高效木质素降解菌的筛选及其对玉米秸秆的降解效果
吉林农业大学食药用菌教育部工程研究中心 吉林 长春 130118
Screening of efficient lignin-degrading fungal strains and their degradation on cornstalk
Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, Jilin 130118, China
责任编辑: 韩丽
收稿日期: 2020-12-25 接受日期: 2021-02-22
| 基金资助: |
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Corresponding authors:
Received: 2020-12-25 Accepted: 2021-02-22
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本研究利用愈创木酚和苯胺蓝固体培养基对菌株进行初筛,利用形态学和分子生物学对筛选出的菌株进行鉴定,以黄孢原毛平革菌Phanerochaete chrysosporium CGMCC 5.0776为对照,利用其对玉米秸秆进行预处理并测定木质素和纤维素的降解率,测定筛选菌株在预处理玉米秸秆过程中漆酶、锰过氧化物酶(manganese peroxidase,MnP)和木质素过氧化物酶(lignin peroxidase,LiP)活性。结果表明:利用愈创木酚和苯胺蓝固体培养基,从16株白腐真菌菌株中筛选出2株具有较高漆酶或MnP活性的菌株,鉴定其为桦栓孔菌Trametes betulina (L.) Pilát(ZT-153)和亚黑管孔菌Bjerkandera fumosa (Pers.) P. Karst.(ZT-307),测定T. betulina ZT-153和B. fumosa ZT-307对玉米秸秆酸不溶木质素降解效率分别为13.60%和21.87%,较对照P. chrysosporium CGMCC 5.0776高1.58%和9.85%,对纤维素的降解率较低,分别为4.10%和4.50%。2株菌株在预处理玉米秸秆过程中,T. betulina ZT-153表现出漆酶和MnP活性,B. fumosa ZT-307只表现出LiP活性。其中B. fumosa ZT-307对玉米秸秆酸不溶木质素的降解效率最高,在秸秆资源的综合利用方面具有较好的潜力和应用前景。
关键词:
Efficient lignin-degrading fungal strains were screened by using guaiacol- and aniline blue-containing solid media. Using Phanerochaete chrysosporium CGMCC 5.0776 as a control, cornstalk was pretreated with the selected strains. The degradation rates of lignin and cellulose, and the activities of laccase, manganese peroxidase (MnP) and lignin peroxidase (LiP) were determined. Two strains with higher activities of laccase or MnP were screened from 16 white-rot fungal strains. Based on morphology and molecular biology, they were identified as Trametes betulina (ZT-153) and B. fumosa (ZT-307). The lignin degradation efficiency on cornstalk was 13.60% by T. betulina ZT-153 and 21.87% by B. fumosa ZT-307, or respectively 1.58% and 9.85% as against P. chrysosporium CGMCC 5.0776, and the degradation rate of cellulose was 4.10% and 4.50% respectively. During the pretreatment of cornstalk, T. betulina ZT-153 showed active in degrading laccase and MnP, while B. fumosa ZT-307 only showed active in degrading LiP. Bjerkandera fumosa ZT-307 showed the highest lignin degradation ability, and it has potential and application prospects in comprehensive utilization of cornstalk resources.
Keywords:
本文引用格式
张芳芳, 张桐, 戴丹, 张振豪, 张波, 李玉.
ZHANG FangFang, ZHANG Tong, DAI Dan, ZHANG ZhenHao, ZHANG Bo, LI Yu.
中国是农业大国,也是秸秆年产量最多的国家。统计数据显示,2015年中国秸秆资源总量约10.4亿吨,以水稻秸秆、小麦秸秆和玉米秸秆为主,在东北地区,玉米秸秆是主要的农业副产物(张强等 2005;蒋泓峰 2016)。秸秆作为一个重要的可再生资源,“用则利,弃则害”(毕于运 2010)。秸秆的主要成分包括木质素、纤维素和半纤维素,木质素和半纤维素以共价键的形式形成一种天然的屏障,将纤维素包裹在其中,防止纤维素被酶解。木质素紧密的碳水化合物结构是影响玉米秸秆利用效率的主要屏障(Buranov & Mazza 2008;宋丽丽 2013;左飒飒 2018)。利用微生物预处理秸秆因具有耗能小、成本低、无污染的特点引起研究者的广泛关注。其中白腐真菌对秸秆进行预处理,破坏秸秆的木质纤维素结构,对于秸秆资源的利用具有重要意义。
我国大型菌物资源丰富(李玉等 2015),其中多孔菌种类繁多,目前达600多种,东北地区达300多种,作为白腐真菌的重要类群,多孔菌为其研究提供了宝贵的资源(戴玉成 2009;Dai 2010;司静等 2011a,2011b,2011c;王伟等 2011;韩美玲等 2017;郑飞等 2017;吴怡等 2019, 2020)。白腐真菌对木质素具有很强的降解能力,能够在纯培养的条件下将木质素完全降解为CO2和H2O(Reid 1995;李慧蓉 2005)。早期Kirk & Tien(1984)研究了白腐真菌模式菌株Phanerochaete chrysosporium Burds.对木质素的降解。此后Wan & Li(2010)利用虫拟蜡孔菌Ceriporiopsis subvermispora (Pilát) Gilb. & Ryvarden降解玉米秸秆,在接种42d时,其对木质素的降解效果达到39.2%,对纤维素的降解效果不足5%。Sun et al.(2011)利用毛栓孔菌Trametes hirsuta (Wulfen) Lloyd 对玉米秸秆进行降解,在预处理42d时,对木质素降解率达到71.91%。宋丽丽等(2017)利用硬毛粗盖孔菌Funalia trogii (Berk.) Bondartsev & Singer预处理玉米秸秆,木质素降解率为33.99%,纤维素降解率为8.77%。甄静等(2017)对T. hirsuta XYG422漆酶发酵条件进行优化,预处理玉米秸秆,木质素降解率达到83.54%。白腐真菌对木质纤维素的降解能力因属、种而异,比较理想的白腐真菌菌株对木质素具有特异性降解效果,微量降解纤维素(Blanchette et al. 1988)。
本研究从16株白腐真菌菌株中筛选得到有较强漆酶或过氧化物酶活性的2株菌,利用其对玉米秸秆进行预处理,发现它们对玉米秸秆中的酸不溶木质素具有较强的降解作用。研究结果为白腐真菌资源的开发利用以及对玉米秸秆木质素降解机制研究提供基础数据。
1 材料与方法
1.1 材料
1.1.1 供试菌株:本试验所用Phanerochaete chrysosporium CGMCC 5.0776购自中国科学院菌种保藏中心,其他16株菌株由作者采集、分离、纯化,现保藏于吉林农业大学菌种保藏中心(CCMJ)。
1.1.2 试验原料:玉米秸秆取自吉林农业大学试验田。
1.1.3 培养基:愈创木酚-PDA固体培养基:200g马铃薯提取液,琼脂20g,葡萄糖20g,愈创木酚0.4mL加水定容到1L,121℃灭菌3min,用于定性测定菌株的产漆酶能力(芦光新等 2014)。苯胺蓝-PDA固体培养基:200g马铃薯提取液,琼脂20g,葡萄糖20g,苯胺蓝0.1g,加水定容到1L,121℃灭菌30min,用于定性测定菌株的产过氧化物酶能力(蔡磊等 2002)。菌株活化培养基:葡萄糖20g,琼脂20g,酵母浸粉5.0g,KH2PO4 1g,MgSO4·7H2O 0.5g,ZnSO4·7H2O 0.05g,加水定容到1L,pH自然,121℃灭菌30min(司静 2014)。液体培养基:葡萄糖20g,酵母浸粉5g,KH2PO4 1g,MgSO4·7H2O 0.5g,ZnSO4·7H2O 50mg,加水定容到1L,pH自然,分装至250mL锥形瓶中,每瓶倒入液体培养基100mL,121℃灭菌30min后,加入维生素B1 40μL。玉米秸秆固体培养基:将玉米秸秆于60℃烘干至恒重后粉碎,过40目筛,按照玉米秸秆:水=1:2.5的比例加入到培养皿中,121℃灭菌30min。
1.2 方法
1.2.1 菌株活化:将于4℃低温保藏的白腐真菌菌株取出,置于室温过夜,接种至菌株活化培养基中,25℃恒温培养至菌丝铺满平板。
1.2.2 菌株筛选:取直径为1cm的菌块分别接种到愈创木酚-PDA固体培养基中25℃培养6d,以及苯胺蓝-PDA固体培养基中25℃培养5d,利用十字划线法,测量培养皿中的菌丝直径、显色圈/褪色圈直径、显色圈/褪色圈直径与菌丝直径的比值,每个菌株设置3个重复。选择菌丝生长较快且漆酶/过氧化物酶活性较高的菌株用于后续试验。
1.2.3 菌株鉴定:(1)形态学鉴定:采用传统分类学方法,观察菌株的宏观特征和微观特征,参照李玉等(2015)和赵继鼎等(1998)的研究进行鉴定。
(2)分子生物学鉴定:取一定量的新鲜菌丝体和子实体,采用基因组DNA提取试剂盒(康为世纪)提取总DNA。PCR扩增引物为ITS5和ITS4(White et al. 1990),PCR反应体系:10×PCR buffer 2.5μL,dNTP(10mmol/L)2μL,引物ITS4和ITS5(10μmol/L)1μL,Taq DNA聚合酶(5U/μL),模板DNA 2μL,补加去离子水至25μL。PCR反应条件:95℃预变性3min;94℃变性40s,54℃退火45s,72℃延伸1min,共35个循环;72℃延伸10min,4℃终止反应。产物送到生工生物工程(上海)股份有限公司测序,结合GenBank的一些已知序列并利用最大似然法和贝叶斯法分析构建系统发育树,选用Boletopsis leucomelaena (Pers.) Fayod和Hydnellum geogenium (Fr.) Banker作为外群,利用MAFFT进行序列的比对(Kazutaka et al. 2005),Gblocks获取序列的保守区域(Talavera & Castresana 2007),ModelFinder选择最佳模型和参数(Kalyaanamoorthy et al. 2017),利用IQtree和MrBayes分别构建系统发育树(Ronquist et al. 2012;Nguyen et al. 2015)。
1.2.4 种子发酵:取直径为1cm的菌块5个,接种至液体培养基中,25℃、150r/min振荡培养6d。
1.2.5 玉米秸秆预处理:以种子发酵液体积:玉米秸秆质量=1:1的比例将种子发酵液接种到玉米秸秆固体培养基中,25℃培养33d后,将样品取出,于60℃烘干至恒重,装入自封袋中备用。测定预处理秸秆酸不溶木质素、纤维素含量,参照王玉万和徐文玉(1987)采用的方法,本方法主要测定酸不溶木质素的含量。
1.2.7 酶活性测定:采用试剂盒(苏州科铭生物技术有限公司)对预处理的玉米秸秆样品中漆酶、锰过氧化物酶(manganese peroxidase,MnP)和木质素过氧化物酶(lignin peroxidase,LiP)活性进行测定。漆酶活力单位的定义(U):在波长420nm下,每分钟将1μmol 2,2′联氮双3乙基苯并噻唑啉6磺酸[2,2′azino bis(3ethylbenzothiazoline6sulfonic acid),ABTS]底物氧化所需的酶量。MnP活力单位的定义(U):在波长465nm下,每分钟将1μmol愈创木酚氧化所需的酶量。LiP活力单位的定义(U):在波长651nm下,每1mL反应体系中每分钟吸光度值变化0.01为一个酶活单位。
1.2.8 数据分析:采用软件SPSS 22.0计算平均值和标准差,使用Duncan’s分析各个处理之间的差异显著性。
2 结果与分析
2.1 菌株筛选
将16株菌接种于愈创木酚PDA固体培养基和苯胺蓝PDA固体培养基上,测量显色圈和变色圈直径(表1)。在愈创木酚PDA固体培养基上生长第6天时,除ZT002、ZT299外,均产生红褐色的显色圈。其中ZT153菌落直径与显色圈直径的比值最大,为1.40,除ZT-070、ZT-079外,菌落直径与显色圈直径的比值显著高于其他菌株,因此判断ZT-153具有较高的漆酶活性,用于后续实验。在苯胺蓝PDA固体培养基上,ZT-070接种第5天,菌丝铺满培养基,菌落直径为84.33mm,未出现褪色圈。其他菌株均产生褪色圈,其中ZT-307的菌落直径为61.36mm;褪色圈直径最大,为59.39mm;变色圈直径与显色圈直径比值为0.97。ZT-218的变色圈直径与显色圈直径比值最大为0.98,与ZT-307无显著性差异,根据褪色圈的大小判断ZT-218和ZT-307具有较强的产过氧化物酶能力,因ZT-307的菌丝直径和褪色圈直径显著高于ZT-218,因此选择ZT-307用于后续试验。
表1 愈创木酚平板显色和苯胺蓝平板褪色结果
Table 1
| 菌株 Strain | 愈创木酚平板显色 Guaiacol-containing plate coloration | 苯胺蓝平板褪色 Aniline blue-containing plate decolorization | ||||
|---|---|---|---|---|---|---|
| 菌落直径 Colony diameter (mm) | 显色圈直径 Coloration circle diameter (mm) | 显色圈直径/ 菌落直径 Coloration circle diameter/ Colony diameter | 菌落直径 Colony diameter (mm) | 褪色圈直径 Decolorization circle diameter (mm) | 褪色圈直径/ 菌落直径 Decolorization circle diameter/ Colony diameter | |
| ZT-002 | 51.33±3.35 cd | 0.00 | 0 | 57.93±1.39 fg | 51.05±3.50 b | 0.88±0.04 b |
| ZT-003 | 49.12±2.78 cd | 53.61±3.03 de | 1.09±0.02 cd | 58.91±4.11 f | 26.88±2.67 fg | 0.46±0.04 g |
| ZT-014 | 63.27±3.25 b | 65.15±3.85 b | 1.03±0.05 cde | 76.08±1.98 bc | 50.88±2.59 b | 0.67±0.05 d |
| ZT-018 | 52.64±3.74 c | 54.01±4.63 de | 1.03±0.03 cde | 68.26±1.07 e | 24.36±8.02 g | 0.36±0.11 h |
| ZT-021 | 43.89±0.31 de | 51.63±1.24 e | 1.18±0.03 bc | 66.51±4.84 e | 36.94±7.44 de | 0.55±0.07 ef |
| ZT-070 | 47.95±10.91 cd | 59.97±1.17 c | 1.30±0.32 ab | 84.33±0.66 a | 0.00 | 0 |
| ZT-079 | 32.52±3.87 f | 44.02±2.13 f | 1.36±0.16 a | 36.16±1.27 g | 9.68±0.27 h | 0.27±0.00 h |
| ZT-123 | 53.74±3.51 c | 46.89±1.76 f | 0.87±0.08 e | 66.90±3.97 e | 32.50±0.27 ef | 0.49±0.03 fg |
| ZT-153 | 33.30±5.13 f | 46.45±5.54 f | 1.40±0.05 a | 54.79±1.52 gh | 15.76±4.36 h | 0.29±0.07 h |
| ZT-156 | 51.50±2.48 cd | 56.92±2.19 cd | 1.10±0.02 cd | 69.45±1.59 de | 40.42±2.92 d | 0.58±0.04 de |
| ZT-157 | 50.21±2.10 cd | 55.21±1.75 cde | 1.10±0.02 cd | 54.86±0.82 gh | 42.15±0.28 cd | 0.77±0.01 c |
| ZT-178 | 71.24±1.05 a | 68.35±1.75 b | 0.96±0.03 de | 77.23±1.16 b | 12.33±0.16 h | 0.16±0.00 i |
| ZT-197 | 72.54±1.57 a | 76.18±0.68 a | 1.05±0.03 cde | 72.64±0.84 cd | 48.13±1.74 bc | 0.66±0.02 d |
| ZT-218 | 40.66±1.28 e | 45.10±0.40 f | 1.11±0.04 cd | 47.53±0.43 i | 46.70±0.67 bc | 0.98±0.01 a |
| ZT-299 | 10±0 g | 0.00 | 0 | 52.97±2.49 h | 14.19±3.53 h | 0.27±0.08 h |
| ZT-307 | 33.35±4.32 f | 31.54±0.95 g | 0.95±0.10 de | 61.36±1.12 f | 59.39±1.37 a | 0.97±0.01 ab |
注:同列数值后不同小写字母表示在P<0.05水平上差异显著
Note: Different lowercase letters after the same column indicate significant differences at P<0.05 level.
2.2 菌株鉴定
ZT-153、ZT-307的形态特征分别与T. betulina和B. fumosa在李玉等(2015)和赵继鼎等(1998)研究中的描述相似。
图1
图1
基于ITS序列构建ZT-153、ZT-307及其相关种的系统发育树
Fig. 1
Phylogenetic tree analysis of ZT-153 and ZT-307 tested strains and their related species based on ITS sequences.
表2 试验菌株
Table 2
| 菌株 Strain | 名称 Name | 采集地 Collecting site |
|---|---|---|
| ZT-153 | 桦栓孔菌Trametes betulina (L.) Pilát | 黑龙江漠河Mohe, Heilongjiang |
| ZT-307 | 亚黑管孔菌Bjerkandera fumosa (Pers.) P. Karst. | 辽宁本溪Benxi, Liaoning |
2.3 菌株对玉米秸秆的预处理效果
以P. chrysosporium CGMCC 5.0776为对照菌株,使用上述试验筛选的T. betulina ZT-153和B. fumosa ZT-307对玉米秸秆进行预处理(图2)。利用王玉万和徐文玉(1987)所采用的方法,测定在玉米秸秆预处理33d时,3株菌对玉米秸秆中酸不溶木质素和纤维素降解效率。结果显示,3株菌均可对玉米秸秆中的木质素和纤维素产生降解作用,P. chrysosporium CGMCC 5.0776对玉米秸秆木质素的降解率为12.02%,对纤维素的降解率为29.63%;B. fumosa ZT-307对木质素的降解率最高,为21.87%,对纤维素的降解率为4.50%;T. betulina ZT-153对木质素的降解率达到13.60%,对纤维素的降解率为4.10%;其中T. betulina ZT-153和B. fumosa ZT-307对木质素的降解率较对照P. chrysosporium CGMCC 5.0776高1.58%和9.85%,但3株菌对木质素的降解率差异不显著;T. betulina ZT-153和B. fumosa ZT-307对纤维素的降解率均小于5%,显著低于P. chrysosporium CGMCC 5.0776(表3)。
图2
图2
三株菌株预处理玉米秸秆33d时的菌丝长势
A:空白玉米秸秆;B:Trametes betulina ZT-153;C:Bjerkandera fumosa ZT-307;D:Phanerochaete chrysosporium CGMCC 5.0776
Fig. 2
Mycelial growth of three tested strains after cornstalk pretreatment for 33d.
A: CK; B: T. betulina ZT-153; C: B. fumosa ZT-307; D: P. chrysosporium CGMCC 5.0776.
表3 三株菌对玉米秸秆的降解效果
Table 3
| 菌株 Strain | 纤维素含量 Cellulose content (%) | 纤维素降解率 Degradation rate of cellulose (%) | 酸不溶木质素含量 Acid-insoluble lignin content (%) | 酸不溶木质素降解率 Degradation rate of acid-insoluble lignin (%) |
|---|---|---|---|---|
| Phanerochaete chrysosporium CGMCC 5.0776 | 12.56±0.42 a | 29.63±2.35 a | 5.61±0.42 a | 12.02±6.52 a |
| Trametes betulina ZT-153 | 17.12±0.54 b | 4.10±3.06 b | 5.51±0.20 a | 13.60±3.19 a |
| Bjerkandera fumosa ZT-307 | 17.05±2.33 b | 4.50±1.57 b | 4.98±0.26 a | 21.87±4.18 a |
注:同列数值后不同小写字母表示在P<0.05水平上差异显著
Note: Different lowercase letters after the same column indicate significant differences at P<0.05 level.
2.4 菌株预处理玉米秸秆过程中酶活性的测定
利用T. betulina ZT-153和B. fumosa ZT-307预处理玉米秸秆,每5d取一次样,提取样品粗酶液,测定其漆酶、MnP和LiP活性(图3)。测定T. betulina ZT-153在预处理玉米秸秆过程中表现出漆酶和MnP活性,B. fumosa ZT-307仅检测到LiP活性。T. betulina ZT-153在预处理玉米秸秆过程中,在第20天时漆酶活力急剧下降,之后迅速上升,在第30天时漆酶活性达到最高值,为21.36U/g;检测到较低的MnP活性,呈现先增高后降低的趋势,在预处理玉米秸秆20天时,达到峰值,为0.32U/g。B. fumosa ZT-307在预处理玉米秸秆过程中,在第10天和第20天时木质素过氧化物酶均达到峰值,为15U/g,测定结果显示在第10在时,其LiP活性比较稳定。
图3
图3
两株菌预处理玉米秸秆过程中酶活性的变化
A:Trametes betulina ZT-153;B:Bjerkandera fumosa ZT-307
Fig. 3
Variations of the enzyme activities during the course of cornstalk pretreatment by two fungal strains.
A: T. betulina ZT-153; B: B. fumosa ZT-307.
3 讨论
本研究从16株白腐真菌菌株中,通过王玉万和徐文玉(1987)所采用的方法测定筛选的2株菌株对玉米秸秆酸不溶木质素的降解效果,其中T. betulina ZT-153和B. fumosa ZT-307对玉米秸秆的木质素降解率高于模式菌株P. chrysosporium CGMCC 5.0776。
研究者利用T. betulina处理山毛榉(Fukasawa et al. 2005)、毛白杨(Wang et al. 2014)、小麦秸秆(Knežević et al. 2013)等基质时,取得了较好的降解木质素的效果,而利用其降解玉米秸秆基质的研究鲜见报道。本研究中,T. betulina ZT-153对玉米秸秆酸不溶木质素的降解率为13.60%,与该菌株对其他基质的降解效果相比,其对玉米秸秆酸不溶木质素的降解优势低于其对其他基质的降解作用,推断一方面是由于同一菌株在不同的培养体系和培养条件下,其降解能力和产酶能力不同(Singh & Chen 2008);同一菌株对不同基质的木质素降解能力不同(Adejoye & Fasidi 2009);同种不同菌株的产酶能力也存在差异(张桐等 2018)。另一方面由于本研究利用72%浓硫酸对秸秆进行处理,过滤后所剩余的残渣即为木质素含量,一些木质素可能因溶解在硫酸中而流失,所测定的木质素含量仅是酸不溶木质素含量(王玉万和徐文玉 1987)。B. fumosa ZT-307是本研究中对玉米秸秆木质素降解率最高的菌株,而利用B. fumosa对不同基质木质素降解的研究未见报道。根据现有的文献调查,较其他白腐真菌菌株相比,B. fumosa对玉米秸秆酸不溶木质素的降解效率较高。吴雪君(2017)利用绒毛栓孔菌T. pubescens Cui 7571预处理玉米秸秆42d,玉米秸秆酸不溶木质素含量由原来的21.65%转变为17.20%,计算后可知其对玉米秸秆酸不溶木质素的降解率为20.55%,而B. fumosa ZT-307在对玉米秸秆预处理33d时酸不溶木质素的降解率已达到21.87%。
在白腐真菌预处理玉米秸秆的过程中,测定T. betulina ZT-153分泌漆酶和MnP,B. fumosa ZT-307仅分泌LiP。木质素的生物降解是一个复杂的反应过程,其酶活性的分泌依赖于菌株、底物和环境条件等因素。在木质素降解过程中,漆酶可能在一个菌株或培养物中起中心作用,而一些菌株在木质素降解过程中,仅表现出MnP或LiP活性或同时表现出漆酶与MnP活性,并在木质素降解过程中发挥关键作用(Sun et al. 2011)。T. betulina ZT-153在预处理玉米秸秆30d时,漆酶仍具有较高活性,且达到其30d内的最大值,可能是由于真菌自溶导致细胞内的酶释放到培养基中所致(Arora et al. 2002)。
本研究筛选出的2株菌均对玉米秸秆中的木质素具有降解作用,其中B. fumosa ZT-307对玉米秸秆酸不溶木质素的降解率较模式菌株P. chrysosporium CGMCC 5.0776高9.85%,可见该菌株在玉米秸秆预处理方面具有较大的开发利用前景,后续还可以对其预处理条件进行优化,或利用此菌株与其他菌株或物理化学方法相结合预处理玉米秸秆,增加其对木质素的降解效果。
致谢:
感谢吉林农业大学饶固和汪阳在系统发育树构建方面提供的技术支持。
参考文献
Biodegradation of agrowastes by some Nigerian white-rot fungi
Involvement of lignin peroxidase, manganese peroxidase and laccase in degradation and selective ligninolysis of wheat straw
Study on straw resources evaluation and utilization in China
Selection of white-rot fungi for biopulping
DOI:10.1016/0144-4565(88)90099-6 URL [本文引用: 1]
Lignin in straw of herbaceous crops
DOI:10.1016/j.indcrop.2008.03.008 URL [本文引用: 1]
Several qualitative methods for the screening of fungi to decompose lignin
The suitable varieties of Auricularia auricular complex substrate screening and nutritional physiology research
A checklist of polypores in China
Species diversity of wood-decaying fungi in Northeast China
Decomposition of Japanese beech wood by diverse fungi isolated from a cool temperate deciduous forest
DOI:10.1007/S10267-004-0215-7 URL [本文引用: 1]
Effects of different lignocellulose as inducers on laccase activities of Pleurotus ostreatus in submerged fermentation
ModelFinder: fast model selection for accurate phylogenetic estimates
DOI:10.1038/nmeth.4285
PMID:28481363
[本文引用: 1]
Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.
MAFFT version 5: improvement in accuracy of multiple sequence alignment
The accuracy of multiple sequence alignment program MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement options, H-INS-i, F-INS-i and G-INS-i, in which pairwise alignment information are incorporated into objective function. These new options of MAFFT showed higher accuracy than currently available methods including TCoffee version 2 and CLUSTAL W in benchmark tests consisting of alignments of >50 sequences. Like the previously available options, the new options of MAFFT can handle hundreds of sequences on a standard desktop computer. We also examined the effect of the number of homologues included in an alignment. For a multiple alignment consisting of approximately 8 sequences with low similarity, the accuracy was improved (2-10 percentage points) when the sequences were aligned together with dozens of their close homologues (E-value < 10(-5)-10(-20)) collected from a database. Such improvement was generally observed for most methods, but remarkably large for the new options of MAFFT proposed here. Thus, we made a Ruby script, mafftE.rb, which aligns the input sequences together with their close homologues collected from SwissProt using NCBI-BLAST.
Lignin-degrading enzyme from Phanerochaete chrysosporium
DOI:10.1007/BF02798954 URL [本文引用: 1]
Lignin degradation by selected fungal species
DOI:10.1016/j.biortech.2013.03.182 URL [本文引用: 1]
Atlas of Chinese macrofungal resources
Study on a laccase-producing fungus from alpine grassland soil in eastern Qilian Mountains: screening, identification, and activity analyses
IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies
DOI:10.1093/molbev/msu300 URL [本文引用: 1]
Biodegradation of lignin
DOI:10.1139/b95-351 URL [本文引用: 1]
MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space
DOI:10.1093/sysbio/sys029
PMID:22357727
[本文引用: 1]
Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
Decolorization of azo dye Congo Red by white rot fungus Trametes pubescens
Primary screening of effective Trametes strains with high laccase- productivity and optimization of conditions on laccase production
Optimization of conditions for laccase production by Perenniporia subacida and its application in dye decolorization
Advances of research on characteristic, molecular biology and applications of laccase from fungi
The white-rot fungus Phanerochaete chrysosporium: conditions for the production of lignin-degrading enzymes
DOI:10.1007/s00253-008-1706-9 URL [本文引用: 1]
Mechanism study on improvement of enzymatic hydrolysis of corn stover by efficient lignin modification with white-rot fungus
Effect of biological pretreatment with Funalia trogii on enzymatic hydrolysis and chemical components of corn stover
Effect of biological pretreatment with Trametes hirsuta yj9 on enzymatic hydrolysis of corn stover
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
Alignment quality may have as much impact on phylogenetic reconstruction as the phylogenetic methods used. Not only the alignment algorithm, but also the method used to deal with the most problematic alignment regions, may have a critical effect on the final tree. Although some authors remove such problematic regions, either manually or using automatic methods, in order to improve phylogenetic performance, others prefer to keep such regions to avoid losing any information. Our aim in the present work was to examine whether phylogenetic reconstruction improves after alignment cleaning or not. Using simulated protein alignments with gaps, we tested the relative performance in diverse phylogenetic analyses of the whole alignments versus the alignments with problematic regions removed with our previously developed Gblocks program. We also tested the performance of more or less stringent conditions in the selection of blocks. Alignments constructed with different alignment methods (ClustalW, Mafft, and Probcons) were used to estimate phylogenetic trees by maximum likelihood, neighbor joining, and parsimony. We show that, in most alignment conditions, and for alignments that are not too short, removal of blocks leads to better trees. That is, despite losing some information, there is an increase in the actual phylogenetic signal. Overall, the best trees are obtained by maximum-likelihood reconstruction of alignments cleaned by Gblocks. In general, a relaxed selection of blocks is better for short alignment, whereas a stringent selection is more adequate for longer ones. Finally, we show that cleaned alignments produce better topologies although, paradoxically, with lower bootstrap. This indicates that divergent and problematic alignment regions may lead, when present, to apparently better supported although, in fact, more biased topologies.
Microbial delignification of corn stover by Ceriporiopsis subvermispora for improving cellulose digestibility
DOI:10.1016/j.enzmictec.2010.04.001 URL [本文引用: 1]
Screening of white rot fungi and preliminary mechanism in their biodegradation on Populus nigra during short-time fermentation
Biological pretreatment with white rot fungi and their co-culture to overcome lignocellulosic recalcitrance for improved enzymatic digestion
Quantitative analysis program of hemicellulose, cellulose and lignin in lignocellulose solid substrate fermentation
A study on the mechanism of degradation and utilization of lignocellulose by Pleurotus ostreatus
Advances on properties, production, purification and immobilization of fungal laccase
Medium optimization for the laccase production by white rot fungus Porodaedalea laricis and its dye decolorizing capacity
Preliminary study on physiological and biochemical characteristics of Grifola frondosa during physiological maturity and fruiting stage
Research progress of alcoholic fermentation of corn stover
Decolorization of thiazine dye methylene blue by three white-rot fungi
Fermentation condition optimization of laccase producing strain Trametes hirsuta XYG422 and its activity on corn straw degradation
Physiological studies on laccase-producing process of white rot fungus Trametes orientalis incubated with two kinds of liquid media
Mechanism of corn stover degradation by white rot fungal treatment and application in production
毛栓孔菌XYG422菌株产漆酶发酵条件优化及对玉米秸秆生物降解的研究
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