Investigation of Salmonella Phage–Bacteria Infection Profiles: Network Structure Reveals a Gradient of Target-Range from Generalist to Specialist Phage Clones in Nested Subsets

Bacteriophages that lyse Salmonella enterica are potential tools to target and control Salmonella infections. Investigating the host range of Salmonella phages is a key to understand their impact on bacterial ecology, coevolution and inform their use in intervention strategies. Virus–host infection networks have been used to characterize the “predator–prey” interactions between phages and bacteria and provide insights into host range and specificity. Here, we characterize the target-range and infection profiles of 13 Salmonella phage clones against a diverse set of 141 Salmonella strains. The environmental source and taxonomy contributed to the observed infection profiles, and genetically proximal phages shared similar infection profiles. Using in vitro infection data, we analyzed the structure of the Salmonella phage–bacteria infection network. The network has a non-random nested organization and weak modularity suggesting a gradient of target-range from generalist to specialist species with nested subsets, which are also observed within and across the different phage infection profile groups. Our results have implications for our understanding of the coevolutionary mechanisms shaping the ecological interactions between Salmonella phages and their bacterial hosts and can inform strategies for targeting Salmonella enterica with specific phage preparations.

Patterns of Nestedness in Carnivorous Mammals in the Arauca-Nía Coastal Mountains of Southern Chile

The probability of existence or not of local extinctions of six species of carnivorous mammals was analyzed by ordering the species composition in nested subsets in 7 fragments of forest habitats in the Coastal Mountains in the Araucanía Region, in southern Chile. Nested Temperature Calculator (NTC) and BINMATNEST computer programs were used to process the results. The first software provided a temperature in the archipelago of 28.21 degree Celsius, whereas the second program showed a nesting temperature of 16.58 degree Celsius. The computer software used in this study suggest that there is no nesting pattern at the level species composition of carnivorous mammal assemblage in the evaluated area, which may be due to the habitat use characteristics of the different carnivorous mammals studied here.

Evolution and networks in ancient and widespread symbioses between Mucoromycotina and liverworts

Like the majority of land plants, liverworts regularly form intimate symbioses with arbuscular mycorrhizal fungi (Glomeromycotina). Recent phylogenetic and physiological studies report that they also form intimate symbioses with Mucoromycotina fungi and that some of these, like those involving Glomeromycotina, represent nutritional mutualisms. To compare these symbioses, we carried out a global analysis of Mucoromycotina fungi in liverworts and other plants using species delimitation, ancestral reconstruction, and network analyses. We found that Mucoromycotina are more common and diverse symbionts of liverworts than previously thought, globally distributed, ancestral, and often co-occur with Glomeromycotina within plants. However, our results also suggest that the associations formed by Mucoromycotina fungi are fundamentally different because, unlike Glomeromycotina, they may have evolved multiple times and their symbiotic networks are un-nested (i.e., not forming nested subsets of species). We infer that the global Mucoromycotina symbiosis is evolutionarily and ecologically distinctive.

Conditional effects of aquatic insects of small tributaries on mainstream assemblages: position within drainage network matters

Tributaries may affect fauna in a mainstream by changing bottom substrate and increasing spatial heterogeneity. Additionally, we hypothesized that fauna in the mainstream may be affected by drifting migrants from tributaries. In nine stream networks, we sampled a similar microhabitat immediately upstream and downstream of two confluences. In each network, one confluence was located in the network centre and one in the periphery, and they were distinguished by low and high ratios of tributary size, respectively. We assessed whether the aquatic fauna at sites downstream from confluences was species-richer, distinct in composition and structure, and whether it included the fauna of upstream sites. We found that richness, rarefied richness, and abundance at downstream sites were not higher than at their upstream counterparts. Faunas at downstream sites were not nested subsets of those at upstream sites. Macroinvertebrate assemblage composition and structure differed between downstream and upstream sites in the peripheral confluences (high tributary to mainstream (T:M) ratios), but not in central confluences (low T:M ratios). Thus, effects of small tributaries on receiving mainstreams are dependent on the T:M ratio.