Amphibacillus iburiensis sp. nov., an alkaliphile that reduces an indigo dye

Hirota, Kikue; Aino, Kenichi; Yumoto, Isao

doi:10.1099/ijs.0.048009-0

Cited by 34 publications

(12 citation statements)

References 37 publications

(33 reference statements)

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“…Therefore, the name Amphibacillus iburiensis sp. nov. was proposed for this strain ( Hirota et al, 2013c ; Table 1 ). The species exhibited similar characteristics to Amphi.…”

Section: Indigo-reducing Bacteria Belonging To the Genera Amentioning

confidence: 99%

Microbial Communities Associated With Indigo Fermentation That Thrive in Anaerobic Alkaline Environments

et al. 2018

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Indigo fermentation, which depends on the indigo-reducing action of microorganisms, has traditionally been performed to dye textiles blue in Asia as well as in Europe. This fermentation process is carried out by naturally occurring microbial communities and occurs under alkaline, anaerobic conditions. Therefore, there is uncertainty regarding the fermentation process, and many unknown microorganisms thrive in this unique fermentation environment. Until recently, there was limited information available on bacteria associated with this fermentation process. Indigo reduction normally occurs from 4 days to 2 weeks after initiation of fermentation. However, the changes in the microbiota that occur during the transition to an indigo-reducing state have not been elucidated. Here, the structural changes in the bacterial community were estimated by PCR-based methods. On the second day of fermentation, a large change in the redox potential occurred. On the fourth day, distinct substitution of the genus Halomonas with the aerotolerant genus Amphibacillus was observed, corresponding to marked changes in indigo reduction. Under open-air conditions, indigo reduction during the fermentation process continued for 6 months on average. The microbiota, including indigo-reducing bacteria, was continuously replaced with other microbial communities that consisted of other types of indigo-reducing bacteria. A stable state consisting mainly of the genus Anaerobacillus was also observed in a long-term fermentation sample. The stability of the microbiota, proportion of indigo-reducing microorganisms, and appropriate diversity and microbiota within the fluid may play key factors in the maintenance of a reducing state during long-term indigo fermentation. Although more than 10 species of indigo-reducing bacteria were identified, the reduction mechanism of indigo particle is riddle. It can be predicted that the mechanism involves electrons, as byproducts of metabolism, being discarded by analogs mechanisms reported in bacterial extracellular solid Fe3+ reduction under alkaline anaerobic condition.

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“…Therefore, the name Amphibacillus iburiensis sp. nov. was proposed for this strain ( Hirota et al, 2013c ; Table 1 ). The species exhibited similar characteristics to Amphi.…”

Section: Indigo-reducing Bacteria Belonging To the Genera Amentioning

confidence: 99%

Microbial Communities Associated With Indigo Fermentation That Thrive in Anaerobic Alkaline Environments

et al. 2018

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“…This bacterium showed unique phenotypic and chemotaxonomic characteristics; therefore, it was accepted as a new genus ( Amphibacillus ) and species ( xylanus ) . Presently, nine species belong to this genus . Amphibacillus xylanus grows well under aerobic and anaerobic conditions, exhibiting the same growth rate and cell yields under both conditions, despite its lack of a respiratory chain .…”

mentioning

confidence: 99%

Intracellular free flavin and its associated enzymes participate in oxygen and iron metabolism in Amphibacillus xylanus lacking a respiratory chain

et al. 2018

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Amphibacillus xylanus is a recently identified bacterium which grows well under both aerobic and anaerobic conditions and may prove useful for biomass utilization. Amphibacillus xylanus, despite lacking a respiratory chain, consumes oxygen at a similar rate to Escherichia coli (130–140 μmol oxygen·min −1 ·g −1 dry cells at 37 °C), suggesting that it has an alternative system that uses a large amount of oxygen. Amphibacillus xylanus NADH oxidase (Nox) was previously reported to rapidly reduce molecular oxygen content in the presence of exogenously added free flavin. Here, we established a quantitative method for determining the intracellular concentrations of free flavins in A. xylanus , involving French pressure and ultrafiltration membranes. The intracellular concentrations of flavin adenine dinucleotide ( FAD ), flavin mononucleotide ( FMN ), and riboflavin were estimated to be approximately 8, 3, and 1 μ m , respectively. In the presence of FAD , the predominant free flavin species, two flavoproteins Nox (which binds FAD ) and NAD (P)H oxidoreductase (Npo, which binds FMN ), were identified as central free flavin‐associated enzymes in the oxygen metabolic pathway. Under 8 μ m free FAD , the catalytic efficiency ( k cat / K m ) of recombinant Nox and Npo for oxygen increased by approximately fivefold and ninefold, respectively. Nox and Npo levels were increased, and intracellular FAD formation was stimulated following exposure of A. xylanus to oxygen. This suggests that these two enzymes and free FAD contribute to effective oxygen detoxification and NAD (P) + regeneration to maintain redox balance during aerobic growth. Furthermore, A. xylanus required iron to grow aerobically. We also discuss the contribution of the free flavin‐associated system to the process of iron utilization.

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“…Under such extreme conditions, there is a gap between the temperatures suitable for metabolism and those suitable for propagation. For example, it has been reported that Amphibacillus iburiensis can survive at pH values higher than 10.5 and exhibits indigoreducing activity at those pH values (Hirota et al, 2013). However, bacterial propagation is observed at relatively low pH values under laboratory conditions.…”

Section: Geobacillus Thermodenitrificans Dsm 465 T (Z26928)mentioning

confidence: 99%

“…However, bacterial propagation is observed at relatively low pH values under laboratory conditions. Although there was apparent metabolic activity in the form of acid production by the inoculated cells in broth adjusted to a pH value greater than pH 10, actual growth was initiated at pH 8.0-9.1, with optimum growth observed at pH 8.9-9.1 (30°C) (Hirota et al, 2013). Thus, we hypothesize that there are bacterial niches that exhibit temperatures lower than that inside the compost and that the temperature range in which bacteria are able to perform metabolic activity is different from the range in which bacterial propagation can occur.…”

Section: Geobacillus Thermodenitrificans Dsm 465 T (Z26928)mentioning

confidence: 99%

Isolation and identification of bacteria from high-temperature compost at temperatures exceeding 90C

Hirota¹,

Miura²,

Motomura³

et al. 2019

Afr. J. Microbiol. Res.

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Conventional composts exhibit temperatures ranging from 50 to 80°C during organic waste degradation by microorganisms. In high-temperature compost, temperatures can reach ≥90°C with appropriate bottom aeration. To elucidate specific characteristics of the bacterial activity in high-temperature compost and to regenerate a high-temperature compost from isolates, bacterial isolation and characterization were performed. Although the isolated taxa varied depending on sample and temperature, the use of gellan gum medium and cultivation at 60°C led to high diversity among the isolated taxa. In addition, combining the use of the compost extract with water-solvent medium led to the isolation of more diverse species. Based on 16S rRNA gene sequencing, the isolates shared ≥99% similarity with Geobacillus thermodenitrificans, Ureibacillus spp. (Ureibacillus suwonensis, Ureibacillus themosphaericus) and Aeribacillus pallidus, and these isolates were isolated from both steady-state and newly prepared small-scale composts. Thus, these taxa were considered to be frequently observed regardless of the composting process. Although the frequency of isolation of mesophilic bacteria from this high-temperature compost was lower than that from ordinary composts, these bacteria have been isolated from ordinary composts and there was a discrepancy between the in situ compost temperature (≥90°C) and their maximum growth temperature (≤70°C).

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Amphibacillus iburiensis sp. nov., an alkaliphile that reduces an indigo dye

Cited by 34 publications

References 37 publications

Microbial Communities Associated With Indigo Fermentation That Thrive in Anaerobic Alkaline Environments

Microbial Communities Associated With Indigo Fermentation That Thrive in Anaerobic Alkaline Environments

Intracellular free flavin and its associated enzymes participate in oxygen and iron metabolism in Amphibacillus xylanus lacking a respiratory chain

Isolation and identification of bacteria from high-temperature compost at temperatures exceeding 90C

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