Kielak Anna M, Barreto Cristine C, Kowalchuk George A, van Veen Johannes A, Kuramae Eiko E
Department of Microbial Ecology, The Netherlands Institute of Ecology - Koninklijke Nederlandse Akademie van Wetenschappen Wageningen, Netherlands.
Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília Brasília, Brazil.
Front Microbiol. 2016 May 31;7:744. doi: 10.3389/fmicb.2016.00744. eCollection 2016.
The phylum Acidobacteria is one of the most widespread and abundant on the planet, yet remarkably our knowledge of the role of these diverse organisms in the functioning of terrestrial ecosystems remains surprisingly rudimentary. This blatant knowledge gap stems to a large degree from the difficulties associated with the cultivation of these bacteria by classical means. Given the phylogenetic breadth of the Acidobacteria, which is similar to the metabolically diverse Proteobacteria, it is clear that detailed and functional descriptions of acidobacterial assemblages are necessary. Fortunately, recent advances are providing a glimpse into the ecology of members of the phylum Acidobacteria. These include novel cultivation and enrichment strategies, genomic characterization and analyses of metagenomic DNA from environmental samples. Here, we couple the data from these complementary approaches for a better understanding of their role in the environment, thereby providing some initial insights into the ecology of this important phylum. All cultured acidobacterial type species are heterotrophic, and members of subdivisions 1, 3, and 4 appear to be more versatile in carbohydrate utilization. Genomic and metagenomic data predict a number of ecologically relevant capabilities for some acidobacteria, including the ability to: use of nitrite as N source, respond to soil macro-, micro nutrients and soil acidity, express multiple active transporters, degrade gellan gum and produce exopolysaccharide (EPS). Although these predicted properties allude to a competitive life style in soil, only very few of these prediction shave been confirmed via physiological studies. The increased availability of genomic and physiological information, coupled to distribution data in field surveys and experiments, should direct future progress in unraveling the ecology of this important but still enigmatic phylum.
酸杆菌门是地球上分布最广、数量最多的门类之一，但令人惊讶的是，我们对这些多样的生物在陆地生态系统功能中所起作用的了解仍然极为有限。这种明显的知识差距在很大程度上源于通过传统方法培养这些细菌所面临的困难。鉴于酸杆菌门在系统发育上的广度，类似于代谢多样的变形菌门，显然有必要对酸杆菌组合进行详细的功能描述。幸运的是，最近的进展让我们得以一窥酸杆菌门成员的生态学。这些进展包括新颖的培养和富集策略、基因组特征分析以及对环境样本宏基因组DNA的分析。在此，我们将这些互补方法的数据结合起来，以更好地了解它们在环境中的作用，从而对这个重要门类的生态学提供一些初步见解。所有已培养的酸杆菌模式种都是异养型的，第1、3和4亚类的成员在碳水化合物利用方面似乎更为多样。基因组和宏基因组数据预测了一些酸杆菌的多种与生态相关的能力，包括：利用亚硝酸盐作为氮源、对土壤大量、微量养分和土壤酸度作出反应、表达多种活性转运蛋白、降解结冷胶并产生胞外多糖（EPS）。尽管这些预测特性暗示了在土壤中的一种竞争性生活方式，但只有极少数这些预测通过生理学研究得到了证实。基因组和生理学信息的可得性增加，再加上实地调查和实验中的分布数据，应该会指导未来在揭示这个重要但仍然神秘的门类生态学方面取得进展。
