一株产纤维素酶菌株的筛选、鉴定及全基因组分析

doi:10.13560/j.cnki.biotech.bull.1985.2024-0448

摘要/Abstract

摘要：

目的筛选纤维素降解酶活性强的微生物菌株，用于青贮饲料的高效发酵。方法从已有菌种库中，利用羧甲基纤维素钠平板筛选产纤维素酶菌株，测定其纤维素酶活性；采用形态观察、生理生化及16S rRNA对菌株进行鉴定；测定该菌株的生长曲线、生长温度及pH、耐盐性等，研究其生长特性；对该菌株的全基因组数据进行生物信息学分析，探究其产纤维素酶基因。结果根据透明圈和菌落直径比值D/d，从菌种库中筛选获得比值最大的菌株为FJAT-25102，其48 h时纤维素酶活性为221.81 U/mL，此外，该菌株具有产蛋白酶和淀粉酶能力。经形态特征、生理生化特征及系统发育分析，将菌株FJAT-25102鉴定为藤黄微球菌（Micrococcus luteus）。菌株FJAT-25102在培养2 h后进入生长起始期，在培养26 h时，OD₆₀₀值达到最大。该菌株在20-50℃、pH 5-11及NaCl浓度为0%-5%时均能生长，具有一定的耐高温性和耐盐碱性。菌株FJAT-25102的基因组由1条环状染色体组成，大小约为2 570 649 bp，GC含量为72.98%。基因组包含2 378个预测的蛋白质编码序列。菌株FJAT-25102中所有可能参与纤维素降解的基因和推定编码的酶包括可能的α-葡萄糖苷酶GH13、内切葡聚糖酶GH74和乙酰木聚糖酯酶CE1、CE7和CE3，其中在FJAT-25102的糖苷水解酶家族中GH13、GH74调控的酶在其降解纤维素的过程中可能起重要作用。菌株FJAT-25102处理的巨菌草青贮饲料的粗纤维、酸性洗涤纤维及中性洗涤纤维含量均显著降低。结论所筛选的藤黄微球菌FJAT-250102可为青贮饲料的发酵提供微生物菌株资源，其全基因组的测定及纤维素酶基因的探究可为后续该菌株产纤维素酶机理研究提供基础。

关键词: 纤维素酶, 藤黄微球菌, 生长特性, 全基因组, 纤维素降解基因

Abstract:

Objective To screen out the microbial strains with strong cellulose degrading enzyme activity for efficient fermentation of silage. Method The cellulase-producing strains were screened by carboxymethyl cellulose sodium plate from existing strain banks and their cellulase activity was determined. Morphological observation, physiological and biochemical analysis and 16S rRNA were used to identify this strain. The growth curve, growth temperature, pH and salt tolerance of strain FJAT-25102 were measured to study its growth characteristics. In further, the whole genome data of this strain was analyzed by bioinformatics to explore the cellulase genes. Result According to the ratio D/d between transparent circle D and colony diameter d, the strain with the highest D/d ratio was FJAT-25102. Further determination of its enzyme activity showed that its cellulase activity was 221.81 U/mL at 48 h. It was found that this strain had the ability to produce protease and amylase. Strain FJAT-25102 was identified as Micrococcus luteus by morphological, physiological, biochemical and phylogenetic analysis. Strain FJAT-25102 was in the growth initiation stage after 2 h of culture, and the OD₆₀₀ value reached the maximum at 26 h of culture. It grew between 20-50℃, pH 5-11 and 0%-5% NaCl concentration, and had certain high temperature resistance and saline-alkaline resistance. The genome of strain FJAT-25102 consisted of a ring chromosome with a size of about 2 570 649 bp and a GC content of 72.98%. The genome contained 2 378 predicted protein-coding sequences. All possible genes involved in cellulose degradation in strain FJAT-25102 included possible alpha-glucosidase GH13, endoglucanase GH74, and acetylxylanesterase CE1, CE7, and CE3. Among them, GH13 and GH74 regulated enzymes in the glycoside hydrolase family of FJAT-25102 may play an important role in the process of cellulose degradation. The contents of crude fiber, acid detergent fiber and neutral detergent fiber in the silage treated by strain FJAT-25102 significantly reduced. Conclusion The selected Micrococcus luteus FJAT-250102 may provide microbial strain resources for silage fermentation. The determination of its whole genome and investigation of cellulase genes may provide the basis for the subsequent research on the cellulase production mechanism of this strain.

Key words: cellulase, Micrococcus luteus, growth characteristics, genome, cellulose degradation genes

车建美, 郑雪芳, 王阶平, 陈燕萍, 陈冰星, 刘波. 一株产纤维素酶菌株的筛选、鉴定及全基因组分析[J]. 生物技术通报, 2025, 41(3): 294-307.

CHE Jian-mei, ZHENG Xue-fang, WANG Jie-ping, CHEN Yan-ping, CHEN Bing-xing, LIU Bo. Screening， Identification and Whole Genome Analysis of a Cellulase Producing Strain[J]. Biotechnology Bulletin, 2025, 41(3): 294-307.

图/表 17

表1 纤维素降解菌株的筛选

Table 1 Screening of cellulose degrading strains

菌株 Strains	菌落直径 Colony diameter （d）/mm	透明圈直径 Diameter of a transparent circle （D）/mm	D/d
FJAT-16079	7.41±0.48	16.60±5.55	2.30
FJAT-16350	6.94±4.37	16.46±6.27	2.99
FJAT-16989	3.91±0.22	7.02±0.70	1.81
FJAT-25102	3.44±0.23	14.59±0.14	4.26
FJAT-17136	9.31±1.03	11.79±0.37	1.28
FJAT-10006	3.03±1.01	8.85±3.61	2.84
FJAT-20218	2.16±0.44	8.70±1.93	4.02
FJAT-22285	6.99±0.59	9.97±0.18	1.43
FJAT-16396	6.19±1.26	13.64±7.30	2.05
FJAT-20520	4.36±0.75	9.79±0.07	2.31
FJAT-20398	2.93±0.42	11.46±1.29	4.06
FJAT-16034	6.93±0.25	13.46±0.02	1.95
FJAT-16517	14.72±0.73	21.16±0.20	1.44
FJAT-26369	10.28±0.37	12.54±0.24	1.22
FJAT-41640	6.96±1.12	10.00±0.16	1.47
FJAT-25102	3.74±0.15	14.71±0.43	3.94
FJAT-22275	2.74±0.54	7.88±0.44	2.96
FJAT-4326	9.05±2.12	20.03±0.82	2.32
FJAT-41635	9.22±1.03	21.28±1.35	2.32

图1 菌株FJAT-25102的纤维素酶活性

Fig. 1 Cellulase activity of strain FJAT-25102

图2 菌株FJAT-25102的产酶特性A：纤维素酶；B：淀粉酶；C：蛋白酶

Fig. 2 Enzymatic characteristics of strain FJAT-25102A: Cellulase. B: Amylase. C: Protease

图3 菌株FJAT-25102的菌落形态（A）和菌体形态（B）

Fig. 3 Colony morphology (A) and cell morphology (B) of strain FJAT-25102

表2 菌株FJAT-25102的API 20E试验结果

Table 2 API 20E results of strain FJAT-25102

项目 Item	结果 Results	项目 Item	结果 Results
精氨酸水解酶Arginine hydrolase	-	苦杏仁苷Amygdalin	-
苯丙氨酸脱氨酶Phenylalanine deaminase	-	甘露醇Mannitol	-
VP反应Voges-Proskauer test	+	肌醇Inositol	-
赖氨酸脱羧酶Lysine decarboxylase	-	山梨醇Sorbitol	-
鸟氨酸脱羧酶Ornithine decarboxylase	-	密二糖Melibiose	-
柠檬酸盐利用Sodium critrate	+	葡萄糖Glucose	-
明胶液化Gelatin hydrolysis	+	阿拉伯糖L-arabinose	-
β-半乳糖苷酶 O-Nitrophenyl-β-D-galactopyranoside enzyme	-	鼠李糖Rhamnose	-
β-半乳糖苷酶 O-Nitrophenyl-β-D-galactopyranoside enzyme	-	蔗糖Sucrose	-
尿素酶Urease	+	吲哚Indole	-
硫化氢Hydrogen sulfide	-	吲哚Indole	-

表3 菌株FJAT-25102的API 50CH试验结果

Table 3 API 50CH experimental results of strain FJAT-25102

项目 Item	结果 Results	项目 Item	结果 Results
甘油Glycerol	-	柳醇Saligenin	-
L-阿拉伯糖L-arabinose	-	纤维二糖Cellobiose	-
D-阿拉伯糖D-arabinose	-	麦芽糖Maltose	-
L-木糖L-xylose	-	D-来苏糖D-lyxose	-
D-木糖D-xylose	-	D-塔格糖D-tagatose	-
β-甲基-D-木糖苷β-methyl-D-xyloside	-	D-松二糖D-turanose	-
赤癣醇Erythritol	-	D-阿糖醇D-arabitol	-
阿东醇Adonitol	-	D-岩糖D-fucose	-
果糖Fructose	-	L-岩糖L-fucose	-
核糖Ribose	-	龙胆二糖Gentiobiose	-
甘露醇Mannitol	-	肝糖Glycogen	-
甘露糖Mannose	-	菊糖Inulin	-
半乳糖Galactose	-	蜜二糖D-melibiose	-
半乳糖醇Dulcitol	-	海藻糖Trehalose	-
肌醇Inositol	-	蔗糖Sucrose	-
山梨醇Sorbitol	-	棉子糖Raffinose	-
山梨糖Sorbose	-	乳糖Lactose	-
葡萄糖Glucose	-	松三糖Melizitose	-
鼠李糖Rhamnose	-	木糖醇Xylitol	-
七叶灵Esculin	+	L-阿糖醇L-arabitol	-
熊果苷Arbutin	-	5-酮基-葡萄糖酸盐5-keto-D-gluconate	-
α-甲基-D-甘露糖苷α-methyl-D-mannose glycosides	-	2-酮基-葡萄糖酸盐2-keto-D-gluconate	-
α-甲基-D-葡萄糖苷α-methyl-D-glucoside	-	葡萄糖酸盐Gluconate	-
N-乙酰-葡糖胺N-acetylglucosamine	-	苦杏仁苷Amygdalin	-
淀粉Starch	-

图4 基于16S rRNA基因序列构建的菌株FJAT-25102的系统发育树括号内序号为该菌株GenBank登录号；标尺0.50代表序列偏差值；内部节点数字为支持度，用于代表该分支结构的可靠程度

Fig. 4 Phylogenetic trees of the strain FJAT-25102 based on the 16S rRNA gene sequencesThe serial number in brackets is the GenBank accession number of the strain. The value of 0.50 indicates the sequence deviation value. The number of internal nodes is support value, which indicates the reliability of the branch structure. The same below

图5 菌株FJAT-25102的生长曲线

Fig. 5 Growth curve of strain FJAT-25102

图6 不同条件对菌株FJAT-25102生长的影响不同小写字母代表不同处理差异显著（P<0.05）。下同

Fig. 6 Effect of different conditions on growth of strain FJAT-25102Different letters indicate significant difference at P<0.05 level among different treatments. The same below

图7 菌株FJAT-25102的基因组圈图圈图的最外面一圈为基因组大小的标识；第二圈和第三圈为正链、负链上的CDS，不同的颜色表示CDS不同的COG的功能分类；第四圈为rRNA和tRNA；第五圈为GC含量，向外的红色部分表示该区域GC含量高于全基因组平均GC含量，峰值越高表示与平均GC含量差值越大，向内的蓝色部分表示该区域GC含量低于全基因组平均GC含量，峰值越高表示与平均GC含量差值越大；最内一圈为GC-Skew值

Fig. 7 Circular genome circle map of strain FJAT-25102The outermost circle is the genome size. The second and third circles are the CDS on the positive and negative strands. The functional classifications of COGs of different CDS are distinguished by different colors. The fourth circle is rRNA and tRNA. The fifth circle is the GC content. The outward red indicates the GC content is higher than the genome level, and the inward blue indicates that the GC content is lower than the genome level. The innermost circle is GC-skew value

图8 菌株FJAT-25102的COG注释分类统计图

Fig. 8 Statistical chart of COG annotation classification of strain FJAT-25102

图9 菌株FJAT-25102的GO注释分类统计图

Fig. 9 Statistical chart of GO annotation classification of strain FJAT-25102

图10 菌株FJAT-25102的KEGG功能注释分类

Fig. 10 KEGG function classification of strain FJAT-25102

图11 菌株FJAT-25102的CAZy分析统计AA：辅助功能酶；CBM：碳水化合物结合组件；CE：碳水化合物酯酶；GH：糖苷水解酶；GT：糖苷转移酶家族的蛋白

Fig. 11 CAZy analysis of strain FJAT-25102AA: Auxiliary activities. CBM: Carbohydrate-binding modules. CE: Carbohydrat esterases. GH: Glycoside hydrolases. GT: Glycosyl transferases

表4 菌株FJAT-25102次级代谢产物合成基因簇预测结果

Table 4 Predicted results of gene clusters of secondary metabolite of strain FJAT-25102

基因簇编号 Cluster ID	基因簇类型 Type	起始位置 Start	终止位置 End	已知基因簇 Similar cluster	相似度 Similarity/%	基因数量 Gene No.
Cluster1	Ectoine	257 860	268 232	-	-	9
Cluster2	Siderophore	1 189 625	1 201 461	-	-	13
Cluster3	Betalactone	1 587 487	1 614 450	五酮安莎霉素 Microansamycin	7	22
Cluster4	NRPS-like	1 653 516	1 696 027	Stenothricin	31	35
Cluster5	Terpene	2 371 418	2 392 315	类胡萝卜素 Carotenoid	50	21

表5 菌株FJAT-25102基因组中纤维素酶相关酶家族

Table 5 Cellulase-related enzyme families in the strain FJAT-25102 genome

基因编号 Gene No.	基因名称 Gene name	酶定义 Definition of enzymes	家族 Family
gene0035	-	Acetyl xylan esterase （EC 3.1.1.72）	CE7
gene0587	metX	Acetyl xylan esterase （EC 3.1.1.72）	CE1
gene0588	-	Acetyl xylan esterase （EC 3.1.1.72）	CE3
gene0589	-	Acetyl xylan esterase （EC 3.1.1.72）	CE1
gene1502	yvaK	Acetyl xylan esterase （EC 3.1.1.72）	CE1
gene0137	malZ	α-glucosidase （EC：3.2.1.20）	GH13
gene0656	-	Endoglucanase （EC 3.2.1.4）	GH74

图12 菌株FJAT-25102对巨菌草青贮饲料营养品质的影响CF：粗纤维；ADF：酸性洗涤纤维；NDF：中性洗涤纤维

Fig. 12 Effect of strain FJAT-25102 on nutrient quality of giganteum silageCF: Crude fiber; ADF: acid detergent fiber; NDF: neutral detergent fiber

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