Prevalence of Methylated Arsenic and Microbial Arsenic Methylation Genes in Paddy Soils of the Mekong Delta

Abstract

Microbially mediated inorganic-methylated arsenic (As) transformation in paddy soil is crucial to rice safety; however, the linkages between the microbial As methylation process and methylated As species remain elusive. Here, 62 paddy soils were collected from the Mekong River delta of Cambodia to profile As-related functional gene composition involved in the As cycle. The soil As concentration ranged from <1 to 16.6 mg kg–1, with average As contents of approximately 81% as methylated As and 54% as monomethylarsenate (MMAs­(V)) in the phosphate- and oxalate-extractable fractions based on As sequential extraction analysis. Quantitative PCR revealed high arsenite-methylating gene (arsM) copy numbers, and metagenomics identified consistently high arsM gene abundance. The abundance of As-related genes was the highest in bacteria, followed by archaea and fungi. Pseudomonas, Bradyrhizobium, Burkholderia, and Anaeromyxobacter were identified as bacteria harboring the most genes related to As biotransformation. Moreover, arsM and arsI (As demethylation) gene-containing operons were identified in the metagenome-assembled genomes (MAGs), implying that arsM and arsI could be transcribed together. The prevalence of methylated As and arsM genes may have been overlooked in tropical paddy fields. The As methylation–demethylation cycle should be considered when manipulating the methylated As pool in paddy fields for rice safety.

Soil Humic Acid Stimulates Potentially Active Dissimilatory Arsenate-Reducing Bacteria in Flooded Paddy Soil as Revealed by Metagenomic Stable Isotope Probing

“…Solution (dissolved) As species was determined by high performance liquid chromatography and inductively coupled plasma mass spectrometry (HPLC-ICP-MS) on the PerkinElmer’s NexSAR instrument (PerkinElmer) using the step-gradient elution mode with an As Spec anion exchange fast column (50 mm × 4.0 mm, PrinCen, Guangzhou, China) (pump: 1.2 mL min –1 , injection volume: 10 μL, autosampler: 4 °C and column compartment: 20 °C). Methods for As speciation analysis were described previously . Concentrations of lactate and its intermediate acetate were analyzed by HPLC on the Agilent 1200 instrument (Agilent) with an Aminex HPX-87H ion exchange column (7.8 mm × 300 mm, Bio-Rad) as described previously .…”

“…Potential function was assigned on the basis of best homology (BLASTx, e-value ≤ 10 –3 ) to proteins within the Kyoto Encyclopedia of Genes and Genomes (KEGG), the national registry databases, and evolutionary genealogy of genes: Nonsupervised Orthologous Groups (eggNOG). Annotation of As genes was performed using a prebuilt As metabolic gene database, which has been well described previously . Homologues of extracellular electron transfer (EET)-related genes were predicted using a Hidden Markov model (HMM)-based search against the Geobacter -like porin-cytochrome complex (pcc) and the EET system in Shewanella sp.…”

Repression of Microbial Arsenite Uptake and Methylation by Dissolved Organic Carbon

“…The microbial transformation of inorganic arsenic (As) into methylated species is an important biogeochemical process regulating As speciation in soil and aquatic environments. − Dimethylarsinic acid (DMA) is readily translocated to rice grains where it influences the toxicity of arsenic in rice, − and it is also phytotoxic and can decrease rice yields by causing straighthead disease. , These impacts have motivated intensive research into microbial As methylation in rice paddy soils. − Arsenic methylation is catalyzed by intracellular arsenite S-adenosylmethionine methyltransferase (ArsM) enzymes, and arsM genes are widely distributed in functionally diverse microorganisms. ,− There has been significant research to identify microbial populations driving methylation reactions − and to characterize the biogeochemical controls on methylation efficiencies. − Despite these efforts, variations in methylation efficiencies between soils, experimental treatments, or geographic locations often go unexplained.…”