Amazon forest-to-agriculture conversion alters rhizosphere microbiome composition while functions are kept

Goss‐Souza, Dennis; Mendes, Lucas William; Borges, Clóvis Daniel; Rodrigues, Jorge L. Mazza; Tsai, Siu Mui

doi:10.1093/femsec/fiz009

Cited by 42 publications

(27 citation statements)

References 82 publications

(98 reference statements)

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“…4c ). Dominance of Proteobacteria recorded in pea rhizosphere samples, with significant increase in the abundance of genera including Pseudomonas, Rhizobium, Pantoae, Enterobacter and Sphingomonas known for plant growth promoting attributes, was in agreement with the previous studies on the rhizosphere microbiome analysis (Mendes et al, 2013; Weinert et al, 2011; Yurgelet al, 2018; Goss-Souza et al, 2019). Pea-Rhizobium symbiosis is well documented in Indian soils (Rahi et al, 2012), hence increase in the abundance of Rhizobium in pea rhizosphere was expected.…”

Section: Discussionsupporting

confidence: 91%

“…In addition to Proteobacteria, a significantly higher abundance of Bacteroidetes and Planctomycetes was also recorded in the rhizosphere soil in comparison to bulk soil samples ( Figs. 3-4 ), positive correlations with increased abundance of Bacteroidetes and Planctomycetes have been observed to increase in organic carbon and phosphorus concentrations, respectively in rhizosphere of soybean (Goss-Souza et al, 2019). The genus Nitrobacter was at higher abundance in pea rhizosphere samples than bulk soils (Fig 4b), suggesting its enrichment by host plant as Nitrobacter converts nitrite to nitrate making nitrogen more readily available to the host plant (Richardson et al, 2009; Hubbard et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

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Homogenization of Rhizosphere Bacterial Communities by Pea (Pisum sativum L.) Cultivated under Different Conservation Agricultural Practices in the Eastern Himalayas

Chaudhari

Rangappa

Das

et al. 2019

Preprint

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Conservation agriculture offers a suitable system to harmonize agriculture with the environment, especially in fragile ecosystems of North-East India. Soil microbes play pivotal roles in ecosystem functioning and act as indispensable indicators of overall fitness of crop plant and soil health. Here we demonstrated that altercations in residue management and tillage practices lead to the development of differential bacterial communities forcing the pea plants to recruit special groups of bacteria leading to highly homogenous rhizosphere communities. Pea rhizosphere and bulk soil samples were collected, and bacterial community structure was estimated by 16S rRNA gene amplicon sequencing and predictive functional analysis was performed using Tax4Fun. The effect on pea plants was evident in the bacterial communities as the overall diversity of rhizosphere samples was significantly higher to that of bulk soil samples. Bacillus, Staphylococcus, Planomicrobium, Enterobacter, Arthrobacter, Nitrobacter, Geobacter, and Sphingomonas were noticed as the most abundant genera in the rhizosphere and bulk soil samples. The abundance of Firmicutes and Proteobacteria altered significantly in the rhizosphere and bulk samples, which was further validated by qPCR. Selection of specific taxa by pea plant was indicated by the higher values of mean proportion of Rhizobium, Pseudomonas, Pantoea, Nitrobacter, Enterobacter and Sphingomonas in rhizosphere samples, and Massilia, Paenibacillus and Planomicrobium in bulk soil samples. Tillage and residue management treatments did not significantly alter the bacterial diversity, while their influence was observed on the abundance of few genera. Recorded results revealed that pea plant selects specific taxa into its rhizosphere plausibly to meet its requirements for nutrient uptake and stress amelioration under the different tillage and residue management practices.

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Section: Discussionsupporting

confidence: 91%

Section: Discussionmentioning

confidence: 99%

Homogenization of Rhizosphere Bacterial Communities by Pea (Pisum sativum L.) Cultivated under Different Conservation Agricultural Practices in the Eastern Himalayas

Chaudhari

Rangappa

Das

et al. 2019

Preprint

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“…The dataset used here is the same as in [34], such that we provide a brief summary of methods used to generate those data. In order to evaluate long-term effects of forestto-agriculture conversion on microbial assembly and ecological process, we analyzed bulk soil and soybean rhizosphere mi-crobial communities found in a chronosequence of amazon soils as follow: first-year of cultivation after deforestation (1year) to tenth (10-year) and twentieth (20year) year of con-secutive cultivation in notill cropping system, with succes-sive rotation of cultures, always with soybean as the main summer culture.…”

Section: Soil Sampling Mesocosms Experiment and Environmental Analysesmentioning

confidence: 99%

“…Overall, from 1-to 20year chronosequence, only functions related to "potassium me-tabolism" have shifted, decreasing with long-term no till cropping. Details regarding taxonomic and functional profiling of microbial metagenomes can be found in [34].…”

Section: Taxonomic and Functional Profiling Of Microbial Metagenomesmentioning

confidence: 99%

“…We noticed that beta diversity in bulk soil did not vary along the chronosequence while it decreased in rhizosphere from 1 to 10 years, with no differences between 10-and 20-year no-till cropping. As we previously found [34] shifts in abundance for several taxa for both bulk soil and rhizosphere along the chronosequence, we depicted the Sørensen beta diversity into turnover (βSIM) and nestedness-resultant dissimilarity (βSNE) components, in order to explain those shifts. For bulk soil, in 1-year no-till ( Fig.…”

Section: Taxonomic and Functional Profiling Of Microbial Metagenomesmentioning

confidence: 99%

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Ecological Processes Shaping Bulk Soil and Rhizosphere Microbiome Assembly in a Long-Term Amazon Forest-to-Agriculture Conversion

et al. 2019

Self Cite

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Forest-to-agriculture conversion has been identified as a major threat to soil biodiversity and soil processes resilience, although the consequences of long-term land use change to microbial community assembly and ecological processes have been often neglected. Here, we combined metagenomic approach with a large environmental dataset, to (i) identify the microbial assembly patterns and,(ii) to evaluate the ecological processes governing microbial assembly, in bulk soil and soybean rhizosphere, along a long-term forest-to-agriculture conversion chronosequence, in Eastern Amazon. We hypothesized that (i) microbial communities in bulk soil and rhizosphere have different assembly patterns and (ii) the weight of the four ecological processes governing assembly differs between bulk soil and rhizosphere and along the chronosequence in the same fraction. Community assembly in bulk soil fitted most the zero-sum multinomial (ZSM) neutral-based model, regardless of time. Low to intermediate dispersal was observed. Decreasing influence of abiotic factors was counterbalanced by increasing influence of biotic factors, as the chronosequence advanced. Undominated ecological processes of dispersal limitation and variable selection governing community assembly were observed in this soil fraction. For soybean rhizosphere, community assembly fitted most the lognormal niche-based model in all chronosequence areas. High dispersal and an increasing influence of abiotic factors coupled with a decreasing influence of biotic factors were found along the chronosequence. Thus, we found a dominant role of dispersal process governing microbial assembly with a secondary effect of homogeneous selection process, mainly driven by decreasing aluminum and increased cations saturation in soil solution, due to long-term no-till cropping. Together, our results indicate that long-term no-till lead community abundances in bulk soil to be in a transient and conditional state, while for soybean rhizosphere, community abundances reach a periodic and permanent distribution state. Dominant dispersal process in rhizosphere, coupled with homogeneous selection, brings evidences that soybean root system selects microbial taxa via trade-offs in order to keep functional resilience of soil processes.

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Structure and putative function of a soil microbial community impacted by the deposition of tailings and subsequent revegetation after the rupture of the Fundao Dam

Cavalcante

Silva

et al. 2022

Land Degrad Dev

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The rupture of the Fundão Dam containing iron‐rich mining tailings, in 2015, was one of the worst environmental disasters in Brazil. The deposition of tailings has generated serious impacts on the soil and, as microorganisms play an important role in these environments, the recovery of the microbial community is a critical step in restoring the soil for sustainable use. Soil microorganisms and their activities are recognized as sensitive bioindicators for environmental changes; however, few experiments have been conducted to investigate the response of the microbial community to the magnitude of the impact caused by the Fundão Dam rupture and the effect of the use of revegetation natural or induced for ecosystem recovery, especially in Brazil. This study aimed to evaluate the dynamics of community structure and putative functions, over time, in response to the deposition of the tailings on the soil by bacterial 16S rRNA sequencing. We evaluated an area affected by tailings, covered with natural and induced revegetation. The results revealed a temporal dynamic of the soil microbiota, which demonstrates that the microbial community structure of these areas differed, mainly in less abundant taxa, and the induced revegetation area was closer to the forest than natural revegetation. These results reveal the importance of implementing revegetation programs to accelerate the initial recovery. Functions related to the use of alternative electron acceptors differed, possibly due to the greater compaction of the affected soil. Despite the improvement of the impacted areas over time, the strong effect of tailings deposition on the bacterial community structure can still be noticed.

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Amazon forest-to-agriculture conversion alters rhizosphere microbiome composition while functions are kept

Abstract: Although the forest-to-agriculture conversion leads to a loss of diversity, the soybean rhizosphere selects a specific microbial community in order to keep important functions in a long-term cropping in Amazon soils.

Cited by 42 publications

References 82 publications

Homogenization of Rhizosphere Bacterial Communities by Pea (Pisum sativum L.) Cultivated under Different Conservation Agricultural Practices in the Eastern Himalayas

Homogenization of Rhizosphere Bacterial Communities by Pea (Pisum sativum L.) Cultivated under Different Conservation Agricultural Practices in the Eastern Himalayas

Ecological Processes Shaping Bulk Soil and Rhizosphere Microbiome Assembly in a Long-Term Amazon Forest-to-Agriculture Conversion

Structure and putative function of a soil microbial community impacted by the deposition of tailings and subsequent revegetation after the rupture of the Fundao Dam

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