Habitat Adaptation Drives Speciation of a Streptomyces Species with Distinct Habitats and Disparate Geographic Origins

Both isolation by distance and isolation by environment occur in bacteria, and different diversification patterns may apply to different species. Streptomyces species, typified by producing useful natural products, are widespread in nature and possess high genetic diversity. However, the ecological processes and evolutionary mechanisms that shape their distribution are not well understood.

Host-symbiont population genomics provide insights into partner fidelity, transmission mode and habitat adaptation in deep-sea hydrothermal vent snails

Symbiont specificity, both at the phylotype and strain level, can have profound consequences for host ecology and evolution. However, except for insights from a few model symbiosis systems, the degree of partner fidelity and the influence of host versus environmental factors on symbiont composition are still poorly understood. Nutritional symbioses between invertebrate animals and chemosynthetic bacteria at deep-sea hydrothermal vents are examples of relatively selective associations, where hosts affiliate only with particular phylotypes of gammaproteobacterial or campylobacterial symbionts. In hydrothermal vent snails of the sister genera Alviniconcha and Ifremeria this phylotype specificity has been shown to play a role in habitat distribution and partitioning among different holobiont species. However, it is currently unknown if fidelity goes beyond species level associations that might influence genetic structuring, connectivity and habitat adaptation of holobiont populations. We used metagenomic analyses to assess sequence variation in hosts and symbionts and identify correlations with geographic and environmental factors. Our analyses indicate that host populations are not differentiated across a ~800 km gradient, while symbiont populations are clearly structured between vent locations due to a combination of neutral and selective processes. Overall, these results suggest that host individuals flexibly associate with local strains of their specific symbiont phylotypes, which confirms a model of horizontal transmission in both Ifremeria and Alviniconcha. Strain flexibility in these snails likely enables host populations to exploit a range of habitat conditions, which might favor wide-spread genetic connectivity and ecological resilience unless physical dispersal barriers are present.

Ecomorphology and ecology of the grassland specialist, Rusingoryx atopocranion (Artiodactyla: Bovidae), from the late Pleistocene of western Kenya

Rusingoryx atopocranion is an extinct alcelaphin bovid from the late Pleistocene of Kenya, known for its distinctive hollow nasal crest. A bonebed of R. atopocranion from the Lake Victoria Basin provides a unique opportunity to examine the nearly complete postcranial ecomorphology of an extinct species, and yields data that are important to studying paleoenvironments and human-environment interaction. With a comparative sample of extant African bovids, we used discriminant function analyses to develop statistical ecomorphological models for 18 skeletal elements and element portions. Forelimb and hindlimb element models overwhelmingly predict that R. atopocranion was an open-adapted taxon. However, the phalanges of Rusingoryx are remarkably short relative to their breadth, a morphology outside the range of extant African bovids, which we interpret as an extreme open-habitat adaptation. It follows that even recently extinct fossil bovids can differ in important morphological ways relative to their extant counterparts, particularly if they have novel adaptations for past environments. This unusual phalanx morphology (in combination with other skeletal indications), mesowear, and dental enamel stable isotopes, demonstrate that Rusingoryx was a grassland specialist. Together, these data are consistent with independent geological and paleontological evidence for increased aridity and expanded grassland habitats across the Lake Victoria Basin.

Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity

Background The increasing availability of microbial genomes and environmental shotgun metagenomes provides unprecedented access to the genomic differences within related bacteria. The human oral microbiome with its diverse habitats and abundant, relatively well-characterized microbial inhabitants presents an opportunity to investigate bacterial population structures at an ecosystem scale. Results Here, we employ a metapangenomic approach that combines public genomes with Human Microbiome Project (HMP) metagenomes to study the diversity of microbial residents of three oral habitats: tongue dorsum, buccal mucosa, and supragingival plaque. For two exemplar taxa, Haemophilus parainfluenzae and the genus Rothia, metapangenomes reveal distinct genomic groups based on shared genome content. H. parainfluenzae genomes separate into three distinct subgroups with differential abundance between oral habitats. Functional enrichment analyses identify an operon encoding oxaloacetate decarboxylase as diagnostic for the tongue-abundant subgroup. For the genus Rothia, grouping by shared genome content recapitulates species-level taxonomy and habitat preferences. However, while most R. mucilaginosa are restricted to the tongue as expected, two genomes represent a cryptic population of R. mucilaginosa in many buccal mucosa samples. For both H. parainfluenzae and the genus Rothia, we identify not only limitations in the ability of cultivated organisms to represent populations in their native environment, but also specifically which cultivar gene sequences are absent or ubiquitous. Conclusions Our findings provide insights into population structure and biogeography in the mouth and form specific hypotheses about habitat adaptation. These results illustrate the power of combining metagenomes and pangenomes to investigate the ecology and evolution of bacteria across analytical scales.

Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity

BackgroundThe increasing availability of microbial genomes and environmental shotgun metagenomes provides unprecedented access to the genomic differences within related bacteria. The human oral microbiome with its diverse habitats and abundant, relatively well-characterized microbial inhabitants presents an opportunity to investigate bacterial population structures at an ecosystem scale.ResultsHere, we employ a metapangenomic approach that combines public genomes with Human Microbiome Project (HMP) metagenomes to study the diversity of microbial residents of three oral habitats: tongue dorsum, buccal mucosa, and supragingival plaque. For two exemplar taxa, Haemophilus parainfluenzae and the genus Rothia, metapangenomes revealed distinct genomic groups based on shared genome content. H. parainfluenzae genomes separated into three distinct subgroups with differential abundance between oral habitats. Functional enrichment analyses identified an operon encoding oxaloacetate decarboxylase as diagnostic for the tongue-abundant subgroup. For the genus Rothia, grouping by shared genome content recapitulated species-level taxonomy and habitat preferences. However, while most R. mucilaginosa were restricted to the tongue as expected, two genomes represented a cryptic population of R. mucilaginosa in many buccal mucosa samples. For both H. parainfluenzae and the genus Rothia, we identified not only limitations in the ability of cultivated organisms to represent populations in their native environment, but also specifically which cultivar gene sequences were absent or ubiquitous.ConclusionsOur findings provide insights into population structure and biogeography in the mouth and form specific hypotheses about habitat adaptation. These results illustrate the power of combining metagenomes and pangenomes to investigate the ecology and evolution of bacteria across analytical scales.

Parasitoids (Hymenoptera) of leaf-spinning moths (Lepidoptera) feeding on Vaccinium uliginosum L. along an ecological gradient in central European peat bogs

Parasitoids of leaf-spinning Lepidoptera associated with two isolated central European peat bogs were investigated. Five families of parasitoid Hymenoptera (Braconidae, lchneumonidae, Eulophidae, Pteromalidae and Encyrtidae) were recorded. Three categories were recognised: (1) primary parasitoids, (2) facultative hyperparasitoids and (3) obligatory hyperparasitoids. Ten species of Braconidae, five species and seven marked morphospecies among lchneumonidae, and three species of Chalcidoidea were identified. Despite of some niche-specific (but less host-specific) parasitoids, all these hymenopterans are likely to be generalists and none of them were confirmed to be habitat and/or host specialists. Unlike their eurytopic (opportunistic tyrphoneutral) parasitoids, the Lepidoptera hosts associated with peat bogs are partially highly stenotopic (tyrphobionts and tyrphophiles). The occurrence of parasitoids compared to their potential hosts was structured along an ecological (mesoclimatic) gradient, so most parasitoids were recorded from margins while stenotopic (narrow habitat adaptation) moths were mostly distributed near the centre of the bog habitat.