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

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.

16S rRNA Gene Amplicon Sequencing Data from Flooded Rice Paddy Mesocosms Treated with Different Silicon-Rich Soil Amendments.

How silicon-rich soil amendments impact the microbial community is unresolved. We report 16S rRNA gene sequencing data from flooded rice paddy mesocosms treated with different silicon amendments sampled over the growing season. We generated 11,678 operational taxonomic units (OTUs) and found that microbial communities were significantly different across treatments, time points, and biospheres.

Si-induced DMA desorption is not the driver for enhanced DMA availability after Si addition to flooded soils.

Silicon (Si) addition to flooded rice paddy soil tends to decrease grain inorganic arsenic (iAs) and increase grain dimethylarsinic acid (DMA) concentrations, but the mechanism for the increase in plant-available DMA is unresolved. It has been suggested that Si displaces DMA from soil solids, rendering it plant-available; however, we hypothesize that Si desorbs primarily iAs from soil solids, which stimulates methylation to DMA. We added silicic acid to a contaminated paddy soil and a flooded upland soil that had been historically contaminated with lead arsenate in a batch incubation experiment, and measured changes in solid-phase As speciation, porewater As speciation, and As-methylating microbial (AsMM) abundance over time. We found that DMA was not detectable in soils prior to the start of the experiment nor throughout the experiment, so it comprised a trace amount of total soil As. Upon Si addition to paddy soil, total As increased in porewater following Si spike and this increase was mainly due to iAs desorption, and an order of magnitude less MMA and DMA was desorbed. The upland soil transitioned to reducing conditions throughout the experiment, but when they were achieved, iAs was desorbed first and this was followed by an increase of MMA and then DMA compared to control soils. Total microbial community abundance increased over the course of the experiments and arsM gene abundance increased from initial conditions, but did not differ between treatments. In the paddy soil, the ratio of arsM:16S gene abundance decreased from the initial conditions, but it increased in the upland soil with historic As contamination. These results suggest that Si-induced desorption of DMA is small and likely does not explain the increases of plant-available DMA upon Si fertilization in prior work. Likely, Si-induced iAs desorption drives microorganisms to methylate iAs, but degree of methylation will differ between soils.

Silicon Decreases Dimethylarsinic Acid Concentration in Rice Grain and Mitigates Straighthead Disorder.

While root Si transporters play a role in the uptake of arsenite and organic As species dimethylarsinic acid (DMA) and monomethylarsonic acid (MMA) in rice ( Oryza sativa L.), the impact of Si addition on the accumulation of DMA and MMA in reproductive tissues has not been directly evaluated, particularly in isolation from inorganic As species. Furthermore, DMA and MMA are suspected causal agents of straighthead disorder. We performed a hydroponic study to disentangle the impact of Si on accumulation of DMA and MMA in rice grain. At 5 µM, MMA was toxic to rice, regardless of Si addition, although Si significantly decreased root MMA concentrations. Plants dosed with 5 µM DMA grew well vegetatively but exhibited straighthead disorder at the lowest Si dose, and this DMA-induced yield loss reversed with increasing solution Si. Increasing Si also significantly decreased DMA concentrations in roots, straw, husk, and grain, particularly in mature plants. Si restricted grain DMA through competition for root uptake and downregulation of root Si transporters particularly at later stages of growth when Si uptake was greatest. Our finding that DMA causes straighthead disorder under low Si availability but not under high Si availability suggests Si as a straighthead management strategy.