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基于拉普拉斯矩阵的流形UniFrac算法
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作者 范业田 宋博 《辽宁大学学报(自然科学版)》 2025年第1期79-85,共7页
UniFrac距离是衡量微生物群落关系的重要且稳健的算法之一,它可以比较不同环境样本的微生物菌群组成,以分析微生物群落结构和功能多样性.但是现有算法没有考虑微生物菌群在生物流形上的分布,并且因为微生物菌群数据的维度高、系统发生... UniFrac距离是衡量微生物群落关系的重要且稳健的算法之一,它可以比较不同环境样本的微生物菌群组成,以分析微生物群落结构和功能多样性.但是现有算法没有考虑微生物菌群在生物流形上的分布,并且因为微生物菌群数据的维度高、系统发生树结构复杂,导致UniFrac算法的计算复杂度极高.为此,基于生物流形局部同构于欧式空间,本文提出了流形UniFrac算法,该算法利用局部生物流形上的UniFrac距离,将样本间的距离由局部推广到全局.此外,通过对流形UniFrac算法进行理论分析,发现其降低了算法的复杂度.数值实验表明,使用不同的UniFrac距离定义,流形UniFrac算法均可以提高微生物菌群的类聚集性,并且随着近邻阶数的增加,流形UniFrac的降维可视化结果可以逐渐收敛到原始UniFrac距离的降维可视化结果. 展开更多
关键词 unifrac距离 流形 拉普拉斯矩阵 微生物组
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Bacterial communities in paddy soils changed by milk vetch as green manure: A study conducted across six provinces in South China 被引量:12
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作者 Songjuan GAO Weidong CAO +1 位作者 Guopeng ZHOU Robert M.REES 《Pedosphere》 SCIE CAS CSCD 2021年第4期521-530,共10页
The use of green manures contributes to sustainable soil and nutrient management in agriculture;however, the responses of soil microbial communities to different fertilization regimes at the regional scale are uncerta... The use of green manures contributes to sustainable soil and nutrient management in agriculture;however, the responses of soil microbial communities to different fertilization regimes at the regional scale are uncertain. A study was undertaken across multiple sites and years in Hunan, Jiangxi, Anhui, Henan,Hubei, and Fujian provinces of South China to investigate the effects of green manuring on the structure and function of soil bacterial communities in rice-green manure cropping systems. The study included four treatments: winter fallow with no chemical fertilizer as a control(NF), milk vetch as green manure without chemical fertilizer(GM), winter fallow and chemical fertilizer(CF), and a combination of chemical fertilizer and milk vetch(GMCF).Significant differences were found in the responses of soil microbial communities at different sites, with sampling sites explaining 72.33%(F = 36.59,P = 0.001) of the community composition variation. The bacterial communities in the soils from Anhui, Henan, and Hubei were broadly similar, while those from Hunan were distinctly different from other locations. The analysis of Weighted UniFrac distances showed that milk vetch changed soil microbial communities compared with winter fallow. Proteobacteria and Chloroflexi predominated in these paddy soils;however, the application of green manures increased the relative abundance of Actinobacteria. There was evidence showing that the functional microbes which play important roles in the cycling of soil carbon, nitrogen(N), and sulfur(S) changed after several years of milk vetch utilization(linear discriminant analysis score > 2). The abundance of methane-oxidizing bacteria and S-reducing bacteria increased, and microbes involved in N fixation, nitrification, and denitrification also increased in some provinces. We concluded that the application of milk vetch changed the bacterial community structure and affected the functional groups related to nutrient transformation in soils at a regional scale. 展开更多
关键词 alpha diversity bacterial composition functional group operational taxonomic unit soil fertility Weighted unifrac distance
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东北湿地沉积物中T4型噬菌体g23基因的多样性 被引量:1
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作者 李想 孙岩 +2 位作者 刘俊杰 姚钦 王光华 《微生物学报》 CAS CSCD 北大核心 2019年第2期364-373,共10页
【目的】揭示我国东北典型湿地沉积物中T4型噬菌体g23基因的多样性,明确湿地环境T4型噬菌体群落分布特征,为噬菌体生态学研究提供数据支撑。【方法】采用简并性引物MZIA1bis和MZIA6对采自东北6个地点不同类型湿地沉积物土壤DNA进行PCR扩... 【目的】揭示我国东北典型湿地沉积物中T4型噬菌体g23基因的多样性,明确湿地环境T4型噬菌体群落分布特征,为噬菌体生态学研究提供数据支撑。【方法】采用简并性引物MZIA1bis和MZIA6对采自东北6个地点不同类型湿地沉积物土壤DNA进行PCR扩增,采用克隆测序方法,解析沉积物中T4型噬菌体g23基因组成,通过UniFrac分析T4型噬菌体群落结构在湿地沉积物中与其他环境中的差异。【结果】在东北湿地沉积物中共得到262条不同的g23基因序列,构建的系统进化树分析表明,我国东北湿地沉积物T4型噬菌体g23基因分布与海洋、湖泊及稻田生态系统中g23基因亲缘关系较近,而与东北旱地黑土g23基因分布较远;以g23基因群集表征的T4型噬菌体群落在不同地点湿地中分异明显。【结论】东北湿地生态系统T4型噬菌体群落结构复杂多样,存在着一些未知的噬菌体类群。 展开更多
关键词 T4型噬菌体 g23基因 湿地沉积物 系统进化树 unifrac分析
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Taxonomic and phylogenetic composition show biotic resistance to exotic invasion in acid seep springs
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作者 David F.Barfknecht David J.Gibson 《Ecological Processes》 SCIE EI 2021年第1期77-88,共12页
Background:Few studies have incorporated the evolutionary insights provided by analysis of phylogenetic structure along with community composition to assess the effects of exotic invasion on freshwater wetlands.Here,w... Background:Few studies have incorporated the evolutionary insights provided by analysis of phylogenetic structure along with community composition to assess the effects of exotic invasion on freshwater wetlands.Here,we assess the taxonomic and phylogenetic relationships among acid seep springs to investigate the potential homogenization or resistance of communities due to invasion of an exotic grass.Results:Multivariate community analyses indicated differences in community and phylogenetic composition and dispersion among acid seep springs,associated with gradients in soil moisture,canopy cover,and phylogenetic diversity.By contrast,univariate analyses showed differences in taxonomic diversity but not phylogenetic diversity among acid seep springs.Conclusions:Despite exotic invasion,individual acid seep springs remained taxonomically and phylogenetically distinct from each other.Taxonomic and phylogenetic diversity metrics revealed different aspects of composition,reinforcing the importance of including both in analyses of plant communities for understanding community assembly following exotic invasion and for management purposes.Within acid seep springs,taxonomic and phylogenetic composition appear to be driven more through environmental filtering by light and moisture than by the competitive effects following invasion of an exotic grass in support of Elton’s biotic resistance hypothesis. 展开更多
关键词 Acid seep springs Diversity Community PHYLOGENETICS Exotic invasion Environmental filtering NMDS unifrac Vector analysis
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