Comparative Genomics of Acetobacterpasteurianus Ab3, an Acetic Acid Producing Strain Isolated from Chinese Traditional Rice Vinegar Meiguichu

Xia, Kai; Li, Yudong; Sun, Jing; Liang, Xinmiao

doi:10.1371/journal.pone.0162172

Cited by 13 publications

(2 citation statements)

References 50 publications

(50 reference statements)

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“…The phylogenetic tree is a two-dimensional graph that shows the relationship between organisms or population classifications based on the history of their evolution. Phylogenetic trees are constructed through the Mega 6.0 software application using the Neighbor-Joining (NJ) method [38] of the Maximum Composite Likelihood and Substitutions models to included: Transitions + Transversions with 1000× boostrap [39,40]. The eubacteria phylogenetic tree is presented in Figure 2.…”

Section: Figure 2 Phylogenetic Tree Of Nitrifying Bacteriamentioning

confidence: 99%

DNA Barcoding and Water Quality Analysis of Nitrifying Bacteria in Lebak Lebung Swamp, South Sumatera

Rarassari,

Yonarta,

Wijayanti

et al. 2024

IJDNE

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Aquaculture development activities in swamp water has the problem of contamination from organic matter, and this waste has the potential for environmental challange. Nitrifying bacteria are a natural instrument that can play a role in maintaining the stability of the quality of swamp waters through their role as bioremediator. Therefore, its presence is important to identify in waters. The aim of the research is to determine the types and characteristics of bioremediation bacteria, construct a phylogenetic tree and the relationship between water quality and the bioremediation process by bacteria so that in the future it can be applied to waters that have the same problems or become a bioindicator for certain pollutants, especially in the area of Lebak Lebung Swamp, Ogan. Ilir, South Sumatra. The method used is taking bacterial samples, isolating bacteria using Nutrient Agar (NA) media, observing bacterial morphology, DNA sequencing, amplifying DNA mitochondria COI using PCR (Polymerase Chain Reaction). The results of BLASTn (Basic Local Alignment Search Tool-nucleotide) analysis showed the highest percentage of identity, namely 93%, with the Burkholderia cepacia strain NBRAJG97 from India and Burkholderia sp. strain 172 1492R comes from Estonia which indicates that the bacteria found belong to the Burkholderia bacteria group. Water quality measurement was temperature 34.7-35.4℃, dissolved oxygen 6.0-6.2 mgL -1 , pH 6.2, ammonia 0.05 mgL -1 . Based on air quality indications such as low ammonia content, this could indicate that the Burkholderia bacteria found in Lebak Lebung Swamp play a role as bioremediation.

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Section: Figure 2 Phylogenetic Tree Of Nitrifying Bacteriamentioning

confidence: 99%

DNA Barcoding and Water Quality Analysis of Nitrifying Bacteria in Lebak Lebung Swamp, South Sumatera

Rarassari,

Yonarta,

Wijayanti

et al. 2024

IJDNE

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“…In order to obtain a whole view as well as a relatively better understanding of the AR mechanisms in AAB, scientists have carried out omics studies within this field. As a result, several genomes of AAB strains participating acetic acid fermentation were sequenced and analyzed ( Azuma et al, 2009 ; Wang et al, 2015b ; Xia et al, 2016a ), while proteomic approaches were extensively exploited and have provided a number of important findings regarding AAB’s AR mechanisms, which have been reviewed and summarized previously ( Nakano and Fukaya, 2008 ; Xia et al, 2017 ; Yang et al, 2022 ). Nowadays, being considered as the important bond linking genome and proteome, transcriptome has been obtaining more and more attentions from the researchers, leading to the reports of many relevant studies.…”

Section: Introductionmentioning

confidence: 99%

RNA-Seq transcriptomic analysis reveals gene expression profiles of acetic acid bacteria under high-acidity submerged industrial fermentation process

Yang

He²,

Liao³

et al. 2022

Front. Microbiol.

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Acetic acid bacteria (AAB) are Gram-negative obligate aerobics in Acetobacteraceae family. Producing acetic acid and brewing vinegars are one of the most important industrial applications of AAB, attributed to their outstanding ability to tolerate the corresponding stresses. Several unique acid resistance (AR) mechanisms in AAB have been revealed previously. However, their overall AR strategies are still less-comprehensively clarified. Consequently, omics analysis was widely performed for a better understanding of this field. Among them, transcriptome has recently obtained more and more attention. However, most currently reported transcriptomic studies were conducted under lab conditions and even in low-acidity environment, which may be unable to completely reflect the conditions that AAB confront under industrialized vinegar-brewing processes. In this study, we performed an RNA-Seq transcriptomic analysis concerning AAB’s AR mechanisms during a continuous and periodical industrial submerged vinegar fermentation process, where a single AAB strain performed the fermentation and the acetic acid concentration fluctuated between ~8% and ~12%, the highest acidity as far we know for transcriptomic studies. Samples were directly taken from the initial (CK), mid, and final stages of the same period of the on-going fermentation. 16S rRNA sequence analysis indicated the participation of Komagataeibacter europaeus in the fermentation. Transcriptomic results demonstrated that more genes were downregulated than upregulated at both mid and final stages. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrich analysis reflected that the upregulated genes mainly carried out tricarboxylic acid cycle and oxidative phosphorylation processes, probably implying a considerable role of acetic acid overoxidation in AR during fermentation. Besides, upregulation of riboflavin biosynthesis pathway and two NAD+-dependent succinate-semialdehyde dehydrogenase-coding genes suggested a critical role of succinate oxidation in AR. Meanwhile, downregulated genes were mainly ribosomal protein-coding ones, reflecting that the adverse impact on ribosomes initiates at the transcription level. However, it is ambiguous whether the downregulation is good for stress responding or it actually reflects the stress. Furthermore, we also assumed that the fermentation stages may have a greater effect on gene expression than acidity. Additionally, it is possible that some physiological alterations would affect the AR to a larger extent than changes in gene expression, which suggests the combination of molecular biology and physiology research will provide deeper insight into the AR mechanisms in AAB.

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Impacts of bioprocess engineering on product formation by Acetobacter pasteurianus

Zheng

Chang

Xie

et al. 2018

Appl Microbiol Biotechnol

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Aerobic Acetobacter pasteurianus is one of the most widely used bacterial species for acetic acid and vinegar production. The acetic acid condition is the primary challenge to the industrial application of A. pasteurianus. Thus, numerous endeavors, including strain improvement and process control, have been performed to improve the product formation and acetic acid tolerance of A. pasteurianus. The metabolic features of A. pasteurianus have been gradually elucidated through omic techniques, such as genomics and proteomics. In this mini review, we summarized bioprocess engineering methods that improved product formation of A. pasteurianus by exploiting its metabolic features. Moreover, given that A. pasteurianus is an important functional microorganism in traditional vinegar production, we discuss its metabolism when cocultured with other microorganisms in traditional vinegar production.

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Comparative Genomics of Acetobacterpasteurianus Ab3, an Acetic Acid Producing Strain Isolated from Chinese Traditional Rice Vinegar Meiguichu

Cited by 13 publications

References 50 publications

DNA Barcoding and Water Quality Analysis of Nitrifying Bacteria in Lebak Lebung Swamp, South Sumatera

DNA Barcoding and Water Quality Analysis of Nitrifying Bacteria in Lebak Lebung Swamp, South Sumatera

RNA-Seq transcriptomic analysis reveals gene expression profiles of acetic acid bacteria under high-acidity submerged industrial fermentation process

Impacts of bioprocess engineering on product formation by Acetobacter pasteurianus

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