基于高通量测序的禁牧对土壤微生物群落结构的影响

麋鹿的采食、躺卧和践踏行为均会对栖息地土壤环境造成影响,进而影响土壤微生物群落结构。利用高通量测序技术,分析江苏大丰麋鹿国家级自然保护区禁牧点和补饲点土壤细菌和真菌群落结构差异,并结合土壤理化性质探究禁牧对土壤微生物群落结构的影响。结果表明细菌群落的优势菌门为变形菌门,真菌群落的优势菌门为子囊菌门。禁牧改变了土壤微生物群落结构,在门水平上提高了变形菌门、放线菌门和担子菌门的相对丰度,降低了绿弯菌门、厚壁菌门和子囊菌门的相对丰度,禁牧点与补饲点土壤微生物群落多样性的相似性较低。冗余分析中,细菌受土壤环境因子的影响大于真菌,其中土壤pH是影响细菌和真菌群落最大的土壤环境因子。研究揭示了禁牧对土壤微生物群落结构的影响,为保护区制定麋鹿生境恢复方案提供参考。     

Insights into Diversity and Imputed Metabolic Potential of Bacterial Communities in the Continental Shelf of Agatti Island

Marine microbes play a key role and contribute largely to the global biogeochemical cycles. This study aims to explore microbial diversity from one such ecological hotspot, the continental shelf of Agatti Island. Sediment samples from various depths of the continental shelf were analyzed for bacterial diversity using deep sequencing technology along with the culturable approach. Additionally, imputed metagenomic approach was carried out to understand the functional aspects of microbial community especially for microbial genes important in nutrient uptake, survival and biogeochemical cycling in the marine environment. Using culturable approach, 28 bacterial strains representing 9 genera were isolated from various depths of continental shelf. The microbial community structure throughout the samples was dominated by phylum Proteobacteria and harbored various bacterioplanktons as well. Significant differences were observed in bacterial diversity within a short region of the continental shelf (1–40 meters) i.e. between upper continental shelf samples (UCS) with lesser depths (i.e. 1–20 meters) and lower continental shelf samples (LCS) with greater depths (i.e. 25–40 meters). By using imputed metagenomic approach, this study also discusses several adaptive mechanisms which enable microbes to survive in nutritionally deprived conditions, and also help to understand the influence of nutrition availability on bacterial diversity.     

山东地区盐碱土花生种子际土壤微生物群落结构的研究

【目的】以不同含盐量的滨海盐土、内陆盐碱土和中等肥力非盐碱土壤为实验对象,探讨花生种子在吸水膨胀与萌发过程中,不同类型盐碱土对种子际土壤微生物多样性变化的影响。【方法】采集不同含盐量的滨海盐土、内陆盐碱土和中等肥力非盐碱土壤,通过对各样品中细菌的16S r RNA基因的V3-V4区进行PCR扩增,利用Illumina Hiseq高通量测序技术对12份V3-V4高变区PCR产物进行测序,并对测序数据进行生物信息学分析。【结果】(1)盐碱土壤的种子际细菌群落多样性高于非盐碱土壤,且以东营青坨滨海盐土种子际土壤细菌群落多样性较高。(2)不同类型土壤样本微生物群落结构在纲水平存在明显差异。4种土壤类型种子际土壤细菌共分属于6个菌纲,分别为Proteobacteria、Actinobacteria、Actinobacteria、Bacteroidetes、Acidobacteria和Firmicutes菌纲,并均以Proteobacteria和Actinobacteria菌纲为主要菌纲。全样本菌落结构分析结果表明,4种类型土壤中不同吸胀时间内种子际微生物菌落在门、属水平上的类型和丰度差异最为显著(P0.05)。(3)beta多样性分析和各样本遗传距离(phylogenetic distances)聚类树图分析表明,4个土壤类型的12个土壤样本种子际土壤中微生物群落均可聚为2大类。【结论】土壤含盐量越高其种子际土壤细菌群落多样性较高。不同类型土壤样本微生物群落结构在纲水平存在明显差异,以Proteobacteria和Actinobacteria菌纲为主要菌纲。种子吸胀萌发时间影响种子际微生物菌落在门、属水平上的类型和丰度,但对相同土壤类型样本间遗传距离无影响。     

基于高通量测序技术的不同年代公园绿地土壤细菌多样性

【背景】细菌多样性对绿地土壤生态功能有重要作用,但不同年代公园绿地土壤的细菌多样性尚未见相关报道。【目的】研究北京市不同年代公园绿地土壤细菌多样性和群落结构特征。【方法】利用IlluminaMiSeq测序技术,分别对北京市代表性古典公园和现代公园绿地土壤细菌群落多样性进行分析。【结果】北京市公园绿地土壤细菌群落共划分为45个已知的菌门,其中变形菌门、酸杆菌门、绿弯菌门和放线菌门为优势细菌群。土壤细菌群落α多样性分析结果表明,古典公园和现代公园的土壤细菌多样性存在差异,表现为古典公园的丰富度和多样性都高于现代公园。此外,土壤细菌群落相似性分析和主坐标分析都表明古典公园和现代公园的土壤细菌群落结构存在显著差异。冗余分析表明,对土壤微生物群落结构产生显著影响的环境因子分别为土壤含水量、有机质和全氮,其它土壤环境因子无统计学意义。首次引入公园年代作为影响因子进行冗余分析的研究结果表明,公园年代为影响公园细菌群落多样性的重要因子。【结论】不同年代公园绿地土壤细菌群落结构和物种多样性具有显著差异,随着公园年代的增加,土壤肥力和微生物多样性增加,绿地生态系统更稳定,可通过制定不同的绿地管理措施改变公园绿地土壤环境,进而优化土壤细菌群落结构,促进土壤碳氮养分循环,提高土壤肥力。     

Effects of tobacco–peanut relay intercropping on soil bacteria community structure

A reasonable cultivation pattern is beneficial to maintain soil microbial activity and optimize the structure of the soil microbial community. To determine the effect of tobacco−peanut (Nicotiana tabacum−Arachis hypogaea) relay intercropping on the microbial community structure in soil, we compared the effects of relay intercropping and continuous cropping on the soil bacteria community structure. We collected soil samples from three different cropping patterns and analyzed microbial community structure and diversity using high-throughput sequencing technology. The number of operational taxonomic units (OTU) for bacterial species in the soil was maximal under continuous peanut cropping. At the phylum level, the main bacteria identified in soil were Proteobacteria, Actinobacteria, and Acidobacteria, which accounted for approximately 70% of the total. The proportions of Actinobacteria and Firmicutes increased, whereas the proportion of Proteobacteria decreased in soil with tobacco–peanut relay intercropping. Moreover, the proportions of Firmicutes and Proteobacteria among the soil bacteria further shifted over time with tobacco–peanut relay intercropping. At the genus level, the proportions of Bacillus and Lactococcus increased in soil with tobacco–peanut relay intercropping. The community structure of soil bacteria differed considerably with tobacco–peanut relay intercropping from that detected under peanut continuous cropping, and the proportions of beneficial bacteria (the phyla Actinobacteria and Firmicutes, and the genera Bacillus and Lactococcus) increased while the proportion of potentially pathogenic bacteria (the genera Variibacter and Burkholderia) decreased. These results provide a basis for adopting tobacco–peanut relay intercropping to improve soil ecology and microorganisms, while making better use of limited cultivable land.     

黄河三角洲滨海湿地微生物多样性及其驱动因子

微生物在湿地的生物地球化学循环和生态功能调节中发挥着重要作用,对全球气候变化具有重大影响,对维持全球生态系统的健康至关重要。以黄河三角洲滨海湿地为研究对象,通过采集代表性植被群落的土壤表层和部分植物根系,探究土壤微生物群落组成、根际微生物、环境因子及其内在的关联性和影响机制。研究结果表明不同植被覆盖地区微生物多样性存在差异,芦苇区和柽柳区微生物丰度高于泥滩区、碱蓬区和棉田,海漫滩微生物丰度高于河漫滩地和泥滩。土壤微生物菌群结构和多样性显著高于根际：土壤细菌的香农指数约为4-5.5,根际微生物的香农指数约为0-4。土壤细菌主要为厚壁菌门、变形菌门、拟杆菌门和放线菌门,占样品总数的90%以上;而根际细菌主要是蓝藻门、变形菌门和放线菌门,二者在属水平上的菌群结构差异更加明显。环境因子的含量与生境类型有关,SO₄^2-和NO₃^-的相关性最高,植被覆盖区土壤中Mn⁴⁺、Fe³⁺和水解氮的含量低于滩涂裸地。冗余分析（RDA）表明,pH值在小空间尺度上对湿地土壤中细菌群落的影响较小,环境因子在门和属水平的解释率分别为89.7%和86.8%,其中K（23.4%）、NO₂^-（11.8%）、Mn⁴⁺（9.8%）和Na（8.0%）是解释门水平微生物区系结构变化和组成的主要因子。研究为理解湿地微生物多样性与湿地生态系统功能之间的影响机制提供了一个生态学视角,有助于了解黄河三角洲滨海湿地土壤和植物根际的细菌分布特征,对黄河三角洲退化滨海湿地的生物修复具有重要的指导意义。     

Global patterns in belowground communities

Although belowground ecosystems have been studied extensively and soil biota play integral roles in biogeochemical processes, surprisingly we have a limited understanding of global patterns in belowground biomass and community structure. To address this critical gap, we conducted a meta-analysis of published data (> 1300 datapoints) to compare belowground plant, microbial and faunal biomass across seven of the major biomes on Earth. We also assembled data to assess biome-level patterns in belowground microbial community composition. Our analysis suggests that variation in microbial biomass is predictable across biomes, with microbial biomass carbon representing 0.6–1.1% of soil organic carbon ( r ² = 0.91) and 1–20% of total plant biomass carbon ( r ² = 0.42). Approximately 50% of total animal biomass can be found belowground and soil faunal biomass represents < 4% of microbial biomass across all biomes. The structure of belowground microbial communities is also predictable: bacterial community composition and fungal : bacterial gene ratios can be predicted reasonably well from soil pH and soil C : N ratios respectively. Together these results identify robust patterns in the structure of belowground microbial and faunal communities at broad scales which may be explained by universal mechanisms that regulate belowground biota across biomes.     

Diversity and dynamics of microbial communities in soils from agro-ecosystems

Soil microbial communities are integrally involved in biogeochemical cycles and their activities are crucial to the productivity of terrestrial ecosystems. Despite the importance of soil microorganisms, little is known about the distribution of microorganisms in the soil or the manner in which microbial community structure responds to changes in land management. We investigated the structure of microbial communities in the soil over two years in a series of replicated plots, that included, cultivated fields, fields abandoned from cultivation and fields with no history of cultivation. Microbial community structure was examined by monitoring the relative abundance of ribosomal RNA (rRNA) from seven of the most common bacterial groups in soil (the Alpha and Beta Proteobacteria, Actinobacteria, Cytophagales, Planctomycetes, Verrucomicrobia and the Acidobacteria) and the Eukarya. These data reveal that soil microbial communities are dynamic, capable of significant change at temporal scales relative to seasonal events. However, despite temporal change in microbial community structure, the rRNA relative abundance of particular microbial groups is affected by the local environment such that recognizable patterns of community structure exist in relation to field management.     

微生物菌剂对猪粪堆肥中细菌群落结构的影响

以猪粪和小麦秸秆做堆肥试验,处理组添加外源微生物菌剂,利用常规方法对堆肥样品进行理化性状测定,采用高通量测序技术分析堆肥过程中细菌群落特征。理化性状测定结果表明: 添加外源菌剂可延长堆肥高温时间,降低堆肥发酵末期的pH,增加全氮含量,加快C/N的下降。主成分分析表明: 外源菌剂影响堆肥样品细菌群落的稳定性。门分类水平上,厚壁菌门、变形菌门和绿弯菌门的相对丰度在处理组中较高;纲分类水平上,梭状芽孢杆菌纲、α-变形菌纲和γ-变形菌纲在处理组的升温期和高温期相对丰度增加;科分类水平上,小单孢菌科和梭状芽孢杆菌纲的消化链球菌科、梭菌科以及盐厌氧菌科的相对丰度在处理组的升温期和高温期均呈上升趋势。Pearson相关性分析表明,盐胞菌属与外源菌剂呈显著正相关,而氨苄芽孢杆菌属与外源菌剂呈显著负相关。研究表明,猪粪堆肥中添加外源菌剂可使堆肥的理化性质和细菌群落结构均发生显著变化。     

Metabolically active microbial communities of yellow and grey colonizations on the walls of Altamira Cave, Spain

Aims: To determine the major components of total and metabolically active microbial communities of yellow and grey colonizations threatening the conservation of palaeolithic paintings in Altamira Cave (Spain). Methods and Results: Micro‐organisms present in yellow and grey colonizations were determined from DNA analysis with those showing metabolic activity determined from RNA analysis. Microbial community fingerprints were obtained by denaturing gradient gel electrophoresis (DGGE) and 16S rDNA libraries were constructed from PCR amplified products. Proteobacteria was the most frequent bacterial phylum. Other phyla detected from RNA‐based microbial surveys were Acidobacteria, Actinobacteria, Firmicutes, Nitrospirae and Gemmatimonadetes. The detected metabolically active micro‐organisms represented only a fraction of the total bacterial community present in the studied colonizations as compared from DGGE analysis. Conclusions: The major bacterial participants in the development of yellow and grey colonizations in Altamira Cave were determined using RNA‐based molecular techniques. Micro‐organisms showing undetectable activity represent a potential risk for the conservation of these paintings if environmental conditions experience variations. Significance and Impact of the Study: Caves with palaeolithic paintings are affected by microbial deterioration. Assessing the composition of the microbial communities colonizing these caves represents a first stage to understand and control these colonizations.