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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

Proportional distribution of total sequence reads and generated OTUs grouped by phyla of fungi from all citrus root samples through blasting against the SILVA database.
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Figure 1: Proportional distribution of total sequence reads and generated OTUs grouped by phyla of fungi from all citrus root samples through blasting against the SILVA database.

Mentions: The overall genetic diversity of AMF colonizing citrus roots is not known, nor is the impact of habitats and host plant genotypes on AMF community structures. To explore these areas, we collected roots of citrus trees grown in eight geographical locations in China. A total of 77 root DNA samples from citrus trees of 23 different genotypes or scion/rootstock combinations (i.e., sample groups) grown under different conditions (For details, see Table S1 and Figure S1, Supporting information) were prepared and used for PCR amplification of the 18S small subunit (SSU) rRNA gene fragment using a pair of largely AMF-specific primers AMV4.5NF/AMDGR. The PCR fragments were purified and subjected to 454-high throughput pyrosequencing. A total of 1,590,218 raw sequence reads were produced. Of which, 7,43,630 were considered to be effective reads (i.e., reads that contain the correct TCMID sequence and the forward primer sequence with a length of ≥200 bp). The effective reads were then assigned to the sequences deposited in SILVA database (v108, http://www.arb-silva.de/), resulting in seven distinct taxonomic groups based on the amplified SSU rRNA gene sequences (Figure 1, Table S2, Supporting information). As expected, the most dominant phylum identified is Glomeromycota to which 6,10,942 effective reads were assigned, accounting for 82.16% of the total effective reads (Table S2). This demonstrates the effectiveness of the AMV4.5NF/AMDGR primer pair in preferential amplification of AMF sequences. Similar to previous studies (Öpik et al., 2009; Lumini et al., 2010; Lin et al., 2012), we also detected some non-AMF sequences that belong to Basidiomycota (90,671 effective reads, accounting for 12.19% of the total effective reads), Ascomycota (1667, 0.22%), Chytridiomycota (953, 0.13%), Blastocladiomycota (66, 0.01%), or Entomophthoromycota (4, nearly 0.00%). A small proportion of amplified sequences (39,327, 5.29%) could not be unambiguously assigned to any of the above phyla (Table S2). To better assess the genetic diversity of the amplified fungal sequences, the 7,43,630 effective reads were clustered into operational taxonomic units (OTU) based on ≥97% sequence similarity, resulting in a total of 3474 OTUs. Among them, 1028 OTUs belong to Glomeromycota (29.59% of the total OTUs), 344 to Basidiomycota (9.90%), 78 to Ascomycota (2.25%), 91 to Chytridiomycota (2.62%), 5 to Blastocladiomycota (0.14%), 1 to Entomophthoromycota (0.03%) and 1927 to the unclassified group (55.47%) (Figure 1, Table S2, Supporting information).


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)

Proportional distribution of total sequence reads and generated OTUs grouped by phyla of fungi from all citrus root samples through blasting against the SILVA database.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 1: Proportional distribution of total sequence reads and generated OTUs grouped by phyla of fungi from all citrus root samples through blasting against the SILVA database.
Mentions: The overall genetic diversity of AMF colonizing citrus roots is not known, nor is the impact of habitats and host plant genotypes on AMF community structures. To explore these areas, we collected roots of citrus trees grown in eight geographical locations in China. A total of 77 root DNA samples from citrus trees of 23 different genotypes or scion/rootstock combinations (i.e., sample groups) grown under different conditions (For details, see Table S1 and Figure S1, Supporting information) were prepared and used for PCR amplification of the 18S small subunit (SSU) rRNA gene fragment using a pair of largely AMF-specific primers AMV4.5NF/AMDGR. The PCR fragments were purified and subjected to 454-high throughput pyrosequencing. A total of 1,590,218 raw sequence reads were produced. Of which, 7,43,630 were considered to be effective reads (i.e., reads that contain the correct TCMID sequence and the forward primer sequence with a length of ≥200 bp). The effective reads were then assigned to the sequences deposited in SILVA database (v108, http://www.arb-silva.de/), resulting in seven distinct taxonomic groups based on the amplified SSU rRNA gene sequences (Figure 1, Table S2, Supporting information). As expected, the most dominant phylum identified is Glomeromycota to which 6,10,942 effective reads were assigned, accounting for 82.16% of the total effective reads (Table S2). This demonstrates the effectiveness of the AMV4.5NF/AMDGR primer pair in preferential amplification of AMF sequences. Similar to previous studies (Öpik et al., 2009; Lumini et al., 2010; Lin et al., 2012), we also detected some non-AMF sequences that belong to Basidiomycota (90,671 effective reads, accounting for 12.19% of the total effective reads), Ascomycota (1667, 0.22%), Chytridiomycota (953, 0.13%), Blastocladiomycota (66, 0.01%), or Entomophthoromycota (4, nearly 0.00%). A small proportion of amplified sequences (39,327, 5.29%) could not be unambiguously assigned to any of the above phyla (Table S2). To better assess the genetic diversity of the amplified fungal sequences, the 7,43,630 effective reads were clustered into operational taxonomic units (OTU) based on ≥97% sequence similarity, resulting in a total of 3474 OTUs. Among them, 1028 OTUs belong to Glomeromycota (29.59% of the total OTUs), 344 to Basidiomycota (9.90%), 78 to Ascomycota (2.25%), 91 to Chytridiomycota (2.62%), 5 to Blastocladiomycota (0.14%), 1 to Entomophthoromycota (0.03%) and 1927 to the unclassified group (55.47%) (Figure 1, Table S2, Supporting information).

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