Sequences, Taxonomic Assignments, And R Script From Comparison Of Lava Cave Bacterial Mat Communities To Overlying Surface Soil Bacterial Communities From Lava Beds National Monument, Usa

This set of files contain the 16S rDNA, taxonomic assignments from the greengenes database, and the R script for processing the data. <strong>Abstract</strong> Lava caves around the world often support extensive microbial mats on ceilings and walls in a range of colors. Little is known about lava cave microbial diversity and how these subsurface mats differ from microbial communities in overlying surface soils. We generated and analyzed bacterial 16S rDNA from 454 pyrosequencing from three colors of microbial mats (tan, white, and yellow) from seven lava caves in Lava Beds National Monument, CA, USA, and compared them with surface soils overlying each cave. <em>Actinobacteria</em> dominated in all samples, with 39% (caves) and 21% (surface soils). <em>Proteobacteria</em> made up 30% of phyla from caves and 36% from surface soil with <em>Gamma</em>- 20% and <em>Alpha</em>- 10% in the caves and <em>Gamma</em>- 18% with <em>Alpha</em>-17% in soil. Other major phyla in caves were <em>Nitrospirae</em> (7%) followed by Minor Phyla (7%), compared to surface soils with <em>Bacteriodetes</em> (8%) and Minor phyla (8%). A very high proportion (53.33%) of the most abundant sequences could not be identified to genus, indicating a high degree of novelty. Surface soil samples had more OTUs and greater diversity indices than cave samples. The same phyla were represented in both soils and cave microbial mats, but the overlap was only 11.2% at the operational taxonomic unit (OTU). Although surface soil microbes immigrate into underlying caves, the environment selects for microbes able to live in the cave habitats, resulting in very different cave microbial communities. In terms of species richness, diversity by mat color differed, but not significantly. Number of entrances per cave, distance from an entrance, cave length, and temperature also contributed to observed differences in diversity. With high levels of novel microbes, caves may represent excellent habitats for the isolation of new bioactive compounds. This study is the first comprehensive comparisons of bacterial communities in lava caves with the overlying soil community.本数据集文件包含16S rDNA、源自Greengenes数据库（Greengenes database）的分类学注释信息，以及用于数据处理的R脚本。 摘要 全球熔岩洞穴的天花板与岩壁上常形成色彩各异的大面积微生物垫。目前学界对熔岩洞穴微生物多样性，以及这类地下微生物垫与上覆表层土壤的微生物群落差异尚所知甚少。本研究对美国加利福尼亚州熔岩床国家纪念公园7处熔岩洞穴中3种颜色（棕褐色、白色、黄色）的微生物垫开展454焦磷酸测序，获取并分析了细菌16S rDNA序列，并将其与各洞穴上覆的表层土壤样本进行比对。 所有样本中放线菌门（Actinobacteria）均为优势类群，在洞穴样本中占比39%，表层土壤中占比21%。变形菌门（Proteobacteria）在洞穴样本中占总菌门的30%，土壤样本中占36%；其中洞穴样本中的γ-变形菌纲（Gamma-）占20%、α-变形菌纲（Alpha-）占10%，而土壤样本中γ-变形菌纲占18%、α-变形菌纲占17%。洞穴样本中的其他主要菌门为硝化螺旋菌门（Nitrospirae，7%），其次为次要菌门（7%）；而表层土壤样本中的主要类群为拟杆菌门（Bacteroidetes，8%）与次要菌门（8%）。 占比高达53.33%的丰度最高序列无法被鉴定到属水平，这表明其中存在大量未被认知的新类群。表层土壤样本的操作分类单元（operational taxonomic unit, OTU）数量与多样性指数均高于洞穴样本。尽管洞穴与土壤样本共享相同的菌门，但在操作分类单元水平上的类群重叠率仅为11.2%。尽管表层土壤微生物可迁移至下方的洞穴生境中，但洞穴环境会筛选出适应洞穴生存的微生物类群，最终形成差异显著的洞穴微生物群落。不同颜色微生物垫的物种丰富度与多样性存在差异，但未达到统计学显著水平。洞穴入口数量、距入口距离、洞穴长度与温度等因素，同样对观测到的多样性差异存在影响。由于蕴藏大量新型微生物，熔岩洞穴或许是分离新型生物活性化合物的优质生境。本研究是首个将熔岩洞穴细菌群落与其上覆土壤群落进行全面对比的学术研究。