title: Insight into the bacterial diversity of fermentation woad dye vats as revealed by PCR-DGGE and pyrosequencing.
abstract: The bacterial diversity in fermenting dye vats with woad (Isatis tinctoria L.) prepared and maintained in a functional state for approximately 12 months was examined using a combination of culture-dependent and -independent PCR-DGGE analyses and next-generation sequencing of 16S rRNA amplicons. An extremely complex ecosystem including taxa potentially contributing to both indigo reduction and formation, as well as indigo degradation was found. PCR-DGGE analyses revealed the presence of Paenibacillus lactis, Sporosarcina koreensis, Bacillus licheniformis, and Bacillus thermoamylovorans, while Bacillus thermolactis, Bacillus pumilus and Bacillus megaterium were also identified but with sequence identities lower than 97%. Dominant operational taxonomic units (OTUs) identified by pyrosequencing included Clostridium ultunense, Tissierella spp., Alcaligenes faecalis, Erysipelothrix spp., Enterococcus spp., Virgibacillus spp. and Virgibacillus panthothenicus, while sub-dominant OTUs included clostridia, alkaliphiles, halophiles, bacilli, moderately thermophilic bacteria, lactic acid bacteria, Enterobacteriaceae, aerobes, and even photosynthetic bacteria. Based on the current knowledge of indigo-reducing bacteria, it is considered that indigo-reducing bacteria constituted only a small fraction in the unique microcosm detected in the natural indigo dye vats.
authors.affiliation: Dipartimento di Scienze Agrarie, Alimentari, ed Ambientali (D3A), Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy.
authors.forename: Vesna
authors.initials: V
authors.lastname: Milanović
authors.affiliation: Dipartimento di Scienze Agrarie, Alimentari, ed Ambientali (D3A), Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Osimani
authors.affiliation: Dipartimento di Scienze Agrarie, Alimentari, ed Ambientali (D3A), Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy.
authors.forename: Manuela
authors.initials: M
authors.lastname: Taccari
authors.affiliation: Dipartimento di Scienze Agrarie, Alimentari, ed Ambientali (D3A), Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy.
authors.forename: Cristiana
authors.initials: C
authors.lastname: Garofalo
authors.affiliation: La Campana Soc. Coop. Agricola, Montefiore dell'Aso, Ascoli Piceno, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Butta
authors.affiliation: Dipartimento di Scienze Agrarie, Alimentari, ed Ambientali (D3A), Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Clementi
authors.affiliation: Dipartimento di Scienze Agrarie, Alimentari, ed Ambientali (D3A), Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy. l.aquilanti@univpm.it.
authors.forename: Lucia
authors.initials: L
authors.lastname: Aquilanti
mesh_terms: D001407:Bacillus / Q000145:classification / Q000302:isolation & purification* / Q000378:metabolism; D003013:Clostridium / Q000302:isolation & purification / Q000378:metabolism; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D004755:Enterobacteriaceae / Q000145:classification / Q000302:isolation & purification / Q000378:metabolism; D005285:Fermentation; D059014:High-Throughput Nucleotide Sequencing; D007203:Indigo Carmine / Q000378:metabolism; D031219:Isatis / Q000737:chemistry / Q000382:microbiology*; D056546:Lactobacillales / Q000145:classification / Q000302:isolation & purification / Q000378:metabolism; D056507:Paenibacillus / Q000302:isolation & purification* / Q000378:metabolism; D012336:RNA, Ribosomal, 16S / Q000235:genetics / Q000302:isolation & purification; D017422:Sequence Analysis, DNA; D058644:Sporosarcina / Q000302:isolation & purification* / Q000378:metabolism
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D007203:Indigo Carmine
keywords: Fermentation liquor; Indigo reduction; Isatis tinctoria L; Microbial diversity; Spore-forming bacteria