Comparative Genomics of Microbacterium Species to Reveal Diversity, Potential for Secondary Metabolites and Heavy Metal Resistance

Erika Corretto,Christoph Höfer,Karivaradharajan Swarnalakshmi,Angela Sessitsch,Günter Brader,Livio Antonielli,Markus Puschenreiter,Siegrid Widhalm

doi:10.3389/fmicb.2020.01869

Abstract

Microbacterium species have been isolated from a wide range of hosts and environments, including heavy metal-contaminated sites. Here, we present a comprehensive analysis on the phylogenetic distribution and the genetic potential of 70 Microbacterium belonging to 20 different species isolated from heavy metal-contaminated and non-contaminated sites with particular attention to secondary metabolites gene clusters. The analyzed Microbacterium species are divided in three main functional clades. They share a small core genome (331 gene families covering basic functions) pointing to high genetic diversity. The most common secondary metabolite gene clusters encode pathways for the production of terpenoids, type III polyketide synthases and non-ribosomal peptide synthetases, potentially responsible of the synthesis of siderophore-like compounds. In vitro tests showed that many Microbacterium strains produce siderophores, ACC deaminase, auxins (IAA) and are able to solubilize phosphate. Microbacterium isolates from heavy metal contaminated sites are on average more resistant to heavy metals and harbor more genes related to metal homeostasis (e.g., metalloregulators). On the other hand, the ability to increase the metal mobility in a contaminated soil through the secretion of specific molecules seems to be widespread among all. Despite the widespread capacity of strains to mobilize several metals, plants inoculated with selected Microbacterium isolates showed only slightly increased iron concentrations, whereas concentrations of zinc, cadmium and lead were decreased.

Highlights

The genus Microbacterium belongs to the Microbacteriaceae family, a high GC actinobacterial taxon, and accounts for more than 90 recognized species that were isolated from a wide range of habitats and hosts (Behrendt et al, 2001; Park et al, 2008; Sharma et al, 2013; Wang et al, 2014; Hadjadj et al, 2016)
The analyzed genomes represent at least 20 different Microbacterium species that were isolated from a broad range of habitats, mainly plants and soils (Supplementary Table S1)
Organisms of polyketide synthases (PKS) cluster type B contain a polyketide cyclase and separate clearly from the cluster type C, harboring genes with PKS/non-ribosomal protein synthetases (NRPS) domains, and type D (Figure 1). These results suggest that Microbacterium species might produce at least four different PKS types which are distributed in groups that largely correspond to the three main operational functional groups (Figure 1)

Summary

Introduction

The genus Microbacterium belongs to the Microbacteriaceae family, a high GC actinobacterial taxon, and accounts for more than 90 recognized species that were isolated from a wide range of habitats and hosts (Behrendt et al, 2001; Park et al, 2008; Sharma et al, 2013; Wang et al, 2014; Hadjadj et al, 2016). Microbacterium strains can survive in heavy metal contaminated environments (Brown et al, 2012; Fidalgo et al, 2016), reduce specific metals such as hexavalent chromium (Henson et al, 2015; Fierros-Romero et al, 2016; Kumar and Saini, 2019) and change the mobility of heavy metals in contaminated soils (Kuffner et al, 2010; Soni et al, 2013) Because of these interesting traits, they have already been used in phytoextraction trials for soil decontamination (Visioli et al, 2015). Bacteria, which can either promote plant growth/health, enhance the stress tolerance and mobilize metals, are considered as an interesting resource for the improvement of such clean-up techniques (Rajkumar et al, 2012; Sessitsch et al, 2013; Ma et al, 2016)

Objectives

Methods

Results

Conclusion