Tle distribution and diversity in metagenomic datasets reveal niche specialization

Abstract

The existence of microbial communities and the complex interactions that govern their dynamics have received considerable attention in recent years. Advances in genomic sequencing technologies have greatly enhanced our understanding of 'what is there'. However, the question as to 'what are they doing' remains less well defined. The continual development of the genomic and metagenomic sequence databases provides an exciting opportunity to interrogate the distribution and prevalence of key microbial systems across a diverse set of ecosystems. The widely distributed type VI secretion system (T6SS) has been shown to play a significant role in bacterial-bacterial and bacterial-host interactions. While several T6SS effectors have been shown to target the cell wall and membrane of competing cells, little is known about the roles these proteins play in different ecosystems. Therefore, the prevalence of a key T6SS effector superfamily known as type six lipase effectors (Tle) was studied in over 2000 metagenomic datasets representing diverse ecosystems and host niches. Increased Tle representation in environmental categories strongly supports the hypothesis of niche specialization and suggests that these effectors may play important niche-specific roles.

A phospholipase A1 antibacterial Type VI secretion effector interacts directly with the C‐terminal domain of the VgrG spike protein for delivery

“…No enzymatic activity has been assigned so far for members of the Tle3 and Tle4 families. Tle5 family members contain a duplicated HXDXXXXG motif characteristic of phospholipase D (PLD) superfamily, and can be divided in two subfamilies (Tle5a and Tle5b), with Tle5a being eukaryotic-like PLD (Russell et al, 2013;Jiang et al, 2014;Egan et al, 2015;Spencer and Brown, 2015). The PLD activities of P. aeruginosa Tle5a PA (known as PldA) and Tle5b PA (known as PldB) have been demonstrated (Russell et al, 2013;Jiang et al, 2014;Spencer and Brown, 2015), while Klebsiella pneumoniae Tle5b KP T6SS toxin presents a cardiolipin synthase activity (Lery et al, 2014).…”

Microbial Surface Colonization and Biofilm Development in Marine Environments

“…However, the T6SSs are found primarily in Gammaproteobacteria among the marine bacteria (732). Recently, T6SSs have also been identified in some bacterial strains, genomes, and marine metagenomes of Bacteroidetes (733)(734)(735)(736), an important group of secondary surface colonizers in marine environments (13,17,108,130,272,574). Therefore, it is reasonable to hypothesize that T6SS-mediated microbial competition may contribute to the successional change and spatial variation of the composition and structure of surface-associated marine microbial communities, in which certain T6SS-harboring bacteria may constitute important groups of secondary colonizers.…”

The Landscape of Type VI Secretion across Human Gut Microbiomes Reveals Its Role in Community Composition

“…Indeed, there are recent reports consistent with the pathway mediating bacterial interaction in environmental communities. For instance, T6S genes were found to be enriched and under positive selection in the barley rhizosphere (Bulgarelli et al, 2015), and T6S phospholipase effectors were detected in metagenomes from diverse sources (Egan et al, 2015). To date, however, systematic studies of the impact of T6S on microbial community assembly are lacking.…”