The microbial constituency of a host-associated microbiome emerges from a complex physical and chemical interplay of microbial colonization factors, host surface conditions, and host immunological responses. To fill unique niches within a host, bacteria encode surface and secreted proteins that enable interactions with and responses to the host and cooccurring microbes.

Temperate phages engage in long-term associations with their hosts that may lead to mutually beneficial interactions, of which the full extent is presently unknown. Here, we describe an environmentally relevant model system with a single host, a species of the Roseobacter clade of marine bacteria, and two genetically similar phages (ɸ-A and ɸ-D). Superinfection of a ɸ-D lysogenized strain (CB-D) with ɸ-A particles resulted in a lytic infection, prophage induction, and conversion of a subset of the host population, leading to isolation of a newly ɸ-A lysogenized strain (CB-A). Phenotypic differences, predicted to result from divergent lysogenic-lytic switch mechanisms, are evident between these lysogens, with CB-A displaying a higher incidence of spontaneous induction. Doubling times of CB-D and CB-A in liquid culture are 75 and 100 min, respectively. As cell cultures enter stationary phase, CB-A viable counts are half of CB-D. Consistent with prior evidence that cell lysis enhances biofilm formation, CB-A produces twice as much biofilm biomass as CB-D. As strains are susceptible to infection by the opposing phage type, co-culture competitions were performed to test fitness effects. When grown planktonically, CB-A outcompeted CB-D three to one. Yet, during biofilm growth, CB-D outcompeted CB-A three to one. These results suggest that genetically similar phages can have divergent influence on the competitiveness of their shared hosts in distinct environmental niches, possibly due to a complex form of phage-mediated allelopathy. These findings have implications for enhanced understanding of the eco-evolutionary dynamics of host-phage interactions that are pervasive in all ecosystems.

In host-associated bacteria, surface and secreted proteins mediate acquisition of nutrients, interactions with host cells, and specificity of host-range and tissue-localization. In Gramnegative bacteria, the mechanism by which many proteins cross, become embedded within, or become tethered to the outer membrane remains unclear. The domain of unknown function (DUF)560 occurs in outer membrane proteins found throughout and beyond the proteobacteria. Functionally characterized DUF560 representatives include NilB, a host-range specificity determinant of the nematode-mutualist Xenorhabdus nematophila and the surface lipoprotein assembly modulators (Slam), Slam1 and Slam2 which facilitate surface exposure of lipoproteins in the human pathogen Neisseria meningitidis. Through network analysis of protein sequence similarity we show that DUF560 subclusters exist and correspond with organism lifestyle rather than with taxonomy, suggesting a role for these proteins in environmental adaptation. Cluster 1 Mauer, Grossman et al. Bacterial Surface/Secreted Protein Associated Outer Membrane Proteins (SPAMs) 2 had the greatest number of representative proteins, was dominated by homologs from animalassociated symbionts, and was composed of subclusters: 1A (containing NilB, Slam1, and Slam2), 1B, and 1C. Genome neighborhood networks revealed that Cluster 1A DUF560 members are strongly associated with TonB, TonB-dependent receptors, and predicted coreceptors such as the Slam1 lipoprotein substrates transferrin binding protein and lactoferrin binding protein. The genome neighborhood network of Cluster 1B sequences are similarly dominated by TonB loci, but typically the associated co-receptors (the presumed DUF560substrates) are predicted to be non-lipidated. We suggest that these subclusters within the DUF560 protein family indicate distinctive activities and that Slam activity may be characteristic of Cluster 1A members but not all DUF560 homologs. For Cluster 1 DUF560 homologs we propose the name SPAM (Surface/Secreted Protein Associated Outer Membrane Proteins) to accommodate the potential for non-lipoprotein substrates or different activities. We show that the repertoire of SPAM proteins in Xenorhabdus correlates with host phylogeny, suggesting that the host environment drives the evolution of these symbiont-encoded proteins. This pattern of selection for specific sequences based on host physiology and/or environmental factors may extend to other clusters of the DUF560 family.

The only known required component of the newly described Type XI secretion system (TXISS) is an outer membrane protein (OMP) of the DUF560 family. TXISSOMPs are broadly distributed across proteobacteria, but properties of the cargo proteins they secrete are largely unexplored. We report biophysical, histochemical, and phenotypic evidence that Xenorhabdus nematophila NilC is surface exposed. Biophysical data and structure predictions indicate that NilC is a two-domain protein with a C-terminal, 8-stranded β-barrel. This structure has been noted as a common feature of TXISS effectors and may be important for interactions with the TXISSOMP. The NilC N-terminal domain is more enigmatic, but our results indicate it is ordered and forms a β-sheet structure, and bioinformatics suggest structural similarities to carbohydrate-binding proteins. X. nematophila NilC and its presumptive TXISSOMP partner NilB are required for colonizing the anterior intestine of Steinernema carpocapsae nematodes: the receptacle of free-living, infective juveniles and the anterior intestinal cecum (AIC) in juveniles and adults. We show that, in adult nematodes, the AIC expresses a Wheat Germ Agglutinin (WGA)-reactive material, indicating the presence of N-acetylglucosamine or N-acetylneuraminic acid sugars on the AIC surface. A role for this material in colonization is supported by the fact that exogenous addition of WGA can inhibit AIC colonization by X. nematophila. Conversely, the addition of exogenous purified NilC increases the frequency with which X. nematophila is observed at the AIC, demonstrating that abundant extracellular NilC can enhance colonization. NilC may facilitate X. nematophila adherence to the nematode intestinal surface by binding to host glycans, it might support X. nematophila nutrition by cleaving sugars from the host surface, or it might help protect X. nematophila from nematode host immunity. Proteomic and metabolomic analyses of wild type X. nematophila compared to those lacking nilB and nilC revealed differences in cell wall and secreted polysaccharide metabolic pathways. Additionally, purified NilC is capable of binding peptidoglycan, suggesting that periplasmic NilC may interact with the bacterial cell wall. Overall, these findings support a model that NilB-regulated surface exposure of NilC mediates interactions between X. nematophila and host surface glycans during colonization. This is a previously unknown function for a TXISS.