瘤胃产甲烷菌定量检测与微生物菌群调控研究
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摘要
瘤胃甲烷的生成不仅是饲料能量的损失,而且通过暖气排入大气的甲烷是一种重要的温室气体。随着全球对温室气体排放的重视,反刍动物瘤胃甲烷生成受到越来越多的关注。本研究在建立分子生物学手段检测瘤胃产甲烷菌及微生物菌群的基础上,通过探讨不同调控途径对瘤胃产甲烷菌和微生物菌群的影响,研究产甲烷菌和微生物菌群与甲烷生成的密切关系。首先利用实时定量PCR方法,建立瘤胃产甲烷菌及微生物菌群的检测技术(第一部分)；然后利用产甲烷菌选择性抑制剂研究产甲烷菌与微生物菌群的变化(第二部分),并以天然调控剂茶皂素为调控手段探讨其对产甲烷菌及瘤胃微生态的影响(第三部分)；最后模拟高粗日粮条件,探讨甲烷生成与瘤胃微生态的关系(第四部分)。
第一部分瘤胃产甲烷菌及微生物菌群分子研究方法的建立
建立实时定量PCR方法检测瘤胃内产甲烷菌、原虫以及主要的纤维降解微生物,并建立产甲烷菌活性检测手段。以产甲烷短杆菌属的模式菌种——反刍兽甲烷短杆菌(Methanobrevibacter ruminantium)为研究对象,建立实时定量PCR绝对定量法。研究发现,荧光定量PCR方法(y)与传统计数法(x)对产甲烷菌的定量结果强相关,y=1.0152x-3×108(r=0.9753；P<0.01)。而后利用反转录Real Time PCR检测mcrA基因表达,表征产甲烷菌的活性。添加2-溴乙烷磺酸(BES)后,反刍兽甲烷短杆菌mcrA基因表达受抑制,培养30小时后其表达量仅为对照组的1%；而添加2,4-二羟基蝶呤(Lumazine)后,mcrA基因表达在前6小时内升高,而后逐渐下降。采用实时定量PCR方法定量分析混合培养微生物中产甲烷菌及主要的纤维降解微生物结果表明,各菌标准曲线可信度高,扩增效率相近(98.4-99.9%)。体外培养24小时后,BES处理组的产甲烷菌显著减少(P<0.01),仅为对照组的10.3%；BES处理组的真菌数量虽然随着培养时间的增加而增长,但其量明显受抑制,在培养12小时和24小时后分别减少40.0和61.9%；甲烷抑制组的产琥珀酸丝状杆菌增加50%,而黄化瘤胃球菌数量无明显变化。
本部分研究结果表明,实时定量PCR方法可以准确定量瘤胃微生物,实践中可根据试验目的选用绝对定量法或相对定量法。
第二部分不同抑制剂对瘤胃产甲烷菌及微生物菌群的调控
以混合培养微生物为研究对象,探讨不同的选择性抑制剂(BES, Lumazine或Mevinolin(甲基四氢蝶呤))对甲烷生成和产甲烷菌的调控作用。研究表明,体外培养24小时后,三种抑制剂对甲烷生成、产甲烷菌含量以及产甲烷菌活性产生不同的影响。BES和Lumazine显著降低了甲烷生成量,分别为对照组的17.2%和83.8%, Mevinolin对甲烷生成量无显著影响。BES和Lumazine显著降低了产甲烷菌的含量,分别为对照组的42.2%和60.0%。Mevinolin对产甲烷菌没有显著影响。培养24小时后,BES显著抑制了产甲烷菌的活性,仅为对照组的1%。Lumazine组mcrA基因表达量在前12小时有所下降,24小时后比对照组高19%。Mevinolin组mcrA基因表达量在前12小时内无显著变化,24小时后比对照组高45%。DGGE结果表明,抑制剂降低了某些优势产甲烷菌的代谢活性。三种抑制剂显著提高了原虫数量,BES、Lumazine和Mevinolin组的原虫数较对照组分别提高42.3%、65.3%和27.5%。BES显著降低了真菌数量(P<0.05),为对照组的71.9%,Lumazine和Mevinolin提高了真菌数量(P<0.05),分别较对照组提高43.8%和37.5%。BES增加产琥珀酸丝状杆菌数量(P<0.05),降低黄色瘤胃球菌数量;Lumazine降低两种纤维降解菌数量；Mevinolin降低产琥珀酸丝状杆菌的数量(P<0.05),增加黄色瘤胃球菌的数量(P<0.05)。PCR-DGGE结果表明,16S rRNA扩增子获得的条带较16S rDNA扩增子获得条带数更多,说明混合微生物中代谢活性微生物菌群与微生物优势菌群的组成不同,而且BES和Lumazine对代谢活性微生物区系的影响更大。
直接作用于甲烷生成途径的BES和Lumazine对产甲烷菌、mcrA基因表达和微生物区系的影响更大,Mevinolin影响产甲烷菌细胞壁的合成,其作用效果不如前二者明显。
第三部分茶皂素对产甲烷菌及瘤胃微生物菌群的调控效果研究
研究茶皂素对瘤胃微生物菌群、产甲烷菌数量与活性和纯培养反刍兽甲烷短杆菌的影响,探讨茶皂素降低瘤胃甲烷生成的作用机理。研究表明,茶皂素减少原虫数量,添加0.2和0.4 mg／ml的茶皂素组中原虫数量分别减少了51.2%和22.9%(P<0.05)。产甲烷细菌的数量并未受茶皂素的影响(P>0.05),表明甲烷产生并不完全对应于产甲烷菌的数量变化。在混合培养微生物中,茶皂素显著抑制了混合培养微生物的mcrA基因表达,茶皂素处理组的mcrA基因表达较对照组降低了76%。以反刍兽甲烷短杆菌为研究对象,发现茶皂素对瘤胃内优势产甲烷菌——反刍兽甲烷短杆菌无明显抑制作用。
这些结果表明,茶皂素可以抑制原虫,从而抑制甲烷的生成。茶皂素对瘤胃内主要产甲烷菌没有直接影响,推测茶皂素通过抑制原虫作用影响氢气生成量,间接降低产甲烷菌活性。产甲烷菌活性,即mcrA基因表达可以更好地预测复杂微生态系统中甲烷生成的变化规律。
第四部分高粗日粮对瘤胃产甲烷菌及微生物菌群的调控研究
试验采用不同纤维来源及水平的NDF模拟高粗日粮条件下瘤胃的发酵模式,比较不同来源及水平的NDF对瘤胃产甲烷菌及微生物菌群的影响。不同来源的NDF对甲烷生成及产甲烷菌产生了显著影响,苜蓿NDF组与全株玉米青贮NDF组的产甲烷菌区系类似,相似性指数为93.3%；黑麦草与黑麦草青贮NDF组区系的相似性指数为87.1%。体外培养24小时后,NDF来源、水平及两者的互作对产甲烷菌产生极显著影响(P<0.01)；苜蓿NDF与淀粉以60：40组合时,产甲烷菌数量最低；100%黑麦草为培养底物时,产甲烷菌数量最高。产甲烷菌与甲烷生成呈负相关关系。不同水平黑麦草青贮NDF对优势产甲烷菌影响不大,产甲烷菌相似性指数在91.1%到96.6%之间；但不同水平NDF影响了微生物区系,其相似性指数降到46%-72%。
甲烷生成量与产甲烷菌和两种纤维降解菌呈负相关关系,与原虫无相关性。产甲烷菌与真菌呈正相关关系(P=0.0099),与其他菌不存在显著相关关系。
综上所述,通过分析产甲烷菌数量及其mcrA基因表达,可以预测瘤胃内甲烷的生成；产甲烷菌数量与原虫数不完全相关,但产甲烷菌与纤维降解微生物呈此长彼长的关系。
Methane production in the rumen represents a loss of energy for the host animal, and, in addition, methane eructated by ruminants may contribute to a greenhouse effect or global warming. Scientists have been recently paying much attention to ruminal methanogens and methanogenesis with the global concerning on greenhouse gas emission. This study, divided into four parts, was carried out to establish molecular techniques to analyze the metanogens in the rumen, and to investigate the relationships among methanogenesis and methanogens and microbial community structure. In Part One, molecular techniques were established to monitor the change of methanogens and other microorganisms in the rumen. In Part Two, three known methnogen-inhibitors were selected to study their influence on ruminal methanogens and microbial populations. Tea saponin was used in Part Three to study rumen methanogenesis and methanogens. Part Four was conducted to study the relationship between methanogens and other microbial population in forage-rich diets in vitro.
Part One:Establishing Real Time PCR technique to monitor ruminal methanogens and microbial population
Real Time PCR technique was conducted to monitor the microbial populations including methanogens, fungi, F. succinogenes and R. flavefaciens, and activity of methanogens as well. Absolute quantification of methanogens was established. There was significant correlation on the quantification of Methanobrevibacter ruminantium by real time PCR (y) and counting (x):y= 1.0152x-3×108(r=0.9753; P<0.01). Then expression of mcrA gene was analyzed to predict the activity of methanogens. BES significantly reduced the mcrA gene expression in whole period of incubation, while lumazine began to reduce the gene expression after 6 h of incubation. Relative quantification was also established to detect the methanogens, fungi, F.succinogenes and R.flavefaciens in mixed culture when treated with BES. All standard curves have high R2 and their amplification efficiency were very close (98.4-99.9%).
Real time PCR could be used to quantify ruminal microbial population. In practice, absolute and relative quantification could be adopted according to different research purpose.
Part Two:Use of inhibitors to manipulate methanogens and microbial population
Manipulation of inhibitors on methanogens and microbial population in mixed culture was investigated. After 24 h of incubation, BES, Lumazine and Mevinolin had different modes of effects on ruminal methanogenesis, methanogens and expression of mcrA gene. BES significantly reduced methane production, methanogens and expression of mcrA gene. Lumazine reduced methane production and methanogens, while Mevinolin had no significant effect. There was difference between present and active methanogens revealed by the DGGE profiles of DNA amplicons from 16S rDNA and 16S rRNA. Protozoa was increased by BES, Lumazine and Mevinolin. DGGE showed that there are big differences between present and active bacteria. BES and Lumazine had greater effect on the community of active bacteria.
BES and Lumazine, which act on the pathway of methanogenesis, had greater effect on methanogenesis, methanogens and microbial community in mixed culture compared to Mevinolin.
Part Three:Manipulation of methanogens and microbial population by tea saponins
To explore the mechanism of tea saponin on reducing methnaogenesis, effect of tea saponin on ruminal microbial community, methanogens and pure culture of Methanobrevibacter ruminantium was investigated. Protozoa was significantly reduced by 51.2 and 22.9%(P<0.05) by the addition of 0.2 and 0.4 mg/ml tea saponin, respectively. Tea saponin did not have obvious effect on methanogens, and there was inconsistency between methanogenesis and methanogens. As the dominant methanogens in the rumen, Methanobrevibacter ruminantium was adopted to explore its response to tea saponin. There was no inhibited effect of tea saponin on Methanobrevibacter ruminantium. However, expression of mcrA gene in mixed culture was reduced by 76% with addition of 0.4 mg/ml tea saponin.
Tea saponin inhibited protozoa and then reduced methane production, while it did not have significant effect on methanogens. It is speculated that tea saponin inhibited protozoa and reduce hydrogen production, and then reduced the activity of methanogens. Expression of mcrA gene is a more reasonable parameter to predict the change of methane production in the complex ecosystem compared to methanogenic population.
Part Four:Manipulation of methanogens and microbial population in forage-rich diet
Different sources and levels of neutral detergent fibers (NDFs) were adopted to simulate forage-rich diet in vitro. Different sources of NDF significantly influenced the methanogenesis and methanogens. As showed by DGGE, methanogens' community structures of NDFs extracted from alfalfa and corn silage were more similar to each other. After incubation of 24 h, NDF source, level and their interaction had significant effects on methanogens. There was negative correlation between methanogens and methanogenesis. Level of NDF had minor effect on the community structure of methanogens, but had strong effect on bacteria community structure and the similarity index was only 46-72% as showed by DGGE.
There were negative correlation of methanogenesis and methanogens, F.succinogenes and R.flavefaciens, while positive correlation existed between methanogens and fungi.
In summary, when considering the change of methanogenesis, methanogen number and mcrA gene expression should be taking into account in the ruminal ecosystem. There is significant correlation between methanogen and protozoa population, while positive correlation exists in methanogen and fibrolytic microorganisms.
第一部分瘤胃产甲烷菌及微生物菌群分子研究方法的建立
建立实时定量PCR方法检测瘤胃内产甲烷菌、原虫以及主要的纤维降解微生物,并建立产甲烷菌活性检测手段。以产甲烷短杆菌属的模式菌种——反刍兽甲烷短杆菌(Methanobrevibacter ruminantium)为研究对象,建立实时定量PCR绝对定量法。研究发现,荧光定量PCR方法(y)与传统计数法(x)对产甲烷菌的定量结果强相关,y=1.0152x-3×108(r=0.9753；P<0.01)。而后利用反转录Real Time PCR检测mcrA基因表达,表征产甲烷菌的活性。添加2-溴乙烷磺酸(BES)后,反刍兽甲烷短杆菌mcrA基因表达受抑制,培养30小时后其表达量仅为对照组的1%；而添加2,4-二羟基蝶呤(Lumazine)后,mcrA基因表达在前6小时内升高,而后逐渐下降。采用实时定量PCR方法定量分析混合培养微生物中产甲烷菌及主要的纤维降解微生物结果表明,各菌标准曲线可信度高,扩增效率相近(98.4-99.9%)。体外培养24小时后,BES处理组的产甲烷菌显著减少(P<0.01),仅为对照组的10.3%；BES处理组的真菌数量虽然随着培养时间的增加而增长,但其量明显受抑制,在培养12小时和24小时后分别减少40.0和61.9%；甲烷抑制组的产琥珀酸丝状杆菌增加50%,而黄化瘤胃球菌数量无明显变化。
本部分研究结果表明,实时定量PCR方法可以准确定量瘤胃微生物,实践中可根据试验目的选用绝对定量法或相对定量法。
第二部分不同抑制剂对瘤胃产甲烷菌及微生物菌群的调控
以混合培养微生物为研究对象,探讨不同的选择性抑制剂(BES, Lumazine或Mevinolin(甲基四氢蝶呤))对甲烷生成和产甲烷菌的调控作用。研究表明,体外培养24小时后,三种抑制剂对甲烷生成、产甲烷菌含量以及产甲烷菌活性产生不同的影响。BES和Lumazine显著降低了甲烷生成量,分别为对照组的17.2%和83.8%, Mevinolin对甲烷生成量无显著影响。BES和Lumazine显著降低了产甲烷菌的含量,分别为对照组的42.2%和60.0%。Mevinolin对产甲烷菌没有显著影响。培养24小时后,BES显著抑制了产甲烷菌的活性,仅为对照组的1%。Lumazine组mcrA基因表达量在前12小时有所下降,24小时后比对照组高19%。Mevinolin组mcrA基因表达量在前12小时内无显著变化,24小时后比对照组高45%。DGGE结果表明,抑制剂降低了某些优势产甲烷菌的代谢活性。三种抑制剂显著提高了原虫数量,BES、Lumazine和Mevinolin组的原虫数较对照组分别提高42.3%、65.3%和27.5%。BES显著降低了真菌数量(P<0.05),为对照组的71.9%,Lumazine和Mevinolin提高了真菌数量(P<0.05),分别较对照组提高43.8%和37.5%。BES增加产琥珀酸丝状杆菌数量(P<0.05),降低黄色瘤胃球菌数量;Lumazine降低两种纤维降解菌数量；Mevinolin降低产琥珀酸丝状杆菌的数量(P<0.05),增加黄色瘤胃球菌的数量(P<0.05)。PCR-DGGE结果表明,16S rRNA扩增子获得的条带较16S rDNA扩增子获得条带数更多,说明混合微生物中代谢活性微生物菌群与微生物优势菌群的组成不同,而且BES和Lumazine对代谢活性微生物区系的影响更大。
直接作用于甲烷生成途径的BES和Lumazine对产甲烷菌、mcrA基因表达和微生物区系的影响更大,Mevinolin影响产甲烷菌细胞壁的合成,其作用效果不如前二者明显。
第三部分茶皂素对产甲烷菌及瘤胃微生物菌群的调控效果研究
研究茶皂素对瘤胃微生物菌群、产甲烷菌数量与活性和纯培养反刍兽甲烷短杆菌的影响,探讨茶皂素降低瘤胃甲烷生成的作用机理。研究表明,茶皂素减少原虫数量,添加0.2和0.4 mg／ml的茶皂素组中原虫数量分别减少了51.2%和22.9%(P<0.05)。产甲烷细菌的数量并未受茶皂素的影响(P>0.05),表明甲烷产生并不完全对应于产甲烷菌的数量变化。在混合培养微生物中,茶皂素显著抑制了混合培养微生物的mcrA基因表达,茶皂素处理组的mcrA基因表达较对照组降低了76%。以反刍兽甲烷短杆菌为研究对象,发现茶皂素对瘤胃内优势产甲烷菌——反刍兽甲烷短杆菌无明显抑制作用。
这些结果表明,茶皂素可以抑制原虫,从而抑制甲烷的生成。茶皂素对瘤胃内主要产甲烷菌没有直接影响,推测茶皂素通过抑制原虫作用影响氢气生成量,间接降低产甲烷菌活性。产甲烷菌活性,即mcrA基因表达可以更好地预测复杂微生态系统中甲烷生成的变化规律。
第四部分高粗日粮对瘤胃产甲烷菌及微生物菌群的调控研究
试验采用不同纤维来源及水平的NDF模拟高粗日粮条件下瘤胃的发酵模式,比较不同来源及水平的NDF对瘤胃产甲烷菌及微生物菌群的影响。不同来源的NDF对甲烷生成及产甲烷菌产生了显著影响,苜蓿NDF组与全株玉米青贮NDF组的产甲烷菌区系类似,相似性指数为93.3%；黑麦草与黑麦草青贮NDF组区系的相似性指数为87.1%。体外培养24小时后,NDF来源、水平及两者的互作对产甲烷菌产生极显著影响(P<0.01)；苜蓿NDF与淀粉以60：40组合时,产甲烷菌数量最低；100%黑麦草为培养底物时,产甲烷菌数量最高。产甲烷菌与甲烷生成呈负相关关系。不同水平黑麦草青贮NDF对优势产甲烷菌影响不大,产甲烷菌相似性指数在91.1%到96.6%之间；但不同水平NDF影响了微生物区系,其相似性指数降到46%-72%。
甲烷生成量与产甲烷菌和两种纤维降解菌呈负相关关系,与原虫无相关性。产甲烷菌与真菌呈正相关关系(P=0.0099),与其他菌不存在显著相关关系。
综上所述,通过分析产甲烷菌数量及其mcrA基因表达,可以预测瘤胃内甲烷的生成；产甲烷菌数量与原虫数不完全相关,但产甲烷菌与纤维降解微生物呈此长彼长的关系。
Methane production in the rumen represents a loss of energy for the host animal, and, in addition, methane eructated by ruminants may contribute to a greenhouse effect or global warming. Scientists have been recently paying much attention to ruminal methanogens and methanogenesis with the global concerning on greenhouse gas emission. This study, divided into four parts, was carried out to establish molecular techniques to analyze the metanogens in the rumen, and to investigate the relationships among methanogenesis and methanogens and microbial community structure. In Part One, molecular techniques were established to monitor the change of methanogens and other microorganisms in the rumen. In Part Two, three known methnogen-inhibitors were selected to study their influence on ruminal methanogens and microbial populations. Tea saponin was used in Part Three to study rumen methanogenesis and methanogens. Part Four was conducted to study the relationship between methanogens and other microbial population in forage-rich diets in vitro.
Part One:Establishing Real Time PCR technique to monitor ruminal methanogens and microbial population
Real Time PCR technique was conducted to monitor the microbial populations including methanogens, fungi, F. succinogenes and R. flavefaciens, and activity of methanogens as well. Absolute quantification of methanogens was established. There was significant correlation on the quantification of Methanobrevibacter ruminantium by real time PCR (y) and counting (x):y= 1.0152x-3×108(r=0.9753; P<0.01). Then expression of mcrA gene was analyzed to predict the activity of methanogens. BES significantly reduced the mcrA gene expression in whole period of incubation, while lumazine began to reduce the gene expression after 6 h of incubation. Relative quantification was also established to detect the methanogens, fungi, F.succinogenes and R.flavefaciens in mixed culture when treated with BES. All standard curves have high R2 and their amplification efficiency were very close (98.4-99.9%).
Real time PCR could be used to quantify ruminal microbial population. In practice, absolute and relative quantification could be adopted according to different research purpose.
Part Two:Use of inhibitors to manipulate methanogens and microbial population
Manipulation of inhibitors on methanogens and microbial population in mixed culture was investigated. After 24 h of incubation, BES, Lumazine and Mevinolin had different modes of effects on ruminal methanogenesis, methanogens and expression of mcrA gene. BES significantly reduced methane production, methanogens and expression of mcrA gene. Lumazine reduced methane production and methanogens, while Mevinolin had no significant effect. There was difference between present and active methanogens revealed by the DGGE profiles of DNA amplicons from 16S rDNA and 16S rRNA. Protozoa was increased by BES, Lumazine and Mevinolin. DGGE showed that there are big differences between present and active bacteria. BES and Lumazine had greater effect on the community of active bacteria.
BES and Lumazine, which act on the pathway of methanogenesis, had greater effect on methanogenesis, methanogens and microbial community in mixed culture compared to Mevinolin.
Part Three:Manipulation of methanogens and microbial population by tea saponins
To explore the mechanism of tea saponin on reducing methnaogenesis, effect of tea saponin on ruminal microbial community, methanogens and pure culture of Methanobrevibacter ruminantium was investigated. Protozoa was significantly reduced by 51.2 and 22.9%(P<0.05) by the addition of 0.2 and 0.4 mg/ml tea saponin, respectively. Tea saponin did not have obvious effect on methanogens, and there was inconsistency between methanogenesis and methanogens. As the dominant methanogens in the rumen, Methanobrevibacter ruminantium was adopted to explore its response to tea saponin. There was no inhibited effect of tea saponin on Methanobrevibacter ruminantium. However, expression of mcrA gene in mixed culture was reduced by 76% with addition of 0.4 mg/ml tea saponin.
Tea saponin inhibited protozoa and then reduced methane production, while it did not have significant effect on methanogens. It is speculated that tea saponin inhibited protozoa and reduce hydrogen production, and then reduced the activity of methanogens. Expression of mcrA gene is a more reasonable parameter to predict the change of methane production in the complex ecosystem compared to methanogenic population.
Part Four:Manipulation of methanogens and microbial population in forage-rich diet
Different sources and levels of neutral detergent fibers (NDFs) were adopted to simulate forage-rich diet in vitro. Different sources of NDF significantly influenced the methanogenesis and methanogens. As showed by DGGE, methanogens' community structures of NDFs extracted from alfalfa and corn silage were more similar to each other. After incubation of 24 h, NDF source, level and their interaction had significant effects on methanogens. There was negative correlation between methanogens and methanogenesis. Level of NDF had minor effect on the community structure of methanogens, but had strong effect on bacteria community structure and the similarity index was only 46-72% as showed by DGGE.
There were negative correlation of methanogenesis and methanogens, F.succinogenes and R.flavefaciens, while positive correlation existed between methanogens and fungi.
In summary, when considering the change of methanogenesis, methanogen number and mcrA gene expression should be taking into account in the ruminal ecosystem. There is significant correlation between methanogen and protozoa population, while positive correlation exists in methanogen and fibrolytic microorganisms.
引文
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