养猪微生物发酵床芽胞杆菌空间生态位特性
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摘要
研究养猪微生物发酵床芽胞杆菌空间生态位特性,理解养殖粪污形成的环境生态位与芽胞杆菌种类的相互关系,为阐明微生物发酵床猪粪降解、臭味消除、猪病防控机理和资源化利用等提供科学数据。采用随机采样法获得微生物发酵床的上层垫料(0—20 cm)和下层垫料(40—60 cm)样本共14个。利用营养条件检测和宏基因组测序的方法,分析垫料样本的营养特性(有机质、全氮、腐殖酸、粗纤维)和生长条件(水分、pH),鉴定芽胞杆菌种类和测定相对丰度(reads);利用聚类分析、相关性分析、空间分布型分析、生态位宽度和重叠,揭示芽胞杆菌空间生态位特性及其因子间相互关系。研究结果表明,从空间生态位样本中共鉴定出芽胞杆菌目8个科中的6个科24个属种类(其中2个属具有芽胞杆菌种名形式,不属于芽胞杆菌),发现微生物发酵床垫料空间生态位中Ammoniibacillus(氨芽胞杆菌属,类芽胞杆菌科)、Desulfuribacillus(脱硫芽胞杆菌属,芽胞杆菌待建立新科)、Tuberibacillus(肿块芽胞杆菌属,芽胞乳杆菌科),国内未见报道,为中国新记录属。在被测生态位中相对含量(reads)最高的前3个属为芽胞杆菌属(Bacillus)(reads=8020)、乳杆菌属(Lactobacillus)(reads=4565)、肿块芽胞杆菌属(Tuberibacillus)(reads=1418);发酵床上层垫料生态位芽胞杆菌属总量与下层相比无显著差异(P>0.05),但属种类和数量结构、亚群落分化差异显著,上层生态位前5位高含量芽胞杆菌优势属(数量平均值)分别为Bacillus(532.86)、Lactobacillus(480.43)、Geobacillus(88.86)、Gracilibacillus(70.00)、Paenibacillus(40.86),而下层为Bacillus(612.86)、Tuberibacillus(188.57)、Lactobacillus(171.71)、Paucisalibacillus(60.00)、Ureibacillus(46.71)。分析表明5个生态位最宽的芽胞杆菌分别为:Bacillus(10.5159)、Ornithinibacillus(8.6094)、Paenibacillus(7.8463)、Oceanobacillus(6.9927)、Rummeliibacillus(5.7417),对发酵床环境条件适应范围较宽、对营养条件要求较低的芽胞杆菌,空间生态位宽度较宽,可利用的资源数较多,反之亦然;分析表明芽胞杆菌各属之间空间生态位重叠Pianka测度范围为0.00—0.99,有些属之间生态位重叠很高,如Gracilibacillus和Ammoniibacillus,有些几乎不重叠,如Desulfuribacillus和Aneurinibacillus;芽胞杆菌空间生态位宽度与生态位重叠存在着相互关系,生态位较宽的属,如芽胞杆菌属(Bacillus),与其他属之间的空间生态位重叠集中在0.20—0.80之间,空间生态位较窄的属,如Geobacillus,与其他属之间的空间生态位重叠主要分布在<0.20或>0.80。
The aim of this study was to investigate the characteristics of the spatial ecological niche of the Bacillus-like genera in a microbial fermentation bed(MFB) used for pig raising. To understand the ecological relationship between the environment and Bacillus-like genera, and thereby clarify the functions of pig feces degradation, odor elimination, pig disease prevention, and resource utilization, the random sampling method was used to obtain a total of 14 samples from the upper(0—20 cm) and under(40—60 cm) layers of the MFB. Nutrition condition analysis and metagenome sequencing methods were used to analyze the nutrition characteristics of the litter samples(organic matter, total nitrogen, humic acid, crude fiber) and growth conditions(moisture, pH), with identification of the Bacillus-like genera and determination of their relative abundance(reads). Cluster analysis, correlation analysis, spatial distribution analysis, and ecological niche width and overlap were used to reveal the characteristics of the spatial ecological niche and the relationships between it and other factors. A total of 24 Bacillus-like genera within six families were identified in the samples from the MFB(including two non-Bacillus genera), of which the genera Ammoniibacillus, Desulfuribacillus, and Tuberibacillus were all newly recorded genera in China. The three genera with the highest relative contents(reads) in the measured ecological niche were Bacillus(reads=8020), Lactobacillus(reads=4565), and Tuberibacillus(reads=1418), respectively. The total numbers of the Bacillus-like genera showed no significant differences(P > 0.05) between the upper and under layers of the ecological niche in the MFB. However, differences in the Bacillus-like genera were found at the level of their subcommunity structure: the top five genera with the highest contents were Bacillus(532.86), Lactobacillus(480.43), Geobacillus(88.86), Gracilibacillus(70.00), and Paenibacillus(40.86) in the upper layer, and Bacillus(612.86), Tuberibacillus(188.57), Lactobacillus(171.71), Paucisalibacillus(60.00), and Ureibacillus(46.71) in the under layer. The results showed that the five highest ecological niche breadth values of Bacillus-like genera were those of Bacillus(10.5159), Ornithinibacillus(8.6094), Paenibacillus(7.8463), Oceanobacillus(6.9927), and Rummeliibacillus(5.7417). The results indicated that the Pianka measurement values of the spatial ecological niche overlap between any two Bacillus-like genera ranged from 0.00—0.99, some of them had a high overlap, such as Gracilibacillus and Ammoniibacillus, while some of them had almost no overlap, such as Desulfuribacillus and Aneurinibacillus. Moreover, there existed a relationship between the ecological niche breadth and ecological niche overlap: the genera with a wide ecological niche breadth, such as Bacillus, had niche overlap values from 0.20—0.80 with the other genera, while those with a narrow ecological niche breadth, such as Geobacillus, had niche overlap values under 0.20 or over 0.80.
The aim of this study was to investigate the characteristics of the spatial ecological niche of the Bacillus-like genera in a microbial fermentation bed(MFB) used for pig raising. To understand the ecological relationship between the environment and Bacillus-like genera, and thereby clarify the functions of pig feces degradation, odor elimination, pig disease prevention, and resource utilization, the random sampling method was used to obtain a total of 14 samples from the upper(0—20 cm) and under(40—60 cm) layers of the MFB. Nutrition condition analysis and metagenome sequencing methods were used to analyze the nutrition characteristics of the litter samples(organic matter, total nitrogen, humic acid, crude fiber) and growth conditions(moisture, pH), with identification of the Bacillus-like genera and determination of their relative abundance(reads). Cluster analysis, correlation analysis, spatial distribution analysis, and ecological niche width and overlap were used to reveal the characteristics of the spatial ecological niche and the relationships between it and other factors. A total of 24 Bacillus-like genera within six families were identified in the samples from the MFB(including two non-Bacillus genera), of which the genera Ammoniibacillus, Desulfuribacillus, and Tuberibacillus were all newly recorded genera in China. The three genera with the highest relative contents(reads) in the measured ecological niche were Bacillus(reads=8020), Lactobacillus(reads=4565), and Tuberibacillus(reads=1418), respectively. The total numbers of the Bacillus-like genera showed no significant differences(P > 0.05) between the upper and under layers of the ecological niche in the MFB. However, differences in the Bacillus-like genera were found at the level of their subcommunity structure: the top five genera with the highest contents were Bacillus(532.86), Lactobacillus(480.43), Geobacillus(88.86), Gracilibacillus(70.00), and Paenibacillus(40.86) in the upper layer, and Bacillus(612.86), Tuberibacillus(188.57), Lactobacillus(171.71), Paucisalibacillus(60.00), and Ureibacillus(46.71) in the under layer. The results showed that the five highest ecological niche breadth values of Bacillus-like genera were those of Bacillus(10.5159), Ornithinibacillus(8.6094), Paenibacillus(7.8463), Oceanobacillus(6.9927), and Rummeliibacillus(5.7417). The results indicated that the Pianka measurement values of the spatial ecological niche overlap between any two Bacillus-like genera ranged from 0.00—0.99, some of them had a high overlap, such as Gracilibacillus and Ammoniibacillus, while some of them had almost no overlap, such as Desulfuribacillus and Aneurinibacillus. Moreover, there existed a relationship between the ecological niche breadth and ecological niche overlap: the genera with a wide ecological niche breadth, such as Bacillus, had niche overlap values from 0.20—0.80 with the other genera, while those with a narrow ecological niche breadth, such as Geobacillus, had niche overlap values under 0.20 or over 0.80.
引文
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