Bacillales: From Taxonomy to Biotechnological and Industrial Perspectives

For a long time, the genus Bacillus has been known and considered among the most applicable genera in several fields. Recent taxonomical developments resulted in the identification of more species in Bacillus-related genera, particularly in the order Bacillales (earlier heterotypic synonym: Caryophanales), with potential application for biotechnological and industrial purposes such as biofuels, bioactive agents, biopolymers, and enzymes. Therefore, a thorough understanding of the taxonomy, growth requirements and physiology, genomics, and metabolic pathways in the highly diverse bacterial order, Bacillales, will facilitate a more robust designing and sustainable production of strain lines relevant to a circular economy. This paper is focused principally on less-known genera and their potential in the order Bacillales for promising applications in the industry and addresses the taxonomical complexities of this order. Moreover, it emphasizes the biotechnological usage of some engineered strains of the order Bacillales. The elucidation of novel taxa, their metabolic pathways, and growth conditions would make it possible to drive industrial processes toward an upgraded functionality based on the microbial nature.

Fermentation Blues: Analyzing the Microbiota of Traditional Indigo Vat Dyeing in Hunan, China

Traditional indigo dyeing through anaerobic fermentation has recently gained worldwide attention in efforts to address concerns regarding the sustainability of industrial indigo dyeing and the impact of toxic reducing agents such as sodium dithionite (Na2S2O4) on human health and the ecological environment. Intriguingly, changes in the microbiota during indigo fermentation are known to potently affect the onset of indigo reduction, and thus elucidation of the microbial community transitions could help develop methods to control the initiation of indigo reduction. Here, we investigated the microbiota associated with the traditional indigo dyeing practiced in Hunan, China. Specifically, we identified the bacterial and fungal components of the microbiota at distinct stages in the indigo fermentation process by analyzing 16S rRNA gene and internal transcribed spacer sequences. Our analyses revealed two substantial changes in the microbiota during the traditional indigo fermentation process. The first change, which was probably caused by the introduction of Chinese liquor (featuring a high alcohol concentration), resulted in decreased bacterial diversity and increased proportions of Pseudomonas, Stenotrophomonas, and Bacillaceae family members. The second change, which could be attributed to the addition of specific plant species, led to an increase in the abundance of Alkalibacterium, Amphibacillus, the obligate anaerobe Turicibacter, the facultative anaerobe Enterococcus, and ZOR0006, as well as to a decrease in the pH and redox potential values. Our results indicate that the specific plant mixture included in the procedure here could be used as an effective additive to accelerate the initiation of indigo reduction during the fermentation process. To the best of our knowledge, this is the first report revealing the fungal diversity during the indigo fermentation process and, furthermore, showing that the fungal diversity has remained in transition despite the relatively stable bacterial diversity in the proper indigo fermentation process. Although traditional indigo fermentation in China is challenging to manage, we can benefit from local knowledge of the fermentation process, and understanding the scientific bases of traditional indigo fermentation will facilitate the development of environmentally friendly procedures. IMPORTANCE Chemical reducing agents included in modern indigo dyeing to initiate indigo reduction can be harmful to both human health and the environment. Given that traditional indigo dyeing involves natural fermentation in a dye vat using natural organic additives without the use of toxic chemicals and that changes in the microbiota during traditional indigo fermentation potently affect the onset of indigo reduction, elucidation of these microbial community transitions could help develop methods to control the initiation of indigo reduction. This study on the microbiota associated with the traditional indigo dyeing practiced in Hunan, China, has identified the bacterial and fungal communities at distinct stages of the indigo fermentation process. Notably, the addition of specific plant species might yield the desired microbial communities and appropriate fermentation conditions, which could be used as an effective additive to accelerate the initiation of indigo reduction. This study has also revealed the fungal diversity during the indigo fermentation process for the first time and shown that the fungal diversity has remained in transition despite the relatively stable bacterial diversity. Thus, this work provides new insights into the traditional indigo fermentation process used in China and substantially enhances current efforts devoted to designing environmentally friendly methods for industrial indigo dyeing.

Fundicoccus fermenti sp. nov., an indigo-reducing facultative anaerobic alkaliphile isolated from indigo fermentation liquor used for dyeing

Two facultative anaerobic and facultative alkaliphilic indigo-reducing strains, designated F-1^T and F-2, were isolated from indigo fermentation liquor produced from couched woad fermentation-based Indian indigo fermentation fluid. The 16S rRNA gene phylogeny showed that Fundicoccus ignavus WS4937^T (99.5%) was the closest neighbour of F-1^T. The isolated bacterial cells were Gram-stain-positive and facultative anaerobic coccoids. Strain F-1^T grew at between 5 and 37 °C with optimum growth between 28‒32 °C. The isolate grew in a pH range of 7.0‒10.5, with optimum growth between pH 9.0‒10.5. The DNA G+C content was 37.6 mol% (HPLC). The whole-cell fatty acid profile mainly consisted (>10 %) of C_16 : 0, C_16 : 1 ω9c, C_18 : 0 and C_18 : 1 ω9c. The digital DNA-DNA hybridization value between strain F-1^T and F. ignavus WS4937^T was 52.9 %. Based on their physiological and biochemical characteristics, and phylogenetic and genomic data, the isolates can be discriminated from F. ignavus WS4937^T. The name Fundicoccus fermenti sp. nov. is proposed. The type strain of this species is F-1^T (JCM 34140^T=NCIMB 15255^T).

Characterization of the microbiota in long- and short-term natural indigo fermentation

The duration for which the indigo-reducing state maintenance in indigo natural fermentation in batch dependent. The microbiota was analyzed in two batches of sukumo fermentation fluids that lasted for different durations (Batch 1: less than 2 months; Batch 2: nearly 1 year) to understand the mechanisms underlying the sustainability and deterioration of this natural fermentation process. The transformation of the microbiota suggested that the deterioration of the fermentation fluid is associated with the relative abundance of Alcaligenaceae. Principal coordinates analysis (PCoA) showed that the microbial community maintained a very stable state in only the long-term Batch 2. Therefore, entry of the microbiota into a stable state under alkaline anaerobic condition is an important factor for maintenance of indigo fermentation for long duration. This is the first report on the total transformation of the microbiota for investigation of long-term maintenance mechanisms and to address the problem of deterioration in indigo fermentation.

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

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.

Azoreductase from alkaliphilic Bacillus sp. AO1 catalyzes indigo reduction

Indigo is an insoluble blue dye historically used for dyeing textiles. A traditional approach for indigo dyeing involves microbial reduction of polygonum indigo to solubilize it under alkaline conditions; however, the mechanism by which microorganisms reduce indigo remains poorly understood. Here, we aimed to identify an enzyme that catalyzes indigo reduction; for this purpose, from alkaline liquor that performed microbial reduction of polygonum indigo, we isolated indigo carmine-reducing microorganisms. All isolates were facultative anaerobic and alkali-tolerant Bacillus spp. An isolate termed AO1 was found to be an alkaliphile that preferentially grows at pH 9.0-11.0 and at 30-35 °C. We focused on flavin-dependent azoreductase as a possible enzyme for indigo carmine reduction and identified its gene (azoA) in Bacillus sp. AO1 using homology-based strategies. azoA was monocistronic but clustered with ABC transporter genes. Primary sequence identities were < 50% between the azoA product (AzoA) and previously characterized flavin-dependent azoreductases. AzoA was heterologously produced as a flavoprotein tolerant to alkaline and organic solvents. The enzyme efficiently reduced indigo carmine in an NADH-dependent manner and showed strict specificity for electron acceptors. Notably, AzoA oxidized NADH in the presence, but not the absence, of indigo. The reaction rate was enhanced by adding organic solvents to solubilize indigo. Absorption spectrum analysis showed that indigo absorption decreased during the reaction. These observations suggest that AzoA can reduce indigo in vitro and potentially in Bacillus sp. AO1. This is the first study that identified an indigo reductase, providing a new insight into a traditional approach for indigo dyeing.