牛粪高温堆肥过程中的物质变化、微生物多样性以及腐熟度评价研究
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摘要
好氧高温堆肥是一种经济、环保的农业固体有机废弃物资源化利用的手段。高温堆肥过程中的物质变化与腐熟度评价以及微生物多样性的研究一直以来都是国内外关注的热点,它们与堆肥产品的质量和堆肥发生的机理密切相关,对堆肥的生产具有指导意义。但是,文献报道的大多数堆肥腐熟度的评价指标测定起来比较复杂,不利于中小型堆肥企业的实际应用。另外,对于堆肥过程中微生物多样性的研究更多的是以实验室规模的小型发酵试验为主,而对于企业应用较多的传统条垛堆肥发酵关注较少,并且分析方法也有一定的缺陷。因此,本文以牛粪和水稻秸秆为原料进行了高温条垛堆肥的发酵,对堆肥过程中的物质变化与腐熟度评价以及微生物多样性进行了研究,主要研究结果如下：
1.通过对堆肥过程中的部分物理指标、化学指标和生物指标的研究表明整个堆肥过程可以明显的分为升温(0-12天)、高温(22-52天)和降温腐熟(62-112天)三个不同的阶段,有机物质的降解和水分的蒸发等主要发生在堆肥的升温和高温阶段(0-52天),而硝化作用和腐殖化作用主要发生在堆肥的降温和腐熟阶段。以测得的各种理化指标进行腐熟度评价发现单个指标并不能很好的评估堆肥的腐熟程度,必须两个或两个以上的指标相结合。以发芽指数(GI)为标准进行相关性分析表明C/N、OM损失和NH4+-N/NO3-N是更为可靠的牛粪堆肥腐熟度的评价指标；各指标综合评价表明以牛粪和水稻秸秆为原料的堆肥62天以后已经达到腐熟。
2.三维荧光光谱与荧光区域指数(EEM-FRI)的研究结果表明在牛粪高温堆肥过程中,蛋白质的含量逐渐低,而腐殖酸和富里酸的含量则逐渐上升；通过EEM-FRI与堆肥过程中的理化指标以及生物指标的相关性分析确定,EEM-FRI与大部分常用的评价堆肥腐熟度的理化指标都显著相关,因此可以用于评价牛粪堆肥的腐熟度,并且具有简单、快速的特点。红外光谱的分析结果则显示随着堆肥的进行,不同时期堆肥样品的红外光谱的峰所在的区域变化不大,只是峰的强度变化较大。
3.分别对五种不同的堆肥DNA提取方法进行了细胞破壁效率、DNA和腐殖酸产量、PCR扩增和微生物多样性等方面的比较,建立了一种适合以牛粪和水稻秸秆为原料的堆肥样品的DNA提取和纯化方法FTSPP. FTSPP法的细胞破壁效率达到了94.6%,纯DNA的产量达到了33.19μg/g dw,并且在1μg/μ1牛血清白蛋白(BSA)存在的条件下成功的进行了PCR扩增,并且通过荧光定量PCR和DGGE分析表明,FTSPP法提取的DNA获得的细菌和放线菌的16S rRNA的拷贝数以及DGGE条带数均高于其他方法。
4.通过平板培养技术对牛粪高温堆肥过程中的常温(30℃)和高温(55℃)微生物的数量进行了研究,结果表明无论常温还是高温可培养微生物的数量在堆肥过程中均经历了一个先增加再降低然后再增加的变化趋势,常温细菌和放线菌的数量在第22天达到最大值,分别为9.331g CFU/gdw和7.181g CFU/gdw,而常温真菌则在第12天达到最大值,为5.121g CFU/g dw;高温细菌和放线菌数量最大值出现的时间比常温微生物明显滞后,均在第32天获得最大值,1g CFU/g dw分别为7.17和5.78,而高温真菌在第22天达到最大值,1gCFU/g dw为3.24。
根据DGGE的研究结果可将整个堆肥过程分为0-12天、22-52天和62-112天三个与根据温度划分相一致的阶段,在堆肥前期(0-12天)微生物种类变化最剧烈,但总体呈现先上升再下降最后再上升的变化趋势,并且高温阶段的样品与降温腐熟阶段的样品的相似性要高于升温阶段的样品。成功测序的DGGE条带的序列比对结果显示,Firmicutes, Bacteroidetes, Proteobacteria和Actinobacteria是堆肥过程中主要的微生物门类,条带M和条带X均与Bacillus属微生物表现出了较高相似性(99%),条带S则与Streptomyces sp.(EF012138)表现出了100%的序列相似性,另外,大部分为未培养的微生物。根据FRI参数与堆肥过程中细菌的种类变化的相关性分析发现PⅡ,n和PⅣ,n与堆肥过程中细菌的种类变化的相关系数分别达到了0.907和0.949,进一步的线性回归分析证明PⅣ,n是更可靠地评价以牛粪和水稻秸秆为原料的堆肥过程中细菌种类变化的参数。
分别对0、12、42和112天的堆肥样品进行了16S rRNA基因克隆丈库的构建和序列分析,成功测序的779个克隆的Genebank登陆号为JQ336994-JQ337772.多样性分析表明四个时间段的Shannon-Wienner指数分别为2.64、3.25、3.18和4.05。序列分析显示Frimicutes、Proteobacteria、Bacteroidetes和Chloroflexi门的微生物在堆肥过程中普遍存在,而Actinobacteria则只存在于堆肥的高温阶段(42天),并且第一次在堆肥后期样品中(112天)发现了BCR1门的微生物。Arthrobacter属的克隆数在高温阶段的样品中(42天)含量最高,达到了21.74%；而Bacillus和Bacillus相关的属包括Soilbacillus, Aneurinibacillus, Marinibacillus和Ureibacillus的相对含量为8.70%,在第112天更是达到了10.25%；另外,第112天的样品中,伴随着新的属包括Flavobacterium, Parapedobacter, Nitrosomonas, Ochrobactrum和Rhizobium的出现；所有文库中有相当一部分序列属于未分类微生物,并且随着堆肥的进行它们所占的比例越来越高。
5.从第82天的新鲜堆肥样品中经过富集、初筛和复筛成功的分离到两株具有较高纤维素酶活的细菌菌株T1和T2,结合生理生化和16S rRNA基因序列分析分别鉴定为Bacillus cereus和Bacillus subtilis.根据NCBI报道的Bacillus subtilis葡聚糖内切酶基因设计引物,克隆到Bacillus subtilis T2的葡聚糖内切酶基因,与报道的内切酶基因均具有99%的相似性,以PET28a为表达载体构建了重组质粒,以E. coli BL21(DE3)为表达菌株,成功的表达了Bacillus subtilis T2的葡聚糖内切酶基因,且在粗酶液检测到了较高的内切酶活性。
Aerobic thermophilic composting is an economical and environmental way for agricultural solid wastes utilization. The materials evolution, microbial diversity and maturity assessment which are related to the quality of composts and mechanism of composting are always being investigated. However, all the indices reported to evaluate the compost maturity are too complicated to be widely used by small-and-medium-sized compost plants. Moreover, many studies of microbial diversity focus on small laboratory-scale composting processes without pay attention to the windrow composting that used extensively by compost plants, and their methods applied may be a little defective too. Thus, the materials evolution, microbial diversity and maturity assessment were studied during the windrow composting of dairy manure and rice stalk, and the main results are as follows:
1. The results of physico-chemical and biological indice shows that the whole composting process could be divided into three distinct phages including the mesophilic phase (0-12day), thermophilic phase (22-52day) and cooling phase (62-112day), and the organic matter degradation and water evaporation were more active in the mesophilic and thermophilic phases, while the nitrification and humification mainly took place during the cooling phases. It is interesting to note that compost maturity was not described by a single property and therefore was best assessed by measuring two or more parameters according to the results of physico-chemical and biological indices analysis. Using GI as the standard of correlation analysis, it is found that the indices of C/N、OM loss and NH4+-N/NO3-N were more reliable to assess the maturity of compost produced from dairy manure and rice stalk, and the compost could be considered mature62days later based on all the physico-chemical and biological indices.
2. The result of Excitation emission matrix-fluorescence regional index (EEM-FRI) reveals that the protein-like substances decreased while the concentration of fulvic-like and humic-like matters increased during composting process; additionally, the EEM-FRI which is determined fast and simply could be used to assess the maturity of compost produced from dairy manure and rice stalk according to the correlation analysis between other maturity indices. The Fourier-transform infrared (FTIR) spectra of all the nine dairy manure compost samples from different stages of composting exhibited similar peaks and the only difference was the intensity of each peak.
3. An effective method suitable for the DNA extraction and purification from compost produced from dairy manure and rice stalk was developed through the comparation of five different DNA extraction methods based on cell lysis efficiency, DNA and humic acid yields, PCR amplification and microbial diversity analysis; by this method, the cell lysis efficiency and the yields of purified DNA achieved were94.6%and33.19μg/g dw respectively, and the purified DNA was clean enough for successful PCR and real-time PCR amplifications in the presence of1μg/μl BSA. In addition, more DGGE bands and16S rRNA gene copies were obtained.
4. The populations of mesophilic and thermophilic aerobic microorganisms at various stages were determined by the traditional dilution plating technique, both of the mesophilic and thermophilic populations increased after the beginning of composting, then decreased significantly with the temperature increase and increased again at the end of the thermophilic phage. The maximum populations of mesophilic bacteria and actinomycetes appeared at day22and the values of1g CFU/g were9.33and7.18respectively, while obtained at day32for the thermophilic bacteria and actinomycetes and the values of1g CFU/g dw were7.17and5.78respectively. The maximum populations of mesophilic fungi was achieved at day12, while at day22for thermophilic fungi, and the values of1g CFU/g were5.12and3.24respectively.
Denaturing gradient gel electrophoresis (DGGE) was applied to investigate community structure and dynamics during the composting process. Continuous variation was observed with the temperature increase during the first12days, and the cluster analysis indicated that the whole composting process could be divided into three continuous phages including0-12,22-52and62-112which were in accordance with the phases divided according to temperature. Additionally, the microbial diversity of the thermophilic phase showed a higher similarity with that of the cooling phase than of the mesophilic phase. The phylum Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria were ubiquitous during composting, and the sequenc results shows that the bands M and X both affiliated with the genus of Bacillus, while the band S shows100%similarity with Streptomyces sp.(EF012138), moreover, most of other sequences were affiliated with uncultured. The EEM-FIR parameters of PH,n and PIV,n showed high correlation with the the evolution of ribotypes that indicated the bacterial community structure and dynamics from DGGE analysis, indicating their potential use for evaluating community structure and dynamics, and a further linear regression analysis demonstrated that PⅣ,n was the most suitable indictor of the community structure and dynamics during the composting process.
Four16S rRNA clone libraries of samples from day0,12,42and112during composting were constructed and a total of779randomly selected clones were sequenced successfully, all the sequences had been deposited in the GenBank sequence database under accession numbers JQ336994-JQ337772. The Shannon-Wiener indices of the four clone libraries were2.64,3.25,3.18and4.05respectly. The phyla Firmicutes, Proteobacteria, Bacteroidetes and Chloroflexi were ubiquitous, while Actinobacteria was dominant only at the thermophilic stage (day42); moreover, sequences belonging to the candidate phylum BCR1were fist determined in sample of day112. In the library of sample day42, the genus Arthrobacter (21.74%), belonging to the phylum of Actinobacteria, and the Bacillus and Bacillus-related genera including Soilbacillus, Aneurinibacillus, Marinibacillus and Ureibacillus (8.70%), belonging to phylum of Firmicutes, showed the largest number of clones, whereas in the library of sample day112, the Bacillus and Bacillus-related genera (10.25%) became the unique dominant group. But new genera, including Flavobacterium, Parapedobacter, Nitrosomonas, Ochrobactrum and Rhizobium appeared; it is interesting to note that as composting progressed, the sequences belonging to unclassified groups continuously increased.
5. Two strains T1, T2with high cellulase activities were isolated from the fresh compost sample of day82. Based on morphological, physiological and biochemical characteristics and16SrDNA sequences, they were identified as Bacillus cereus and Bacillus subtilis respectively. Tthrough the alignment of the endoglucanase genes of Bacillus subtilis downloaded from NCBI database, the primers were designed, and the endoglucanase gene of the isolated Bacillus subtilis T2strain was cloned, and showed99%similarity to the endoglucanase genes reported. Moreover, the endoglucanase gene was successfully expressed in the E. coli BL21(DE3) with PET28a as the expression plasmid, and high endoglucanase activity was determined in the crude enzyme solution.
1.通过对堆肥过程中的部分物理指标、化学指标和生物指标的研究表明整个堆肥过程可以明显的分为升温(0-12天)、高温(22-52天)和降温腐熟(62-112天)三个不同的阶段,有机物质的降解和水分的蒸发等主要发生在堆肥的升温和高温阶段(0-52天),而硝化作用和腐殖化作用主要发生在堆肥的降温和腐熟阶段。以测得的各种理化指标进行腐熟度评价发现单个指标并不能很好的评估堆肥的腐熟程度,必须两个或两个以上的指标相结合。以发芽指数(GI)为标准进行相关性分析表明C/N、OM损失和NH4+-N/NO3-N是更为可靠的牛粪堆肥腐熟度的评价指标；各指标综合评价表明以牛粪和水稻秸秆为原料的堆肥62天以后已经达到腐熟。
2.三维荧光光谱与荧光区域指数(EEM-FRI)的研究结果表明在牛粪高温堆肥过程中,蛋白质的含量逐渐低,而腐殖酸和富里酸的含量则逐渐上升；通过EEM-FRI与堆肥过程中的理化指标以及生物指标的相关性分析确定,EEM-FRI与大部分常用的评价堆肥腐熟度的理化指标都显著相关,因此可以用于评价牛粪堆肥的腐熟度,并且具有简单、快速的特点。红外光谱的分析结果则显示随着堆肥的进行,不同时期堆肥样品的红外光谱的峰所在的区域变化不大,只是峰的强度变化较大。
3.分别对五种不同的堆肥DNA提取方法进行了细胞破壁效率、DNA和腐殖酸产量、PCR扩增和微生物多样性等方面的比较,建立了一种适合以牛粪和水稻秸秆为原料的堆肥样品的DNA提取和纯化方法FTSPP. FTSPP法的细胞破壁效率达到了94.6%,纯DNA的产量达到了33.19μg/g dw,并且在1μg/μ1牛血清白蛋白(BSA)存在的条件下成功的进行了PCR扩增,并且通过荧光定量PCR和DGGE分析表明,FTSPP法提取的DNA获得的细菌和放线菌的16S rRNA的拷贝数以及DGGE条带数均高于其他方法。
4.通过平板培养技术对牛粪高温堆肥过程中的常温(30℃)和高温(55℃)微生物的数量进行了研究,结果表明无论常温还是高温可培养微生物的数量在堆肥过程中均经历了一个先增加再降低然后再增加的变化趋势,常温细菌和放线菌的数量在第22天达到最大值,分别为9.331g CFU/gdw和7.181g CFU/gdw,而常温真菌则在第12天达到最大值,为5.121g CFU/g dw;高温细菌和放线菌数量最大值出现的时间比常温微生物明显滞后,均在第32天获得最大值,1g CFU/g dw分别为7.17和5.78,而高温真菌在第22天达到最大值,1gCFU/g dw为3.24。
根据DGGE的研究结果可将整个堆肥过程分为0-12天、22-52天和62-112天三个与根据温度划分相一致的阶段,在堆肥前期(0-12天)微生物种类变化最剧烈,但总体呈现先上升再下降最后再上升的变化趋势,并且高温阶段的样品与降温腐熟阶段的样品的相似性要高于升温阶段的样品。成功测序的DGGE条带的序列比对结果显示,Firmicutes, Bacteroidetes, Proteobacteria和Actinobacteria是堆肥过程中主要的微生物门类,条带M和条带X均与Bacillus属微生物表现出了较高相似性(99%),条带S则与Streptomyces sp.(EF012138)表现出了100%的序列相似性,另外,大部分为未培养的微生物。根据FRI参数与堆肥过程中细菌的种类变化的相关性分析发现PⅡ,n和PⅣ,n与堆肥过程中细菌的种类变化的相关系数分别达到了0.907和0.949,进一步的线性回归分析证明PⅣ,n是更可靠地评价以牛粪和水稻秸秆为原料的堆肥过程中细菌种类变化的参数。
分别对0、12、42和112天的堆肥样品进行了16S rRNA基因克隆丈库的构建和序列分析,成功测序的779个克隆的Genebank登陆号为JQ336994-JQ337772.多样性分析表明四个时间段的Shannon-Wienner指数分别为2.64、3.25、3.18和4.05。序列分析显示Frimicutes、Proteobacteria、Bacteroidetes和Chloroflexi门的微生物在堆肥过程中普遍存在,而Actinobacteria则只存在于堆肥的高温阶段(42天),并且第一次在堆肥后期样品中(112天)发现了BCR1门的微生物。Arthrobacter属的克隆数在高温阶段的样品中(42天)含量最高,达到了21.74%；而Bacillus和Bacillus相关的属包括Soilbacillus, Aneurinibacillus, Marinibacillus和Ureibacillus的相对含量为8.70%,在第112天更是达到了10.25%；另外,第112天的样品中,伴随着新的属包括Flavobacterium, Parapedobacter, Nitrosomonas, Ochrobactrum和Rhizobium的出现；所有文库中有相当一部分序列属于未分类微生物,并且随着堆肥的进行它们所占的比例越来越高。
5.从第82天的新鲜堆肥样品中经过富集、初筛和复筛成功的分离到两株具有较高纤维素酶活的细菌菌株T1和T2,结合生理生化和16S rRNA基因序列分析分别鉴定为Bacillus cereus和Bacillus subtilis.根据NCBI报道的Bacillus subtilis葡聚糖内切酶基因设计引物,克隆到Bacillus subtilis T2的葡聚糖内切酶基因,与报道的内切酶基因均具有99%的相似性,以PET28a为表达载体构建了重组质粒,以E. coli BL21(DE3)为表达菌株,成功的表达了Bacillus subtilis T2的葡聚糖内切酶基因,且在粗酶液检测到了较高的内切酶活性。
Aerobic thermophilic composting is an economical and environmental way for agricultural solid wastes utilization. The materials evolution, microbial diversity and maturity assessment which are related to the quality of composts and mechanism of composting are always being investigated. However, all the indices reported to evaluate the compost maturity are too complicated to be widely used by small-and-medium-sized compost plants. Moreover, many studies of microbial diversity focus on small laboratory-scale composting processes without pay attention to the windrow composting that used extensively by compost plants, and their methods applied may be a little defective too. Thus, the materials evolution, microbial diversity and maturity assessment were studied during the windrow composting of dairy manure and rice stalk, and the main results are as follows:
1. The results of physico-chemical and biological indice shows that the whole composting process could be divided into three distinct phages including the mesophilic phase (0-12day), thermophilic phase (22-52day) and cooling phase (62-112day), and the organic matter degradation and water evaporation were more active in the mesophilic and thermophilic phases, while the nitrification and humification mainly took place during the cooling phases. It is interesting to note that compost maturity was not described by a single property and therefore was best assessed by measuring two or more parameters according to the results of physico-chemical and biological indices analysis. Using GI as the standard of correlation analysis, it is found that the indices of C/N、OM loss and NH4+-N/NO3-N were more reliable to assess the maturity of compost produced from dairy manure and rice stalk, and the compost could be considered mature62days later based on all the physico-chemical and biological indices.
2. The result of Excitation emission matrix-fluorescence regional index (EEM-FRI) reveals that the protein-like substances decreased while the concentration of fulvic-like and humic-like matters increased during composting process; additionally, the EEM-FRI which is determined fast and simply could be used to assess the maturity of compost produced from dairy manure and rice stalk according to the correlation analysis between other maturity indices. The Fourier-transform infrared (FTIR) spectra of all the nine dairy manure compost samples from different stages of composting exhibited similar peaks and the only difference was the intensity of each peak.
3. An effective method suitable for the DNA extraction and purification from compost produced from dairy manure and rice stalk was developed through the comparation of five different DNA extraction methods based on cell lysis efficiency, DNA and humic acid yields, PCR amplification and microbial diversity analysis; by this method, the cell lysis efficiency and the yields of purified DNA achieved were94.6%and33.19μg/g dw respectively, and the purified DNA was clean enough for successful PCR and real-time PCR amplifications in the presence of1μg/μl BSA. In addition, more DGGE bands and16S rRNA gene copies were obtained.
4. The populations of mesophilic and thermophilic aerobic microorganisms at various stages were determined by the traditional dilution plating technique, both of the mesophilic and thermophilic populations increased after the beginning of composting, then decreased significantly with the temperature increase and increased again at the end of the thermophilic phage. The maximum populations of mesophilic bacteria and actinomycetes appeared at day22and the values of1g CFU/g were9.33and7.18respectively, while obtained at day32for the thermophilic bacteria and actinomycetes and the values of1g CFU/g dw were7.17and5.78respectively. The maximum populations of mesophilic fungi was achieved at day12, while at day22for thermophilic fungi, and the values of1g CFU/g were5.12and3.24respectively.
Denaturing gradient gel electrophoresis (DGGE) was applied to investigate community structure and dynamics during the composting process. Continuous variation was observed with the temperature increase during the first12days, and the cluster analysis indicated that the whole composting process could be divided into three continuous phages including0-12,22-52and62-112which were in accordance with the phases divided according to temperature. Additionally, the microbial diversity of the thermophilic phase showed a higher similarity with that of the cooling phase than of the mesophilic phase. The phylum Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria were ubiquitous during composting, and the sequenc results shows that the bands M and X both affiliated with the genus of Bacillus, while the band S shows100%similarity with Streptomyces sp.(EF012138), moreover, most of other sequences were affiliated with uncultured. The EEM-FIR parameters of PH,n and PIV,n showed high correlation with the the evolution of ribotypes that indicated the bacterial community structure and dynamics from DGGE analysis, indicating their potential use for evaluating community structure and dynamics, and a further linear regression analysis demonstrated that PⅣ,n was the most suitable indictor of the community structure and dynamics during the composting process.
Four16S rRNA clone libraries of samples from day0,12,42and112during composting were constructed and a total of779randomly selected clones were sequenced successfully, all the sequences had been deposited in the GenBank sequence database under accession numbers JQ336994-JQ337772. The Shannon-Wiener indices of the four clone libraries were2.64,3.25,3.18and4.05respectly. The phyla Firmicutes, Proteobacteria, Bacteroidetes and Chloroflexi were ubiquitous, while Actinobacteria was dominant only at the thermophilic stage (day42); moreover, sequences belonging to the candidate phylum BCR1were fist determined in sample of day112. In the library of sample day42, the genus Arthrobacter (21.74%), belonging to the phylum of Actinobacteria, and the Bacillus and Bacillus-related genera including Soilbacillus, Aneurinibacillus, Marinibacillus and Ureibacillus (8.70%), belonging to phylum of Firmicutes, showed the largest number of clones, whereas in the library of sample day112, the Bacillus and Bacillus-related genera (10.25%) became the unique dominant group. But new genera, including Flavobacterium, Parapedobacter, Nitrosomonas, Ochrobactrum and Rhizobium appeared; it is interesting to note that as composting progressed, the sequences belonging to unclassified groups continuously increased.
5. Two strains T1, T2with high cellulase activities were isolated from the fresh compost sample of day82. Based on morphological, physiological and biochemical characteristics and16SrDNA sequences, they were identified as Bacillus cereus and Bacillus subtilis respectively. Tthrough the alignment of the endoglucanase genes of Bacillus subtilis downloaded from NCBI database, the primers were designed, and the endoglucanase gene of the isolated Bacillus subtilis T2strain was cloned, and showed99%similarity to the endoglucanase genes reported. Moreover, the endoglucanase gene was successfully expressed in the E. coli BL21(DE3) with PET28a as the expression plasmid, and high endoglucanase activity was determined in the crude enzyme solution.
引文
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