Genome Sequences of 11 Conspecific Streptomyces sp. Strains.
ABSTRACT: The genomes of 11 conspecific Streptomyces strains, i.e., from the same species and inhabiting the same ecological niche, were sequenced and assembled. This data set offers an ideal framework to assess the genome evolution of Streptomyces species in their ecological context.
Project description:The genomes of five Streptomyces strains belonging to the same soil community were sequenced and assembled. The strains, which were isolated at microscale, belonged to different Streptomyces species. This sample provides access to understand the functioning of a Streptomyces community in an ecological context.
Project description:Mammals kill both conspecific infants and adults. Whereas infanticide has been profusely studied, the killing of non-infants (adulticide) has seldom attracted the attention of researchers. Mammals kill conspecific adults by at least four, non-exclusive reasons: during intrasexual aggression for mating opportunities, to defend valuable resources, to protect their progeny and to prey upon conspecifics. In this study, we test which reason is most likely to explain male and female adulticide in mammals. For this, we recorded the presence of adulticide, the ecological and behavioural traits, and the phylogenetic relationship for more than 1000 species. Adulticide has been recorded in over 350 species from the most important Mammalian clades. Male adulticide was phylogenetically correlated with the presence of size dimorphism and intrasexually selected weapons. Female adulticide was phylogenetically associated with the occurrence of infanticide. These results indicate that the evolutionary pathways underlying the evolution of adulticide differ between sexes in mammals. Whereas males commit adulticide to increase breeding opportunities and to compete with other males for mating, females commit adulticide mainly to defend offspring from infanticidal conspecifics.
Project description:Forest community structure may be influenced by seedling density dependence, however, the effect is loosely coupled with population dynamics and diversity in the short term. In the long term the strength of conspecific density dependence may fluctuate over time because of seedling abundance, yet few long-term studies exist. Based on 11 years of seedling census data and tree census data from a 25-ha temperate forest plot in Northeast China, we used generalized linear mixed models to test the relative effects of local neighborhood density and abiotic factors on seedling density and seedling survival. Spatial point pattern analysis was used to determine if spatial patterns of saplings and juveniles, in relation to conspecific adults, were in accordance with patterns uncovered by conspecific negative density dependence at the seedling stage. Our long-term results showed that seedling density was mainly positively affected by conspecific density, suggesting dispersal limitation of seedling development. The probability of seedling survival significantly decreased over 1 year with increasing conspecific density, indicating conspecific negative density dependence in seedling establishment. Although there was variation in conspecific negative density dependence at the seedling stage among species and across years, a dispersed pattern of conspecific saplings relative to conspecific adults at the local scale (<10 m) was observed in four of the 11 species examined. Overall, sapling spatial patterns were consistent with the impacts of conspecific density on seedling dynamics, which suggests that conspecific negative density dependence is persistent over the long term. From the long-term perspective, conspecific density dependence is an important driver of species coexistence in temperate forests.
Project description:Social information use for decision-making is common and affects ecological and evolutionary processes, including social aggregation, species coexistence, and cultural evolution. Despite increasing ecological knowledge on social information use, very little is known about its genetic basis and therefore its evolutionary potential. Genetic variation in a trait affecting an individual's social and nonsocial environment may have important implications for population dynamics, interspecific interactions, and, for expression of other, environmentally plastic traits. We estimated repeatability, additive genetic variance, and heritability of the use of conspecific and heterospecific social cues (abundance and breeding success) for breeding site choice in a population of wild collared flycatchers Ficedula albicollis. Repeatability was found for two social cues: previous year conspecific breeding success and previous year heterospecific abundance. Yet, additive genetic variances for these two social cues, and thus heritabilities, were low. This suggests that most of the phenotypic variation in the use of social cues and resulting conspecific and heterospecific social environment experienced by individuals in this population stems from phenotypic plasticity. Given the important role of social information use on ecological and evolutionary processes, more studies on genetic versus environmental determinism of social information use are needed.
Project description:<h4>Background</h4>Antibiotic-producing Streptomyces bacteria are ubiquitous in nature, yet most studies of its diversity have focused on free-living strains inhabiting diverse soil environments and those in symbiotic relationship with invertebrates.<h4>Results</h4>We studied the draft genomes of 73 Streptomyces isolates sampled from the skin (wing and tail membranes) and fur surfaces of bats collected in Arizona and New Mexico. We uncovered large genomic variation and biosynthetic potential, even among closely related strains. The isolates, which were initially identified as three distinct species based on sequence variation in the 16S rRNA locus, could be distinguished as 41 different species based on genome-wide average nucleotide identity. Of the 32 biosynthetic gene cluster (BGC) classes detected, non-ribosomal peptide synthetases, siderophores, and terpenes were present in all genomes. On average, Streptomyces genomes carried 14 distinct classes of BGCs (range = 9-20). Results also revealed large inter- and intra-species variation in gene content (single nucleotide polymorphisms, accessory genes and singletons) and BGCs, further contributing to the overall genetic diversity present in bat-associated Streptomyces. Finally, we show that genome-wide recombination has partly contributed to the large genomic variation among strains of the same species.<h4>Conclusions</h4>Our study provides an initial genomic assessment of bat-associated Streptomyces that will be critical to prioritizing those strains with the greatest ability to produce novel antibiotics. It also highlights the need to recognize within-species variation as an important factor in genetic manipulation studies, diversity estimates and drug discovery efforts in Streptomyces.
Project description:Conspecific adults have strong negative effect on the survival of nearby early-stage seedlings and thus can promote species coexistence by providing space for the regeneration of heterospecifics. The leaf litter fall from the conspecific adults, and it could mediate this conspecific negative adult effect. However, field evidence for such effect of conspecific leaf litter remains absent. In this study, we used generalized linear mixed models to assess the effects of conspecific leaf litter on the early-stage seedling survival of four dominant species (Machilus leptophylla, Litsea elongate, Acer pubinerve and Distylium myricoides) in early-stage seedlings in a subtropical evergreen broad-leaved forest in eastern China. Our results consistently showed that the conspecific leaf litter of three species negatively affected the seedling survival. Meanwhile, the traditional conspecific adult neighborhood indices failed to detect this negative conspecific adult effect. Our study revealed that the accumulation of conspecific leaf litter around adults can largely reduce the survival rate of nearby seedlings. Ignoring it could result in underestimation of the importance of negative density dependence and negative species interactions in the natural forest communities.
Project description:Microbial diversity studies using small subunit (SSU) rRNA gene sequences continue to advance our understanding of biological and ecological systems. Although a good predictor of overall diversity, using this gene to infer the presence of a species in a sample is more controversial. Here, we present a detailed polyphasic analysis of 10 bacterial strains isolated from three coastal lichens Lichina confinis, Lichina pygmaea and Roccella fuciformis with SSU rRNA gene sequences identical to the type strain of Streptomyces cyaneofuscatus. This analysis included phenotypic, microscopic, genetic and genomic comparisons and showed that despite their identical SSU rRNA sequences the strains had markedly different properties, and could be distinguished as 5 different species. Significantly, secondary metabolites profiles from these strains were also found to be different. It is thus clear that SSU rRNA based operational taxonomy units, even at the most stringent cut-off can represent multiple bacterial species, and that at least for the case of Streptomyces, strain de-replication based on SSU gene sequences prior to screening for bioactive molecules can miss potentially interesting novel molecules produced by this group that is notorious for the production of drug-leads.
Project description:Negative interspecific mating interactions, known as reproductive interference, can hamper species coexistence in a local patch and promote niche partitioning or geographical segregation of closely related species. Conspecific sperm precedence (CSP), which occurs when females that have mated with both conspecific and heterospecific males preferentially use conspecific sperm for fertilization, might contribute to species coexistence by mitigating the costs of interspecific mating and hybridization. We discussed whether two species exhibiting CSP can coexist in a local environment in the presence of reproductive interference. First, using a behaviorally explicit mathematical model, we demonstrated that two species characterized by negative mating interactions are unlikely to coexist because the costs of reproductive interference, such as loss of mating opportunity with conspecific partners, are inevitably incurred when individuals of both species are present. Second, we experimentally examined differences in mating activity and preference in two <i>Harmonia</i> ladybird species known to exhibit CSP. These behavioral differences may lead to local extinction of <i>H. yedoensis</i> because of reproductive interference by <i>H. axyridis</i>. This prediction is consistent with field observations that <i>H. axyridis</i> uses various food sources and habitats whereas <i>H. yedoensis</i> is confined to a less preferred prey item and a pine tree habitat. Finally, by a comparative approach, we observed that niche partitioning or parapatric distribution, but not sympatric coexistence in the same habitat, is maintained between species with CSP belonging to a wide range of taxa, including vertebrates and invertebrates living in aquatic or terrestrial environments. Taken together, it is possible that reproductive interference may destabilize local coexistence even in closely related species that exhibit CSP.
Project description:UNLABELLED:We show that Streptomyces biogeography in soils across North America is influenced by the regional diversification of microorganisms due to dispersal limitation and genetic drift.Streptomyces spp. form desiccation-resistant spores, which can be dispersed on the wind, allowing for a strong test of whether dispersal limitation governs patterns of terrestrial microbial diversity. We employed an approach that has high sensitivity for determining the effects of genetic drift. Specifically, we examined the genetic diversity and phylogeography of physiologically similar Streptomyces strains isolated from geographically distributed yet ecologically similar habitats. We found that Streptomyces beta diversity scales with geographic distance and both beta diversity and phylogenetic diversity manifest in a latitudinal diversity gradient. This pattern of Streptomyces biogeography resembles patterns seen for diverse species of plants and animals, and we therefore evaluated these data in the context of ecological and evolutionary hypotheses proposed to explain latitudinal diversity gradients. The data are consistent with the hypothesis that niche conservatism limits dispersal, and historical patterns of glaciation have limited the time for speciation in higher-latitude sites. Most notably, higher-latitude sites have lower phylogenetic diversity, higher phylogenetic clustering, and evidence of range expansion from lower latitudes. In addition, patterns of beta diversity partition with respect to the glacial history of sites. Hence, the data support the hypothesis that extant patterns of Streptomyces biogeography have been driven by historical patterns of glaciation and are the result of demographic range expansion, dispersal limitation, and regional diversification due to drift. IMPORTANCE:Biogeographic patterns provide insight into the evolutionary and ecological processes that govern biodiversity. However, the evolutionary and ecological processes that govern terrestrial microbial diversity remain poorly characterized. We evaluated the biogeography of the genus Streptomyces to show that the diversity of terrestrial bacteria is governed by many of the same processes that govern the diversity of many plant and animal species. While bacteria of the genus Streptomyces are a preeminent source of antibiotics, their evolutionary history, biogeography, and biodiversity remain poorly characterized. The observations we describe provide insight into the drivers of Streptomyces biodiversity and the processes that underlie microbial diversification in terrestrial habitats.
Project description:In this work, by comparing genomes of closely related individuals of Streptomyces isolated at a spatial microscale (millimeters or centimeters), we investigated the extent and impact of horizontal gene transfer in the diversification of a natural Streptomyces population. We show that despite these conspecific strains sharing a recent common ancestor, all harbored significantly different gene contents, implying massive and rapid gene flux. The accessory genome of the strains was distributed across insertion/deletion events (indels) ranging from one to several hundreds of genes. Indels were preferentially located in the arms of the linear chromosomes (ca. 12 Mb) and appeared to form recombination hot spots. Some of them harbored biosynthetic gene clusters (BGCs) whose products confer an inhibitory capacity and may constitute public goods that can favor the cohesiveness of the bacterial population. Moreover, a significant proportion of these variable genes were either plasmid borne or harbored signatures of actinomycete integrative and conjugative elements (AICEs). We propose that conjugation is the main driver for the indel flux and diversity in Streptomyces populations.IMPORTANCE Horizontal gene transfer is a rapid and efficient way to diversify bacterial gene pools. Currently, little is known about this gene flux within natural soil populations. Using comparative genomics of Streptomyces strains belonging to the same species and isolated at microscale, we reveal frequent transfer of a significant fraction of the pangenome. We show that it occurs at a time scale enabling the population to diversify and to cope with its changing environment, notably, through the production of public goods.