The genome of the obligate endobacterium of an AM fungus reveals an interphylum network of nutritional interactions

Abstract

As obligate symbionts of most land plants, arbuscular mycorrhizal fungi (AMF) have a crucial role in ecosystems, but to date, in the absence of genomic data, their adaptive biology remains elusive. In addition, endobacteria are found in their cytoplasm, the role of which is unknown. In order to investigate the function of the Gram-negative Candidatus Glomeribacter gigasporarum, an endobacterium of the AMF Gigaspora margarita, we sequenced its genome, leading to an B1.72-Mb assembly. Phylogenetic analyses placed Ca. G. gigasporarum in the Burkholderiaceae whereas metabolic network analyses clustered it with insect endobacteria. This positioning of Ca. G. gigasporarum among different bacterial classes reveals that it has undergone convergent evolution to adapt itself to intracellular lifestyle. The genome annotation of this mycorrhizal-fungal endobacterium has revealed an unexpected genetic mosaic where typical determinants of symbiotic, pathogenic and freeliving bacteria are integrated in a reduced genome. Ca. G. gigasporarum is an aerobic microbe that depends on its host for carbon, phosphorus and nitrogen supply; it also expresses type II and type III secretion systems and synthesizes vitamin B12, antibiotics-and toxin-resistance molecules, which may contribute to the fungal host's ecological fitness. Ca. G. gigasporarum has an extreme dependence on its host for nutrients and energy, whereas the fungal host is itself an obligate biotroph that relies on a photosynthetic plant. Our work represents the first step towards unraveling a complex network of interphylum interactions, which is expected to have a previously unrecognized ecological impact.

Detection of a novel intracellular microbiome hosted in arbuscular mycorrhizal fungi

“…For example, in Mre, we found evidence of recombination, which was not apparent in CaGg. This finding was supported by some genomic features of CaGg genome: notwithstanding its high repetitive DNA (15%), CaGg contains a low number of active insertion sequences, which are considered important determinants for recombination (Ghignone et al, 2012). Indeed, a recent study of CaGg, using a set of four marker genes, revealed that recombination is not entirely absent from the CaGg evolutionary The quantification was performed for batches of 1, 5 and 10 spores considering at least five biological replicates.…”

“…In addition, by using codiverging partner pairs, Mondo et al (2012) demonstrated that this fungal/bacterial association is ancient (at least 400 million years old) and evolutionarily stable. Analysis of the 1.72 Mb CaGg genome (Ghignone et al, 2012) revealed that it is reduced when compared with the free-living related Burkholderia species, and that the metabolic profile of CaGg unambiguously clusters with insect endobacteria, including essential endosymbionts like Buchnera and Wigglesworthia (Moran et al, 2008). These data suggest that CaGg has undergone functional convergent evolution with phylogenetically distant endobacteria.…”

“…However, genome annotation also shows functional similarities with the secondary non-essential symbionts (for example H. defensa). On the basis of these considerations, we concluded that CaGg is an obligate intracellular symbiont, characterized by a genetic mosaic where determinants for different nutritional strategies are integrated in a reduced genome (Ghignone et al, 2012). Collectively, its life history features (that is, a strict vertical transmission) as well as molecular evolution and genomic features seem to share patterns from both essential and non-essential endosymbionts of insects.…”

“…The 16S rRNA gene was used as a target gene, but while in the CaGg genome the 16S rRNA gene is present in a single copy (Ghignone et al, 2012), in Mre one or at most two rRNA gene copies are expected based on the comparison with the closest microbes already sequenced (Fraser et al, 1995;Glass et al, 2000;Jaffe et al, 2004;Minion et al, 2004;Vasconcelos et al, 2005;Bai et al, 2006). The accuracy of qPCR primers of CaGg and Mre was confirmed by assessing the melting profile generated by each primer pair (Supplementary Figure S2).…”

“…The CaGg genome sequence (Ghignone et al, 2012) revealed that Glomeribacter endobacteria are nutritionally dependent on the fungal host and have a possible role in providing the fungus with essential factors like vitamin B12 (Ghignone et al, 2012). Phenotypic consequences of CaGg removal from the host include important morphological changes as well as reduced proliferation of host presymbiotic hyphae.…”