,008 effective reads, 12.33% of the 5,27,394 effective reads assigned in MAARJAM database), Glomus.MO-G17_VTX00114 (3rd, 37,932 effective reads, 7.19%) and Glomus.Afrothismia.foertheriana.symbiont_VTX00111 (16th, 9320 effective reads, 1.77%) presented in all the 8 habitats and 14 host genotypes (Figure S3).

Bottom Line: However, the AMF community structure of citrus is largely unknown.Over 7,40,000 effective sequences were obtained from 77 citrus root samples.These sequences were assigned to 75 AMF virtual taxa, of which 66 belong to Glomus, highlighting an absolute dominance of this AMF genus in symbiosis with citrus roots.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University Wuhan, China.

ABSTRACT
Citrus roots have rare root hairs and thus heavily depend on arbuscular mycorrhizal fungi (AMF) for mineral nutrient uptake. However, the AMF community structure of citrus is largely unknown. By using 454-pyrosequencing of 18S rRNA gene fragment, we investigated the genetic diversity of AMF colonizing citrus roots, and evaluated the impact of habitats and rootstock and scion genotypes on the AMF community structure. Over 7,40,000 effective sequences were obtained from 77 citrus root samples. These sequences were assigned to 75 AMF virtual taxa, of which 66 belong to Glomus, highlighting an absolute dominance of this AMF genus in symbiosis with citrus roots. The citrus AMF community structure is significantly affected by habitats and host genotypes. Interestingly, our data suggests that the genotype of the scion exerts a greater impact on the AMF community structure than that of the rootstock where the physical root-AMF association occurs. This study not only provides a comprehensive assessment for the community composition of the AMF in citrus roots under different conditions, but also sheds novel insights into how the AMF community might be indirectly influenced by the spatially separated yet metabolically connected partner-the scion-of the grafted citrus tree.

No MeSH data available.


Related in: MedlinePlus