Unraveling the interaction between soil microbiomes and their potential for restoring polluted soils

Soils are not exempt from anthropogenic pollution,which can eventually cause disturbance of the microbial communities and areas without any kind of productivity.Among soil microbiota,bacteria play an important role in pollutant degradation,enabling them to thrive in contaminated sites.Given this,several techniques have been used to increase the number of pollutantdegrading bacteria in situ or for subsequent addition.Additionally,bacteriophages exhibit a high tolerance to pollutants and enhance bacterial metabolic activity through phage-encoded auxiliary metabolic genes(AMGs),thereby augmenting their skills for nutrient assimilation,resistance to phage infection,antibiotic resistance,heavy metal resistance,and degradation of pesticides and xenobiotics,among others.Several phage-encoded AMGs have been described during the last few years,but their diversity,distribution,and function have not been extensively explored,warranting further studies.Here,we highlight soil microbiome interactions,especially bacterium and phage interactions to understand this unexplored world with a high potential for restoring polluted soils.

A Novel Vibriophage vB_VcaS_HC Containing Lysogeny-Related Gene Has Strong Lytic Ability against Pathogenic Bacteria

To avoid the negative effects of antibiotics,using phage to prevent animal disease becomes a promising method in aquaculture.Here,a lytic phage provisionally named vB_Vca S_HC that can infect the pathogen(i.e.,Vibrio campbellii 18)of prawn was isolated.The phage has an isometric head and a non-contractile tail.During phage infection,the induced host mortality in 5.5 h reached ca.96%,with a latent period of 1.5 h and a burst size of 172 PFU/cell.It has an 81,566 bp circular ds DNA genome containing 121 open reading frames(ORFs),and ca.71%of the ORFs are functionally unknown.Comparative genomic and phylogenetic analysis revealed that it is a novel phage belonging to Delepquintavirus,Siphoviridae,Caudovirales.In the phage genome,besides the ordinary genes related to structure assembly and DNA metabolism,there are 10 auxiliary metabolic genes.For the first time,the pyruvate phosphate dikinase(PPDK)gene was found in phages whose product is a key rate-limiting enzyme involving Embden-Meyerhof-Parnas(EMP)reaction.Interestingly,although the phage has a strong bactericidal activity and contains a potential lysogeny related gene,i.e.,the recombinase(Rec A)gene,we did not find the phage turned into a lysogenic state.Meanwhile,the phage genome does not contain any bacterial virulence gene or antimicrobial resistance gene.This study represents the first comprehensive characterization of a lytic V.campbellii phage and indicates that it is a promising candidate for the treatment of V.campbellii infections.

Another piece of puzzle for the human microbiome: the gut virome under dietary modulation

The virome is the most abundant and highly variable microbial consortium in the gut.Because of difficulties in isolating and culturing gut viruses and the lack of reference genomes,the virome has remained a rela-tively elusive aspect of the human microbiome.In recent years,studies on the virome have accumulated growing evidence showing that the virome is diet-modulated and widely involved in regulating health.Here,we review the responses of the gut virome to dietary intake and the potential health implications,presenting changes in the gut viral community and preferences of viral members to particular diets.We further discuss how viral-bacterial interactions and phage lifestyle shifts shape the gut microbiota.We also discuss the specific functions conferred by diet on the gut virome and bacterial community in the context of horizontal gene transfer,as well as the import of new viral members along with the diet.Collating these studies will expand our understanding of the dietary regulation of the gut virome and inspire dietary in-terventions and health maintenance strategies targeting the gut microbiota.