Comparative genomic analysis of Paenibacillus sp. SSG-1 and its closely related strains reveals the effect of glycometabolism on environmental adaptation

Abstract

The extensive environmental adaptability of the genus Paenibacillus is related to the enormous diversity of its gene repertoires. Paenibacillus sp. SSG-1 has previously been reported, and its agar-degradation trait has attracted our attention. Here, the genome sequence of Paenibacillus sp. SSG-1, together with 76 previously sequenced strains, was comparatively studied. The results show that the pan-genome of Paenibacillus is open and indicate that the current taxonomy of this genus is incorrect. The incessant flux of gene repertoires resulting from the processes of gain and loss largely contributed to the difference in genomic content and genome size in Paenibacillus. Furthermore, a large number of genes gained are associated with carbohydrate transport and metabolism. It indicates that the evolution of glycometabolism is a key factor for the environmental adaptability of Paenibacillus species. Interestingly, through horizontal gene transfer, Paenibacillus sp. SSG-1 acquired an approximately 150 kb DNA fragment and shows an agar-degrading characteristic distinct from most other non-marine bacteria. This region may be transported in bacteria as a complete unit responsible for agar degradation. Taken together, these results provide insights into the evolutionary pattern of Paenibacillus and have implications for studies on the taxonomy and functional genomics of this genus.

Bacteria From the Multi-Contaminated Tinto River Estuary (SW, Spain) Show High Multi-Resistance to Antibiotics and Point to Paenibacillus spp. as Antibiotic-Resistance-Dissemination Players

“…In the second place, Paenibacillus species have been described in a variety of environments, some of them interacting with other organisms (Finkelshtein et al, 2015;Grady et al, 2016;Xie et al, 2016), which suggests their potential for affecting ecology. Also, strains of the same species showed numerous variations in genome sequences with a high rate of recombination, which makes them prone to exchange DNA fragments by horizontal genetic exchange (Xie et al, 2016;Xu et al, 2017). Likewise, several species of the genus produce diverse antibiotic substances (Zhao et al, 2018;Pasari et al, 2019), which could make them players in the shaping of their ecosystems.…”

“…Likewise, several species of the genus produce diverse antibiotic substances (Zhao et al, 2018;Pasari et al, 2019), which could make them players in the shaping of their ecosystems. Furthermore, Paenibacillus genomes have a plethora of genes for adaptation, some of which considered to be acquired by HGT (Xie et al, 2016;Xu et al, 2017). Moreover, some studies have considered that the species of the genus evolve not as individual species, but inter-related in a pan-genomic evolution model (Xu et al, 2017).…”

“…Furthermore, Paenibacillus genomes have a plethora of genes for adaptation, some of which considered to be acquired by HGT (Xie et al, 2016;Xu et al, 2017). Moreover, some studies have considered that the species of the genus evolve not as individual species, but inter-related in a pan-genomic evolution model (Xu et al, 2017). Finally, the resistance elements found in genomes of some Paenibacillus species could be the origin of resistance elements found in other genera (Guardabassi et al, 2005;Liu et al, 2016); and, thus, they show mobilization potential.…”

Green Technology: Bacteria-Based Approach Could Lead to Unsuspected Microbe–Plant–Animal Interactions

“…Comparative genome analyses of Paenibacillus spp. revealed that this capacity is related to a highly diverse gene repertoire and to the HGT trend [143].…”

Paenibacillussp. strain UY79, isolated from a root nodule ofArachis villosa, displays a broad spectrum of antifungal activity

“…spectrum of pathogens and would be a potential and valuable strain to be further 48 assessed for the development of biofungicides.…”