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Verrucomicrobial community structure and abundance as indicators for changes in chemical factors linked to soil fertility.

Navarrete AA, Soares T, Rossetto R, van Veen JA, Tsai SM, Kuramae EE - Antonie Van Leeuwenhoek (2015)

Bottom Line: Terminal restriction fragment length polymorphism fingerprint and real-time quantitative PCR assay were used to analyze changes in verrucomicrobial communities associated with contrasting soil nutrient conditions in tropical regions.In case study Model I ("Slash-and-burn deforestation") the verrucomicrobial community structures revealed disparate patterns in nutrient-enriched soils after slash-and-burn deforestation and natural nutrient-poor soils under an adjacent primary forest in the Amazonia (R = 0.819, P = 0.002).In nutrient-enriched soils, verrucomicrobial community structures were related to soil factors linked to soil fertility, such as total nitrogen, phosphorus, potassium and sum of bases, i.e., the sum of calcium, magnesium and potassium contents.

View Article: PubMed Central - PubMed

Affiliation: Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of São Paulo USP, Piracicaba, SP, Brazil.

ABSTRACT
Here we show that verrucomicrobial community structure and abundance are extremely sensitive to changes in chemical factors linked to soil fertility. Terminal restriction fragment length polymorphism fingerprint and real-time quantitative PCR assay were used to analyze changes in verrucomicrobial communities associated with contrasting soil nutrient conditions in tropical regions. In case study Model I ("Slash-and-burn deforestation") the verrucomicrobial community structures revealed disparate patterns in nutrient-enriched soils after slash-and-burn deforestation and natural nutrient-poor soils under an adjacent primary forest in the Amazonia (R = 0.819, P = 0.002). The relative proportion of Verrucomicrobia declined in response to increased soil fertility after slash-and-burn deforestation, accounting on average, for 4 and 2 % of the total bacterial signal, in natural nutrient-poor forest soils and nutrient-enriched deforested soils, respectively. In case study Model II ("Management practices for sugarcane") disparate patterns were revealed in sugarcane rhizosphere sampled on optimal and deficient soil fertility for sugarcane (R = 0.786, P = 0.002). Verrucomicrobial community abundance in sugarcane rhizosphere was negatively correlated with soil fertility, accounting for 2 and 5 % of the total bacterial signal, under optimal and deficient soil fertility conditions for sugarcane, respectively. In nutrient-enriched soils, verrucomicrobial community structures were related to soil factors linked to soil fertility, such as total nitrogen, phosphorus, potassium and sum of bases, i.e., the sum of calcium, magnesium and potassium contents. We conclude that community structure and abundance represent important ecological aspects in soil verrucomicrobial communities for tracking the changes in chemical factors linked to soil fertility under tropical environmental conditions.

No MeSH data available.


Related in: MedlinePlus

Constrained ordination diagram for sample plots (deforested and forest soil samples) in the first two redundancy analysis (RDA) axes based on the soil chemical characteristics of the different sampling sites and their relationship with the verrucomicrobial T-RFLP generated by restriction with enzymes AluI, MspI and HhaI. Symbols refer to individual replicates (A, B, C, D and E) of the following sampling sites: open squares forest site located at Area 1 (FS1), open diamonds forest site located at Area 2 (FS2), open circle forest site located at Area 3 (FS3), black squares deforested site located at Area 1 (DS1), black diamonds deforested site located at Area 2 (DS2), black circle deforested site located at Area 3 (DS3)
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Fig2: Constrained ordination diagram for sample plots (deforested and forest soil samples) in the first two redundancy analysis (RDA) axes based on the soil chemical characteristics of the different sampling sites and their relationship with the verrucomicrobial T-RFLP generated by restriction with enzymes AluI, MspI and HhaI. Symbols refer to individual replicates (A, B, C, D and E) of the following sampling sites: open squares forest site located at Area 1 (FS1), open diamonds forest site located at Area 2 (FS2), open circle forest site located at Area 3 (FS3), black squares deforested site located at Area 1 (DS1), black diamonds deforested site located at Area 2 (DS2), black circle deforested site located at Area 3 (DS3)

Mentions: The relationship between soil chemical characteristics and verrucomicrobial community structures revealed by T-RFLP fingerprinting for nutrient-enriched soils after slash-and-burn deforestation (deforested soils) and natural nutrient-poor soils (forest soils) were calculated by redundancy analysis (RDA). A total of 64.3 % of all variation was explained by the first two RDA axes (Fig. 2). RDA results showed that community structures from deforested soils were related to soil chemical factors linked to soil fertility, such as total nitrogen (Ntot), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), sum of bases (the sum of Ca, Mg and K), and soil pH. Verrucomicrobial community structures from forest soils were related to manganese (Mn), copper (Cu), iron (Fe) and organic matter (OM) content as well as cation exchange capacity (CEC) and potential acidity (H + Al) (Fig. 2).Fig. 2


Verrucomicrobial community structure and abundance as indicators for changes in chemical factors linked to soil fertility.

Navarrete AA, Soares T, Rossetto R, van Veen JA, Tsai SM, Kuramae EE - Antonie Van Leeuwenhoek (2015)

Constrained ordination diagram for sample plots (deforested and forest soil samples) in the first two redundancy analysis (RDA) axes based on the soil chemical characteristics of the different sampling sites and their relationship with the verrucomicrobial T-RFLP generated by restriction with enzymes AluI, MspI and HhaI. Symbols refer to individual replicates (A, B, C, D and E) of the following sampling sites: open squares forest site located at Area 1 (FS1), open diamonds forest site located at Area 2 (FS2), open circle forest site located at Area 3 (FS3), black squares deforested site located at Area 1 (DS1), black diamonds deforested site located at Area 2 (DS2), black circle deforested site located at Area 3 (DS3)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4525199&req=5

Fig2: Constrained ordination diagram for sample plots (deforested and forest soil samples) in the first two redundancy analysis (RDA) axes based on the soil chemical characteristics of the different sampling sites and their relationship with the verrucomicrobial T-RFLP generated by restriction with enzymes AluI, MspI and HhaI. Symbols refer to individual replicates (A, B, C, D and E) of the following sampling sites: open squares forest site located at Area 1 (FS1), open diamonds forest site located at Area 2 (FS2), open circle forest site located at Area 3 (FS3), black squares deforested site located at Area 1 (DS1), black diamonds deforested site located at Area 2 (DS2), black circle deforested site located at Area 3 (DS3)
Mentions: The relationship between soil chemical characteristics and verrucomicrobial community structures revealed by T-RFLP fingerprinting for nutrient-enriched soils after slash-and-burn deforestation (deforested soils) and natural nutrient-poor soils (forest soils) were calculated by redundancy analysis (RDA). A total of 64.3 % of all variation was explained by the first two RDA axes (Fig. 2). RDA results showed that community structures from deforested soils were related to soil chemical factors linked to soil fertility, such as total nitrogen (Ntot), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), sum of bases (the sum of Ca, Mg and K), and soil pH. Verrucomicrobial community structures from forest soils were related to manganese (Mn), copper (Cu), iron (Fe) and organic matter (OM) content as well as cation exchange capacity (CEC) and potential acidity (H + Al) (Fig. 2).Fig. 2

Bottom Line: Terminal restriction fragment length polymorphism fingerprint and real-time quantitative PCR assay were used to analyze changes in verrucomicrobial communities associated with contrasting soil nutrient conditions in tropical regions.In case study Model I ("Slash-and-burn deforestation") the verrucomicrobial community structures revealed disparate patterns in nutrient-enriched soils after slash-and-burn deforestation and natural nutrient-poor soils under an adjacent primary forest in the Amazonia (R = 0.819, P = 0.002).In nutrient-enriched soils, verrucomicrobial community structures were related to soil factors linked to soil fertility, such as total nitrogen, phosphorus, potassium and sum of bases, i.e., the sum of calcium, magnesium and potassium contents.

View Article: PubMed Central - PubMed

Affiliation: Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of São Paulo USP, Piracicaba, SP, Brazil.

ABSTRACT
Here we show that verrucomicrobial community structure and abundance are extremely sensitive to changes in chemical factors linked to soil fertility. Terminal restriction fragment length polymorphism fingerprint and real-time quantitative PCR assay were used to analyze changes in verrucomicrobial communities associated with contrasting soil nutrient conditions in tropical regions. In case study Model I ("Slash-and-burn deforestation") the verrucomicrobial community structures revealed disparate patterns in nutrient-enriched soils after slash-and-burn deforestation and natural nutrient-poor soils under an adjacent primary forest in the Amazonia (R = 0.819, P = 0.002). The relative proportion of Verrucomicrobia declined in response to increased soil fertility after slash-and-burn deforestation, accounting on average, for 4 and 2 % of the total bacterial signal, in natural nutrient-poor forest soils and nutrient-enriched deforested soils, respectively. In case study Model II ("Management practices for sugarcane") disparate patterns were revealed in sugarcane rhizosphere sampled on optimal and deficient soil fertility for sugarcane (R = 0.786, P = 0.002). Verrucomicrobial community abundance in sugarcane rhizosphere was negatively correlated with soil fertility, accounting for 2 and 5 % of the total bacterial signal, under optimal and deficient soil fertility conditions for sugarcane, respectively. In nutrient-enriched soils, verrucomicrobial community structures were related to soil factors linked to soil fertility, such as total nitrogen, phosphorus, potassium and sum of bases, i.e., the sum of calcium, magnesium and potassium contents. We conclude that community structure and abundance represent important ecological aspects in soil verrucomicrobial communities for tracking the changes in chemical factors linked to soil fertility under tropical environmental conditions.

No MeSH data available.


Related in: MedlinePlus