The Ecology of Acidobacteria: Moving beyond Genes and Genomes.

Anna M Kielak,Eiko E Kuramae,George A Kowalchuk,Johannes A Van Veen,Cristine C Barreto

doi:10.3389/fmicb.2016.00744

Abstract

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.

Highlights

The Acidobacteria were only recognized as a phylum relatively recently, their abundance across a range of ecosystems, especially soils, has demanded research into their ecology. 16S rRNA gene-based approaches as well as environmental shotgun metagenomic analyses have revealed that the Acidobacteria represent a highly diverse phylum resident to a wide range of habitats around the globe
Changes in the traditional methods for culturing bacteria from soils have significantly improved the isolation of Acidobacteria strains in recent years
The 16S rRNA data provided by generation sequencing together with soil chemicals can help to elaborate specific culture medium for different Acidobacteria subdivisions isolation

Summary

Introduction

The Acidobacteria were only recognized as a phylum relatively recently, their abundance across a range of ecosystems, especially soils, has demanded research into their ecology. 16S rRNA gene-based approaches as well as environmental shotgun metagenomic analyses have revealed that the Acidobacteria represent a highly diverse phylum resident to a wide range of habitats around the globe (Chow et al, 2002; Kuske et al, 2002; Gremion et al, 2003; Quaiser et al, 2003; Fierer et al, 2005; Stafford et al, 2005; Janssen, 2006; Sanguin et al, 2006; de Carcer et al, 2007; Ecology of AcidobacteriaKim et al, 2007; Singh et al, 2007; DeAngelis et al, 2009; Jesus et al, 2009; Kielak et al, 2009; Navarrete et al, 2010, 2013b; Zhang et al, 2014). In 2009, the first sequenced genomes of acidobacteria strains became available, providing preliminary genetic insights into the potential physiology and environment functions of several members of this phylum (Ward et al, 2009) In these first genomic studies, five aspects of physiological received particular attention: (i) carbon usage, (ii) nitrogen assimilation, (iii) metabolism of iron, (iv) antimicrobials, and (v) abundance of transporters. Besides genome sequencing of cultivated isolates, addition information regarding genomic properties of acidobacteria has been derived from metagenomics studies (Liles et al, 2003; Quaiser et al, 2003, 2008; Riaz et al, 2008; Jones et al, 2009; Kielak et al, 2010; Parsley et al, 2011; Faoro et al, 2012; Navarrete et al, 2013b; Mendes et al, 2014)

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Conclusion