Contrasting the microbiomes from forest rhizosphere and deeper bulk soil from an Amazon rainforest reserve

Fonseca, Jose Pedro; Hoffmann, Luísa; Cabral, Bianca Catarina Azeredo; Dias, Victor Hugo Giordano; Miranda, Maximiliano; Martins, Allan Cézar de Azevedo; Boschiero, Clarissa; Bastos, Wanderley Rodrigues; Silva, Rosane

doi:10.1016/j.gene.2017.11.039

Cited by 43 publications

(23 citation statements)

References 44 publications

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“…At the phylum level, the three most abundant bacteria in both rhizosphere and bulk soil samples were Proteobacteria, Actinobacteria and Acidobacteria, consistent with the ndings of Fonseca et al (2018). The relative abundance of Actinobacteria and Verrucomocrobia decreased from F to T, while Proteobacteria showed an opposite trend ( Figure.…”

Section: Discussionsupporting

confidence: 80%

Impact of Robinia pseudoacacia stand conversion on soil bacterial communities composition and soil properties in Mount Tai, China

Li¹,

Han²,

Ni³

et al. 2020

Preprint

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Background: Robinia pseudoacacia is a widely planted pioneer tree species in reforestations on barren mountains in northern China. Because of its nitrogen-fixing ability, it can play a positive role in soil and forest restoration. After clear-cutting of planted stands, R. pseudoacacia stands become coppice plantations. The impacts of shifting from seedling to coppice plantations on soil bacterial community and soil properties have not been well described. This study aims to quantify how soil properties and bacterial community composition vary between planted seedling versus coppice stands.Methods: Three 20×20 m plots were randomly selected in each seedling and coppice stand. The bulk soil and rhizosphere soil were sampled in the nine above-mentioned sample plots in the summer of 2017. Bulk soil was sampled at 10 cm from the soil surface using a soil auger. Rhizosphere soil samples were collected by brush. The soil samples were transported to the laboratory for chemical analysis and bacterial community composition and diversity was obtanied through DNA extraction, 16S rRNA gene amplification and high throughput sequencing.Results: The results showed that, compared to seedling plantations, soil quality decreased significantly in coppice stands, but without affecting soil exchangeable Mg2+ and K+. Total carbon (C) and nitrogen (N) were lower in the rhizosphere than in bulk soil, whereas nutrient availability showed an opposite trend. The conversion from seedling to coppice plantations was also related to significant differences in soil bacterial community structure and to the reduction of soil bacterial α-diversity. Principal component analysis (PCA) showed that, bacterial community composition was similar in both bulk and rhizosphere soils in second generation coppice plantations. Specially, the conversion from seedling to coppice increased the relative abundance of Proteobacteria and Rhizobium, but reduced that of Actinobacteria, which may result in a decline of soil nutrient availability. Mantel tests revealed that C, N, Soil organic matter (SOM), nitrate nitrogen (NO3--N) and available phosphorus positively correlated with bacterial community composition, while a variation partition analysis (VPA) showed that NO3--N explained a relatively greater proportion of bacterial distribution (15.12%), compared with C and SOM. Surprinsingly, N showed no relationship with bacterial community composition, which may be related to nitrogen transportation. Conclusions: The conversion from seedling to coppice stands reduced soil quality and led to spatial-temporal homogenization of the soil bacterial community structure in both the rhizosphere and bulk soils. Such imbalance in microbial structure can accelerate the decline of R. pseudoacacia. This may affect the role of R. pseudoacacia coppice stands in soil and forest restoration of barren lands in mountain areas.

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Section: Discussionsupporting

confidence: 80%

Impact of Robinia pseudoacacia stand conversion on soil bacterial communities composition and soil properties in Mount Tai, China

Li¹,

Han²,

Ni³

et al. 2020

Preprint

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“…At the phylum level, the three most abundant bacteria in both rhizosphere and bulk soil samples were Proteobacteria, Actinobacteria and Acidobacteria, in accordance with the ndings of Fonseca et al (2018). The relative abundance of Actinobacteria and Verrucomocrobia decreased from F to T stands, while Proteobacteria showed an opposite trend ( Figure 1A).…”

Section: Discussionsupporting

confidence: 78%

“…Rhizosphere is a critical interface supporting the exchange of resources between plants and the surrounding soil environment, which provides microhabitats and niches for diverse microorganisms and microbial species (Philippot et al 2013;Mendes et al 2013). Rhizosphere microorganisms play a key role in plant growth and soil properties, especially in the rhizosphere niche (Philippot et al 2013;Zhang et al 2018a), which in uences several plant physiological processes such as growth and energy metabolism affecting overall plant health (Fonseca et al 2018). Generally, there are signi cant differences between rhizosphere and bulk soil microenvironments, the most obvious of which is that the higher nutrient content and root exudates in the rhizosphere contribute to improving soil carbon and nitrogen concentrations (Yin et al 2018).…”

Section: Introductionmentioning

confidence: 99%

Impact of Robinia pseudoacacia stand conversion on soil properties and bacterial community composition in Mount Tai, China

Han

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Robinia pseudoacacia is a widely planted pioneer tree species in reforestations on barren mountains in northern China. Because of its nitrogen-fixing ability, it can play a positive role in soil and forest restoration. After clear-cutting of planted stands, R. pseudoacacia stands become coppice plantations. The impacts of shifting from seedling to coppice stands on soil bacterial community and soil properties have not been well described. This study aims to quantify how soil properties and bacterial community composition vary between planted seedling versus coppice stands.Methods: Nine 20×20 m plots were randomly selected in seedling and coppice stands. The bulk soil and rhizosphere soil were sampled in summer 2017. Bulk soil was sampled at 10 cm from the soil surface using a soil auger. Rhizosphere soil samples were collected using a brush. The soil samples were transported to the laboratory for chemical analysis, and bacterial community composition and diversity was obtained through DNA extraction, 16S rRNA gene amplification and high-throughput sequencing.Results: The results showed that, compared to seedling plantations, soil quality decreased significantly in coppice stands, but without affecting soil exchangeable Mg2+ and K+. Total carbon (C) and nitrogen (N) were lower in the rhizosphere than in bulk soil, whereas nutrient availability showed an opposite trend. The conversion from seedling to coppice plantations was also related to significant differences in soil bacterial community structure and to the reduction of soil bacterial α-diversity. Principal component analysis (PCA) showed that bacterial community composition was similar in both bulk and rhizosphere soils in second generation coppice plantations. Specially, the conversion from seedling to coppice stands increased the relative abundance of Proteobacteria and Rhizobium, but reduced that of Actinobacteria, which may result in a decline of soil nutrient availability. Mantel tests revealed that C, N, Soil organic matter (SOM), nitrate nitrogen (NO3--N) and available phosphorus positively correlated with bacterial community composition, while a variation partition analysis (VPA) showed that NO3--N explained a relatively greater proportion of bacterial distribution (15.12%), compared with C and SOM. Surprisingly, N showed no relationship with bacterial community composition, which may be related to nitrogen transportation.Conclusions: The conversion from seedling to coppice stands reduced soil quality and led to spatial-temporal homogenization of the soil bacterial community structure in both the rhizosphere and bulk soils. Such imbalance in microbial structure can accelerate the decline of R. pseudoacacia. This may affect the role of R. pseudoacacia coppice stands in soil and forest restoration of barren lands in mountain areas.

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“…The microorganisms found in these samples were collected in pH 4.0 to 4.7 at 35°C. The group of bacteria and archaea described here can be found in soil at pH 3.7 to 4.5 [ 20 , 21 ]. Indeed, some microbial populations from acidic forest soils are more tolerant to acidic cultivation conditions [ 22 ].…”

Section: Discussionmentioning

confidence: 99%

Microbial enrichment and gene functional categories revealed on the walls of a spent fuel pool of a nuclear power plant

et al. 2018

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Microorganisms developing in the liner of the spent fuel pool (SFP) and the fuel transfer channel (FTC) of a Nuclear Power Plant (NPP) can form high radiation resistant biofilms and cause corrosion. Due to difficulties and limitations to obtain large samples from SFP and FTC, cotton swabs were used to collect the biofilm from the wall of these installations. Molecular characterization was performed using massively parallel sequencing to obtain a taxonomic and functional gene classification. Also, samples from the drainage system were evaluated because microorganisms may travel over the 12-meter column of the pool water of the Brazilian Nuclear Power Plant (Angra1), which has been functioning since 1985. Regardless of the treatment of the pool water, our data reveal the unexpected presence of Fungi (Basidiomycota and Ascomycota) as the main contaminators of the SFP and FTC. Ustilaginomycetes (Basidiomycota) was the major class contributor (70%) in the SFP and FTC reflecting the little diversity in these sites; nevertheless, Proteobacteria, Actinobacteria, Firmicutes (Bacilli) were present in small proportions. Mapping total reads against six fungal reference genomes indicate that there is, in fact, a high abundance of fungal sequences in samples collected from SFP and FTC. Analysis of the ribosomal internal transcribed spacer (ITS) 1 and 2 regions and the protein found in the mitochondria of eukaryotic cells, cytochrome b (cytb) grouped our sample fungi in the clade 7 as Ustilago and Pseudozyma. In contrast, in the drainage system, Alphaproteobacteria were present in high abundances (55%). The presence of Sphingopyxis, Mesorhizobium, Erythrobacter, Sphingomonas, Novosphingobium, Sphingobium, Chelativorans, Oceanicaulis, Acidovorax, and Cyanobacteria was observed. Based on genomic annotation data, the assessment of the biological function found a higher proportion of protein-coding sequences related to respiration and protein metabolism in SFP and FTC samples. The knowledge of this biological inventory present in the system may contribute to further studies of potential microorganisms that might be useful for bioremediation of nuclear waste.

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Contrasting the microbiomes from forest rhizosphere and deeper bulk soil from an Amazon rainforest reserve

Cited by 43 publications

References 44 publications

Impact of Robinia pseudoacacia stand conversion on soil bacterial communities composition and soil properties in Mount Tai, China

Impact of Robinia pseudoacacia stand conversion on soil bacterial communities composition and soil properties in Mount Tai, China

Impact of Robinia pseudoacacia stand conversion on soil properties and bacterial community composition in Mount Tai, China

Microbial enrichment and gene functional categories revealed on the walls of a spent fuel pool of a nuclear power plant

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