Ijaz Ali Z, Jeffries Thomas C, Ijaz Umer Z, Hamonts Kelly, Singh Brajesh K
Hawkesbury Institute for the Environment, Western Sydney University, Penrith, Australia.
School of Science & Health, Western Sydney University, Penrith, Australia.
PeerJ. 2017 Oct 10;5:e3827. doi: 10.7717/peerj.3827. eCollection 2017.
Understanding how the environment selects a given taxon and the diversity patterns that emerge as a result of environmental filtering can dramatically improve our ability to analyse any environment in depth as well as advancing our knowledge on how the response of different taxa can impact each other and ecosystem functions. Most of the work investigating microbial biogeography has been site-specific, and logical environmental factors, rather than geographical location, may be more influential on microbial diversity. SEQenv, a novel pipeline aiming to provide environmental annotations of sequences emerged to provide a consistent description of the environmental niches using the ENVO ontology. While the pipeline provides a list of environmental terms on the basis of sample datasets and, therefore, the annotations obtained are at the dataset level, it lacks a taxa centric approach to environmental annotation. The work here describes an extension developed to enhance the SEQenv pipeline, which provided the means to directly generate environmental annotations for taxa under different contexts. 16S rDNA amplicon datasets belonging to distinct biomes were selected to illustrate the applicability of the extended SEQenv pipeline. A literature survey of the results demonstrates the immense importance of sequence level environmental annotations by illustrating the distribution of both taxa across environments as well as the various environmental sources of a specific taxon. Significantly enhancing the SEQenv pipeline in the process, this information would be valuable to any biologist seeking to understand the various taxa present in the habitat and the environment they originated from, enabling a more thorough analysis of which lineages are abundant in certain habitats and the recovery of patterns in taxon distribution across different habitats and environmental gradients.
了解环境如何选择特定的分类群以及环境过滤所产生的多样性模式，能够极大地提高我们深入分析任何环境的能力，同时增进我们对不同分类群的响应如何相互影响以及生态系统功能的认识。大多数研究微生物生物地理学的工作都是针对特定地点的，对微生物多样性而言，合乎逻辑的环境因素可能比地理位置更具影响力。SEQenv是一种新颖的流程，旨在提供序列的环境注释，它利用ENVO本体论对环境生态位进行一致的描述。虽然该流程基于样本数据集提供了一份环境术语列表，因此获得的注释是在数据集层面，但它缺乏以分类群为中心的环境注释方法。本文所述的工作描述了对SEQenv流程的扩展，该扩展提供了在不同背景下直接为分类群生成环境注释的方法。选择了属于不同生物群落的16S rDNA扩增子数据集来说明扩展后的SEQenv流程的适用性。对结果的文献调查通过展示分类群在不同环境中的分布以及特定分类群的各种环境来源，证明了序列水平环境注释的巨大重要性。在此过程中显著增强了SEQenv流程，这些信息对于任何想要了解栖息地中存在的各种分类群及其起源环境的生物学家来说都是有价值的，从而能够更全面地分析哪些谱系在某些栖息地中丰富，以及恢复不同栖息地和环境梯度下分类群分布的模式。
