Seigo Amachi

Bacteria Mediate Methylation of Iodine in Marine and Terrestrial Environments

ABSTRACT Methyl iodide (CH3I) plays an important role in the natural iodine cycle and participates in atmospheric ozone destruction. However, the main source of this compound in nature is still unclear. Here we report that a wide variety of bacteria including terrestrial and marine bacteria are capable of methylating the environmental level of iodide (0.1 μM). Of the strains tested, Rhizobium sp. strain MRCD 19 was chosen for further analysis, and it was found that the cell extract catalyzed the methylation of iodide withS-adenosyl-l-methionine as the methyl donor. These results strongly indicate that bacteria contribute to iodine transfer from the terrestrial and marine ecosystems into the atmosphere.

Arsenic release from flooded paddy soils is influenced by speciation, Eh, pH, and iron dissolution

Arsenic (As) is highly mobilized when paddy soil is flooded, causing increased uptake of As by rice. We investigated factors controlling soil-to-solution partitioning of As under anaerobic conditions. Changes in As and iron (Fe) speciation due to flooded incubation of two paddy soils (soils A and B) were investigated by HPLC/ICP-MS and XANES. The flooded incubation resulted in a decrease in Eh, a rise in pH, and an increase in the As(III) fraction in the soil solid phase up to 80% of the total As in the soils. The solution-to-soil ratio of As(III) and As(V) (R(L/S)) increased with pH due to the flooded incubation. The R(L/S) for As(III) was higher than that for As(V), indicating that As(III) was more readily released from soil to solution than was As(V). Despite the small differences in As concentrations between the two soils, the amount of As dissolved by anaerobic incubation was lower in soil A. With the development of anaerobic conditions, Fe(II) remained in the soil solid phase as the secondary mineral siderite, and a smaller amount of Fe was dissolved from soil A than from soil B. The dissolution of Fe minerals rather than redox reaction of As(V) to As(III) explained the different dissolution amounts of As in the two paddy soils. Anaerobic incubation for 30 d after the incomplete suppression of microbial activity caused a drop in Eh. However, this decline in Eh did not induce the transformation of As(V) to As(III) in either the soil solid or solution phases, and the dissolution of As was limited. Microbial activity was necessary for the reductive reaction of As(V) to As(III) even when Eh reached the condition necessary for the dominance of As(III). Ratios of released As to Fe from the soils were decreased with incubation time during both anaerobic incubation and abiotic dissolution by sodium ascorbate, suggesting that a larger amount of As was associated with an easily soluble fraction of Fe (hydr) oxide in amorphous phase and/or smaller particles.

Arsenic Dissolution from Japanese Paddy Soil by a Dissimilatory Arsenate-Reducing Bacterium Geobacter sp. OR-1

Dissimilatory As(V) (arsenate)-reducing bacteria may play an important role in arsenic release from anoxic sediments in the form of As(III) (arsenite). Although respiratory arsenate reductase genes (arrA) closely related to Geobacter species have been frequently detected in arsenic-rich sediments, it is still unclear whether they directly participate in arsenic release, mainly due to lack of pure cultures capable of arsenate reduction. In this study, we isolated a novel dissimilatory arsenate-reducing bacterium, strain OR-1, from Japanese paddy soil, and found that it was phylogenetically closely related to Geobacter pelophilus. OR-1 also utilized soluble Fe(III), ferrihydrite, nitrate, and fumarate as electron acceptors. OR-1 catalyzed dissolution of arsenic from arsenate-adsorbed ferrihydrite, while Geobacter metallireducens GS-15 did not. Furthermore, inoculation of washed cells of OR-1 into sterilized paddy soil successfully restored arsenic release. Arsenic K-edge X-ray absorption near-edge structure analysis revealed that strain OR-1 reduced arsenate directly on the soil solid phase. Analysis of putative ArrA sequences from paddy soils suggested that Geobacter-related bacteria, including those closely related to OR-1, play an important role in arsenic release from paddy soils. Our results provide direct evidence for arsenic dissolution by Geobacter species and support the hypothesis that Geobacter species play a significant role in reduction and mobilization of arsenic in flooded soils and anoxic sediments.

Microbiology of inorganic arsenic : From metabolism to bioremediation

Arsenic (As) contamination of drinking water and soils poses a threat to a large number of people worldwide, especially in Southeast Asia. The predominant forms of As in soils and aquifers are inorganic arsenate [As(V)] and arsenite [As(III)], with the latter being more mobile and toxic. Thus, redox transformations of As are of great importance to predict its fate in the environment, as well as to achieve remediation of As-contaminated water and soils. Although As has been recognized as a toxic element, a wide variety of microorganisms, mainly bacteria, can use it as an electron donor for autotrophic growth or as an electron acceptor for anaerobic respiration. In addition, As detoxification systems in which As is oxidized to the less toxic form or reduced for subsequent excretion are distributed widely in microorganisms. This review describes current development of physiology, biochemistry, and genomics of arsenic-transforming bacteria. Potential application of such bacteria to removal of As from soils and water is also highlighted.

Active Transport and Accumulation of Iodide by Newly Isolated Marine Bacteria

ABSTRACT Iodide (I−)-accumulating bacteria were isolated from marine sediment by an autoradiographic method with radioactive 125I−. When they were grown in a liquid medium containing 0.1 μM iodide, 79 to 89% of the iodide was removed from the medium, and a corresponding amount of iodide was detected in the cells. Phylogenetic analysis based on 16S rRNA gene sequences indicated that iodide-accumulating bacteria were closely related to Flexibacter aggregans NBRC15975 and Arenibacter troitsensis, members of the family Flavobacteriaceae. When one of the strains, strain C-21, was cultured with 0.1 μM iodide, the maximum iodide content and the maximum concentration factor for iodide were 220 ± 3.6 (mean ± standard deviation) pmol of iodide per mg of dry cells and 5.5 × 103, respectively. In the presence of much higher concentrations of iodide (1 μM to 1 mM), increased iodide content but decreased concentration factor for iodide were observed. An iodide transport assay was carried out to monitor the uptake and accumulation of iodide in washed cell suspensions of iodide-accumulating bacteria. The uptake of iodide was observed only in the presence of glucose and showed substrate saturation kinetics, with an apparent affinity constant for transport and a maximum velocity of 0.073 μM and 0.55 pmol min−1 mg of dry cells−1, respectively. The other dominant species of iodine in terrestrial and marine environments, iodate (IO3−), was not transported.

Production of fructooligosaccharides by crude enzyme preparations of β-fructofuranosidase from Aureobasidium pullulans

Fructooligosaccharides (FOS) were produced from sucrose by using crude enzyme preparations of β-fructofuranosidases (FFases) obtained from sucrose-cultured cells of Aureobasidium pullulans DSM 2404. When the preparation mainly consisted of FFase I, that has high transfructosylating activity, the FOS yield was 62%. When the reaction was carried out with additional commercial glucose isomerase (GI) at an activity ratio of FFase and GI of 1:2, the maximum FOS yield reached 69%. This value was higher than those obtained previously using other Aureobasidium spp. (53–59%).

Dissimilatory Iodate Reduction by Marine Pseudomonas sp. Strain SCT

ABSTRACT Bacterial iodate (IO3−) reduction is poorly understood largely due to the limited number of available isolates as well as the paucity of information about key enzymes involved in the reaction. In this study, an iodate-reducing bacterium, designated strain SCT, was newly isolated from marine sediment slurry. SCT is phylogenetically closely related to the denitrifying bacterium Pseudomonas stutzeri and reduced 200 μM iodate to iodide (I−) within 12 h in an anaerobic culture containing 10 mM nitrate. The strain did not reduce iodate under the aerobic conditions. An anaerobic washed cell suspension of SCT reduced iodate when the cells were pregrown anaerobically with 10 mM nitrate and 200 μM iodate. However, cells pregrown without iodate did not reduce it. The cells in the former category showed methyl viologen-dependent iodate reductase activity (0.31 U mg−1), which was located predominantly in the periplasmic space. Furthermore, SCT was capable of anaerobic growth with 3 mM iodate as the sole electron acceptor, and the cells showed enhanced activity with respect to iodate reductase (2.46 U mg−1). These results suggest that SCT is a dissimilatory iodate-reducing bacterium and that its iodate reductase is induced by iodate under anaerobic growth conditions.

Release of Arsenic from Soil by a Novel Dissimilatory Arsenate- Reducing Bacterium, Anaeromyxobacter sp. Strain PSR-1

ABSTRACT A novel arsenate-reducing bacterium, designated strain PSR-1, was isolated from arsenic-contaminated soil. Strain PSR-1 was phylogenetically closely related to Anaeromyxobacter dehalogenans 2CP-1T with 16S rRNA gene similarity of 99.7% and coupled the oxidation of acetate with the reduction of arsenate. Arsenate reduction was inhibited almost completely by respiratory inhibitors such as dicumarol and 2-heptyl-4-hydroxyquinoline N-oxide. Strain PSR-1 also utilized soluble Fe(III), ferrihydrite, nitrate, oxygen, and fumarate as electron acceptors. Strain PSR-1 catalyzed the release of arsenic from arsenate-adsorbed ferrihydrite. In addition, inoculation of washed cells of strain PSR-1 into sterilized soil successfully reproduced arsenic release. Arsenic K-edge X-ray absorption near-edge structure (XANES) analysis revealed that the proportion of arsenite in the soil solid phase actually increased from 20% to 50% during incubation with washed cells of strain PSR-1. These results suggest that strain PSR-1 is capable of reducing not only dissolved arsenate but also arsenate adsorbed on the soil mineral phase. Arsenate reduction by strain PSR-1 expands the metabolic versatility of Anaeromyxobacter dehalogenans. Considering its distribution throughout diverse soils and anoxic sediments, Anaeromyxobacter dehalogenans may play a role in arsenic release from these environments.

Hydrogen Peroxide-Dependent Uptake of Iodine by Marine Flavobacteriaceae Bacterium Strain C-21

ABSTRACT The cells of the marine bacterium strain C-21, which is phylogenetically closely related to Arenibacter troitsensis, accumulate iodine in the presence of glucose and iodide (I−). In this study, the detailed mechanism of iodine uptake by C-21 was determined using a radioactive iodide tracer, 125I−. In addition to glucose, oxygen and calcium ions were also required for the uptake of iodine. The uptake was not inhibited or was only partially inhibited by various metabolic inhibitors, whereas reducing agents and catalase strongly inhibited the uptake. When exogenous glucose oxidase was added to the cell suspension, enhanced uptake of iodine was observed. The uptake occurred even in the absence of glucose and oxygen if hydrogen peroxide was added to the cell suspension. Significant activity of glucose oxidase was found in the crude extracts of C-21, and it was located mainly in the membrane fraction. These findings indicate that hydrogen peroxide produced by glucose oxidase plays a key role in the uptake of iodine. Furthermore, enzymatic oxidation of iodide strongly stimulated iodine uptake in the absence of glucose. Based on these results, the mechanism was considered to consist of oxidation of iodide to hypoiodous acid by hydrogen peroxide, followed by passive translocation of this uncharged iodine species across the cell membrane. Interestingly, such a mechanism of iodine uptake is similar to that observed in iodine-accumulating marine algae.

Iodide Oxidation by a Novel Multicopper Oxidase from the Alphaproteobacterium Strain Q-1

ABSTRACT Alphaproteobacterium strain Q-1 is able to oxidize iodide (I−) to molecular iodine (I2) by an oxidase-like enzyme. One of the two isoforms of the iodide-oxidizing enzyme (IOE-II) produced by this strain was excised from a native polyacrylamide gel, eluted, and purified. IOE-II appeared as a single band (51 kDa) and showed significant in-gel iodide-oxidizing activity in sodium dodecyl sulfate-polyacrylamide gel electrophoresis without heat treatment. However, at least two bands with much higher molecular masses (150 and 230 kDa) were observed with heat treatment (95°C, 3 min). IOE-II was inhibited by NaN3, KCN, EDTA, and a copper chelator, o-phenanthroline. In addition to iodide, IOE-II showed significant activities toward phenolic compounds such as syringaldazine, 2,6-dimethoxy phenol, and p-phenylenediamine. IOE-II contained copper atoms as prosthetic groups and had UV/VIS absorption peaks at 320 and 590 nm. Comparison of several internal amino acid sequences obtained from trypsin-digested IOE-II with a draft genome sequence of strain Q-1 revealed that the products of two open reading frames (IoxA and IoxC), with predicted molecular masses of 62 and 71 kDa, are involved in iodide oxidation. Furthermore, subsequent tandem mass spectrometric analysis repeatedly detected peptides from IoxA and IoxC with high sequence coverage (32 to 40%). IoxA showed homology with the family of multicopper oxidases and included four copper-binding regions that are highly conserved among various multicopper oxidases. These results suggest that IOE-II is a multicopper oxidase and that it may occur as a multimeric complex in which at least two proteins (IoxA and IoxC) are associated.