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Reduces Bacterial Diversity and Prolongs the Preservation Time of Volvariella Volvacea

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Reduces Bacterial Diversity and Prolongs the Preservation Time of Volvariella Volvacea microorganisms Article ◦ Low Temperature (15 C) Reduces Bacterial Diversity and Prolongs the Preservation Time of Volvariella volvacea 1,2, 1, 1 1 1, Xiuling Wang y, Shunjie Liu y, Mingjie Chen , Changxia Yu , Yan Zhao * , Huanling Yang 1, Lei Zha 1 and Zhengpeng Li 1 1 Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; [email protected] (X.W.); [email protected] (S.L.); [email protected] (M.C.); [email protected] (C.Y.); [email protected] (H.Y.); [email protected] (L.Z.); [email protected] (Z.L.) 2 College of Life Sciences, Shihezi University, Shihezi 832003, China * Correspondence: [email protected]; Tel.: +86-21-3719-6813 These authors contributed equally to this work. y Received: 30 August 2019; Accepted: 18 October 2019; Published: 20 October 2019 Abstract: Straw mushroom (Volvariella volvacea) is the most commonly cultivated edible fungus in the world, but the challenges associated with the preservation have limited its marketability. Microbiology, especially bacteria, play a key role in the deterioration of food, this study aimed to reveal the succession of the bacterial community on the surfaces of V. volvacea fruit bodies under different temperature conditions. We amplified 16S rRNA genes of V4 regions, obtained the bacterial species information by using high-throughput sequencing technology, and analyzed the effects of environmental temperature and preservation time on bacterial communities. The relative abundances of Firmicutes, Bacilli, and Bacillales increased significantly when straw mushrooms began to rot. Furthermore, the relative abundances of Paenibacillus, Lysinibacillus and Solibacillus, which belong to Bacillales, increased with the decay of straw mushroom. The Shannon and Simpson indices of V. volvacea stored at 30 ◦C were significantly higher than those of V. volvacea stored at 15 ◦C, which indicates that a high temperature contributes to the improvement in the species diversity. According to the linear discriminant analysis (LDA) effect size (LEfSe) results, the number of biomarkers in the 30 ◦C group (32, 42.11%) was significantly higher than that in the 15 ◦C group (17, 22.37%), indicating that a high temperature has a clustering effect on some bacterial communities. A Spearman correlation analysis showed that Pseudomonas, Stenotrophomonas and Solibacillus promoted the decay of straw mushroom. In conclusion, a high temperature increases the bacterial diversity on the straw mushroom surfaces and has a clustering effect on the bacterial communities. The bacterial community consisting of Firmicutes, Bacilli, Bacillales, Paenibacillus, Lysinibacillus, Pseudomonas, Stenotrophomonas and Solibacillus could promote the decay of straw mushroom, so new preservation materials research can focus on inhibiting anaerobic and decay-causing bacteria to prolong preservation time. Keywords: Volvariella volvacea; food preservation; bacterial community; Firmicutes; Solibacillus 1. Introduction Straw mushroom (Volvariella volvacea), also known as Guangdong mushroom and Chinese mushroom, is one of the largest cultivated edible fungi in the world and one of the main exported mushrooms in China [1,2]. China began cultivating straw mushroom 300 years ago and was the first country to do so [3]. Straw mushroom is a kind of high-temperature mushroom that is not only delicious but also has a high nutritional value [4,5]. Its antioxidant, low-fat and high-protein properties make straw mushroom Microorganisms 2019, 7, 475; doi:10.3390/microorganisms7100475 www.mdpi.com/journal/microorganisms Microorganisms 2019, 7, 475 2 of 14 a typically healthy food in the public mind [6,7]. V. volvacea grows in hot and rainy environments in tropical and subtropical areas, and the optimum growth temperature of this mushroom is 30–32 ◦C, which is similar to the average summer temperature of its main production area. However, the high temperature is not conducive to the storage of the fruit body of V. volvacea. During transport, straw mushroom is placed in paper boxes at 5 kg per box. Due to the respiration of the picked V. volvacea, the temperature at the center of each package can be as high as 50 ◦C, which is extremely unfavorable for the preservation of V. volvacea. To date, there has been much advancement in V. volvacea cultivation, resulting in the ready availability of this mushroom [8–11], while the preservation of V. volvacea remains a serious problem. V. volvacea is unable to withstand low temperatures: when it is stored at 4 ◦C, the mycelium disintegrates and dies, and the fruit body softens and undergoes autolysis [12,13], which complicates the preservation of V. volvacea. At the same time, researchers found that the storage time of V. volvacea was significantly extended when the temperature was approximately 15 ◦C[3,14,15]. While it is expensive to maintain V. volvacea at the ideal storage temperature (15 ◦C), it is also difficult to control the temperature at the center of the box at 15 ◦C. Numerous studies have shown that bacteria are an important reason for food spoilage and degradation [16–20]. To prolong the shelf life of the V. volvacea fruit bodies, this study focused on the bacterial community succession process on the surfaces of postharvest fruit bodies of V. volvacea and aimed to find a solution for V. volvacea fruit body preservation. The bacterial community structures differ greatly among different stages of food spoilage, so investigation of the succession of the bacterial communities could help the identification of decay-causing bacteria [21]. To explore the succession of bacteria on the surfaces of V. volvacea fruit bodies during the process of spoilage, a high-throughput sequencing of the V4 16S rRNA gene was performed to identify bacterial species. The purpose of this research was to identify the bacterial community that played a key role in the process of V. volvacea fruit body decay, thus providing a reference for the preservation of V. volvacea fruit bodies. 2. Methods 2.1. Experimental Design and Simple Process Considering the growth conditions of V. volvacea, we established 30 ◦C as the storage temperature of the fruitbody of V. volvacea. Additionally, previous studies have shown that 15 ◦C was an excellent temperature suitable for the storage of V. volvacea. Thus, this study used 15 and 30 ◦C as the storage temperatures for postharvest V. volvacea. We labeled the fresh fruit bodies of V. volvacea as the D0 group, and we used a letter-plus-number system (D0 group is not fully applicable because no letter was added in front of the group to indicate temperature) to label all the samples. The first letter in the label represents the storage temperature, i.e., A represents a storage temperature of 30 ◦C and B represents a storage temperature of 15 ◦C. The second letter, D, represents the day, the third character (the number between the letter and the decimal point) represents the storage time (number of days); and the fourth character represents the number of biological replicates. V. volvacea fruit bodies were stored at 30 ◦C for 5 days and sampled every 24 h, or stored at 15 ◦C for 12 days and sampled every 48 h (Figure1). The mushrooms were sampled by selecting one sample that was close to the average state from the three V. volvacea fruit body samples in the crisper, i.e., the one that represented the overall preservation condition of all the V. volvacea fruit body samples was selected. The selected sample was then placed in a triangular flask containing 500 mL of double-distilled water and shaken for 3 min. The solution was filtered using filter paper with a 0.22-nm pore size, after which the filter paper was placed in a 50-mL centrifuge tube and stored at 80 C. − ◦ Microorganisms 2019, 7, 475 3 of 14 Microorganisms 2019, 7, x FOR PEER REVIEW 3 of 14 Figure 1. The sensory quality of the V. volvacea fruit bodies stored at 30 and 15 C. Figure 1. The sensory quality of the V. volvacea fruit bodies stored at 30 and 15 °C. ◦ 2.2. Sequencing 2.2. Sequencing 2.2.1. DNA Extraction 2.2.1. DNA Extraction TheThe total genomic DNA DNA was was ex extractedtracted from from microorganisms microorganisms on onthe thesurfaces surfaces of the of V. the volvaceaV. volvacea fruit bodyfruit samplesbody samples using using the cetyl the trimethylcetyl trimethyl ammonium ammonium bromide bromide (CTAB) (CTAB) method. method. The DNAThe DNA concentration andconcentration purity were and quantified purity were on quantified 1% agarose on 1% gels agarose (Life Technologies,gels (Life Technologies, Grand Island, Grand NY,Island, USA). NY, Based on theUSA). determined Based on the concentration, determined concentr the DNAation, was the diluted DNA was to 1 diluted ng/µL to using 1 ng/ sterileμL using water. sterile water. 2.2.2.2.2.2. Amplicon Generation Generation TheThe 16S16S rRNArRNA genesgenes fromfrom thethe distinctdistinct 16S16S V4V4 regions regions werewere amplified amplified usingusing thethe specificspecific barcoded primersbarcoded 515F-806R primers 515F-806R [22]. All [22]. PCRs All were PCRs carried were carried out with out Phusion with Phusion® High-Fidelity® High-Fidelity PCR PCR Master Mix (NewMaster England Mix (New Biolabs, England Ipswich, Biolabs, MA,Ipswich, USA). MA, USA). 2.2.3.2.2.3. PCR Product Product Mixing Mixing and and Purification Purification An equal volume of 1× loading buffer (containing SYBR Green) was mixed with the PCR An equal volume of 1 loading buffer (containing SYBR Green) was mixed with the PCR products, products, and electrophoresis× was performed on a 2% agarose gel for detection. The PCR products andwere electrophoresis mixed at equal was concentrations. performed on Then, a 2% agarosethe mixed gel PCR for detection. products Thewere PCR purified products with were the mixed at equalGeneJET™ concentrations. Gel Extraction Then, Kit the(Thermo mixed Scientific, PCR products Waltham, were MA, purified USA). with the GeneJET™ Gel Extraction Kit (Thermo Scientific, Waltham, MA, USA).
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