Silicon-rich soil amendments impact microbial community composition and the composition of arsM bearing microbes

Dykes, Gretchen E.; Limmer, Matt A.; Seyfferth, Angelia L.

doi:10.1007/s11104-021-05103-8

Cited by 10 publications

(4 citation statements)

References 67 publications

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“…Details on soil chemistry and treatments, including fertilization, and water management can be found in the Materials and Methods section. Previous studies of the microbial community showed that Si amendments had less of an impact than redox status ( 43 , 44 ). Given the variability in chemistry and community composition across the 12 paddies, here we show chemistry (plaque iron content and mineralogy) for each paddy individually ( 45 ), and then aggregate samples from all treatments to evaluate the most abundant FeOB and FeRB across all conditions.…”

Section: Resultsmentioning

confidence: 97%

“…Paddies were amended prior to planting in 2015 and did not receive further Si amendments in 2016 ( 46 ) or in 2017. Treatments had less of an impact than redox status and microhabitats on the microbial community ( 43 , 44 ); therefore, the present study focused on the diversity and abundance of microbes associated with Fe cycling over the rice life cycle and data are averaged across all four treatments. Prior to planting in 2016 and in 2017, only roots from the previous year were tilled into the soil and paddies were fertilized with 112 kg N/ha as urea and 135 kg K 2 O/ha as KCl based on soil testing and fertility recommendations.…”

Section: Methodsmentioning

confidence: 99%

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Gallionellaceae in rice root plaque: metabolic roles in iron oxidation, nutrient cycling, and plant interactions

Chan,

Dykes,

Hoover

et al. 2023

Appl Environ Microbiol

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On the roots of wetland plants such as rice, Fe(II) oxidation forms Fe(III) oxyhydroxide-rich plaques that modulate plant nutrient and metal uptake. The microbial roles in catalyzing this oxidation have been debated and it is unclear if these iron-oxidizers mediate other important biogeochemical and plant interactions. To investigate this, we studied the microbial communities, metagenomes, and geochemistry of iron plaque on field-grown rice, plus the surrounding rhizosphere and bulk soil. Plaque iron content (per mass root) increased over the growing season, showing continuous deposition. Analysis of 16S rRNA genes showed abundant Fe(II)-oxidizing and Fe(III)-reducing bacteria (FeOB and FeRB) in plaque, rhizosphere, and bulk soil. FeOB were enriched in relative abundance in plaque, suggesting FeOB affinity for the root surface. Gallionellaceae FeOB Sideroxydans were enriched during vegetative and early reproductive rice growth stages, while a Gallionella was enriched during reproduction through grain maturity, suggesting distinct FeOB niches over the rice life cycle. FeRB Anaeromyxobacter and Geobacter increased in plaque later, during reproduction and grain ripening, corresponding to increased plaque iron. Metagenome-assembled genomes revealed that Gallionellaceae may grow mixotrophically using both Fe(II) and organics. The Sideroxydans are facultative, able to use non-Fe substrates, which may allow colonization of rice roots early in the season. FeOB genomes suggest adaptations for interacting with plants, including colonization, plant immunity defense, utilization of plant organics, and nitrogen fixation. Taken together, our results strongly suggest that rhizoplane and rhizosphere FeOB can specifically associate with rice roots, catalyzing iron plaque formation, with the potential to contribute to plant growth. IMPORTANCE In waterlogged soils, iron plaque forms a reactive barrier between the root and soil, collecting phosphate and metals such as arsenic and cadmium. It is well established that iron-reducing bacteria solubilize iron, releasing these associated elements. In contrast, microbial roles in plaque formation have not been clear. Here, we show that there is a substantial population of iron oxidizers in plaque, and furthermore, that these organisms ( Sideroxydans and Gallionella ) are distinguished by genes for plant colonization and nutrient fixation. Our results suggest that iron-oxidizing and iron-reducing bacteria form and remodel iron plaque, making it a dynamic system that represents both a temporary sink for elements (P, As, Cd, C, etc.) as well as a source. In contrast to abiotic iron oxidation, microbial iron oxidation results in coupled Fe-C-N cycling, as well as microbe-microbe and microbe-plant ecological interactions that need to be considered in soil biogeochemistry, ecosystem dynamics, and crop management.

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Section: Resultsmentioning

confidence: 97%

Section: Methodsmentioning

confidence: 99%

Gallionellaceae in rice root plaque: metabolic roles in iron oxidation, nutrient cycling, and plant interactions

Chan,

Dykes,

Hoover

et al. 2023

Appl Environ Microbiol

Self Cite

View full text Add to dashboard Cite

show abstract

“…Paddies were amended prior to planting in 2015 and did not receive further Si amendments in 2016 (44) or in 2017. Treatments had less of an impact than redox status and microhabitats on the microbial community (98, 99); therefore, the present study focused on diversity and abundance of microbes associated with Fe cycling over the rice life cycle and data are averaged across all four treatments. Prior to planting in 2016 and in 2017, only roots from the previous year were tilled into the soil and paddies were fertilized with 112 kg N/ha as urea and 135 kg K 2 O/ha as KCl based on soil testing and fertility recommendations.…”

Section: Methodsmentioning

confidence: 99%

“…Details on soil chemistry and treatments, including fertilization, and water management can be found in the Methods section. Previous studies of the microbial community showed that Si amendments had less of an impact than redox status (98,99). Given the 7 variability in chemistry and community composition across the 12 paddies, here we show chemistry (plaque iron content and mineralogy) for each paddy individually (43), and then aggregate samples from all treatments to evaluate the most abundant FeOB and FeRB across all conditions.…”

Section: Rice Paddy Experimentsmentioning

confidence: 99%

Gallionellaceae in rice root plaque: metabolic roles in iron oxidation, nutrient cycling, and plant interactions

Chan

Dykes

Hoover

et al. 2023

Preprint

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On the roots of wetland plants such as rice, iron oxidation forms iron-rich plaques that modulate plant nutrient and metal uptake. An enduring question is whether microbes catalyze this iron oxidation and, furthermore, if these iron-oxidizers mediate other important biogeochemical and plant interactions. To investigate this, we studied the microbial communities, metagenomes, and geochemistry of iron plaque on field-grown rice, as well as the surrounding rhizosphere and bulk soil. Plaque iron content (per mass root) increased over the growing season, showing continuous deposition. Analysis of 16S rRNA genes showed abundant iron-oxidizing and iron-reducing bacteria (FeOB and FeRB) in plaque, rhizosphere and bulk soil. FeOB were enriched in plaque, suggesting FeOB affinity for the root surface. Gallionellaceae FeOBSideroxydanswere enriched during the vegetative and early reproductive rice growth stages, while aGallionellawas enriched during reproduction through grain maturity, suggesting distinct FeOB niches over the rice life cycle. FeRBAnaeromyxobacterandGeobacterincreased in plaque later, during reproduction and grain ripening, corresponding to increased plaque iron. Metagenome-assembled genomes reveal that the Gallionellaceae may grow mixotrophically using both Fe(II) and organics. TheSideroxydansare facultative, able to use non-Fe substrates, which may allow colonization of rice roots early in the season. FeOB genomes suggest adaptations for interacting with plants, including colonization, immunity, utilization of plant organics, and nitrogen fixation. Together, our results strongly suggest that rhizoplane and rhizosphere FeOB are specifically associated with the rice plants, catalyzing the formation of iron plaque, with the potential to contribute to plant growth.

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Controlling exposure to As and Cd from rice via irrigation management

Limmer,

Seyfferth

2024

Environ Geochem Health

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Irrigation management controls biogeochemical cycles in rice production. Under flooded paddy conditions, arsenic becomes plant-available as iron-reducing conditions ensue, while oxic conditions lead to increased plant availability of Cd in acidic soils. Because Cd enters rice through Mn transporters, we hypothesized that irrigation resulting in intermediate redox could simultaneously limit both As and Cd in rice grain due to As retention in soil and Mn competition for Cd uptake. In a 2 year field study, we used 6 irrigation managements that varied in extent and frequency of inundation, and we observed strong effects of irrigation management on porewater chemistry, soil redox potentials, plant As and Cd concentrations, plant nutrient concentrations, and methane emissions. Plant As decreased with drier irrigation management, but in the grain this effect was stronger for organic As than for inorganic As. Grain organic As, but not inorganic As, was strongly and positively correlated with cumulative methane emissions. Conversely, plant Cd increased under more aerobic irrigation management and grain Cd was negatively correlated with porewater Mn. A hazard index approach showed that in the tested soil with low levels of As and Cd (5.4 and 0.072 mg/kg, respectively), irrigation management could not simultaneously decrease grain As and Cd. Many soil properties, such as reducible As, available Cd, soil pH, available S, and soil organic matter should be considered when attempting to optimize irrigation management when the goal is decreasing the risk of As and Cd in rice grain.

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Silicon-rich soil amendments impact microbial community composition and the composition of arsM bearing microbes

Cited by 10 publications

References 67 publications

Gallionellaceae in rice root plaque: metabolic roles in iron oxidation, nutrient cycling, and plant interactions

Gallionellaceae in rice root plaque: metabolic roles in iron oxidation, nutrient cycling, and plant interactions

Gallionellaceae in rice root plaque: metabolic roles in iron oxidation, nutrient cycling, and plant interactions

Controlling exposure to As and Cd from rice via irrigation management

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