Interspecific coexistence selects for variants enhancing mutualism and productivity. Paenibacillus amylolyticus strain variants
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ABSTRACT:
PROVIDER: PRJEB18991 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1795433.fastq.gz | Fastqsanger.gz | |||
| ERR1795433_1.fastq.gz | Fastqsanger.gz | |||
| ERR1795433_2.fastq.gz | Fastqsanger.gz | |||
| ERR1795434.fastq.gz | Fastqsanger.gz | |||
| ERR1795434_1.fastq.gz | Fastqsanger.gz |
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Project description:Interspecific coexistence selects for variants enhancing mutualism and productivity. Xanthomonas retroflexus strain variants.
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Project description:This is the supplementary material for "Slower-growing species promote interspecific cooperation and coexistence under acid stress through cross-feeding"
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Project description:All interactions between multiple species invading together (coinvasion) must be accounted for to predict species coexistence patterns across space. Mutualisms, particularly, are known to influence species' population dynamics and their invasive ability (e.g., mycorrhizal fungi with partner plants). Yet, while modeling coinvasion, their role in mediating coexistence is overlooked. Here, we build a spatially explicit model of coinvasion of two competing plant species with a shared fungal mutualist to study how mutualism and competition interact to shape the local and regional coexistence of competitors. We observe four main results. First, mutualist presence generates regional coexistence between competitors even when local coexistence between them is impossible. Second, increasing partner mutualist dispersal leads to abrupt changes in competitor coexistence outcomes. Third, differences in mutualist partner dependence and competitive ability interact to produce a variety of local and regional coexistence outcomes. Fourth, asymmetry in the dispersal ability arising from dependence-dispersal trade-offs leads to greater exclusion of species less dependent on mutualist partners for growth. In toto, incorporating mutualism-specific trait trade-offs and dispersal asymmetries into coinvasion models offers new insights into regional coexistence and invasive species distributions.
| S-EPMC11848128 | biostudies-literature
Project description:It is well known that bacteria often exist in naturally formed multispecies biofilms. Within these biofilms, interspecies interactions seem to play an important role in ecological processes. Little is known about the effects of interspecies interactions on gene expression in these multispecies biofilms. This study presents a comparative gene expression analysis of the Xanthomonas retroflexus transcriptome when grown in a single-species biofilm and in dual- and four-species consortia with Stenotrophomonas rhizophila, Microbacterium oxydans and Paenibacillus amylolyticus. The results revealed complex interdependent interaction patterns in the multispecies biofilms. Many of the regulated functions are related to interactions with the external environment and suggest a high phenotypic plasticity in response to coexistence with other species. Furthermore, the changed expression of genes involved in aromatic and branched chain amino acid biosynthesis suggests nutrient cross feeding as an contribution factor for the observed synergistic biofilm production when these four species coexists in a biofilm. X. retroflexus was cultivated in three replicates of single-species biofilm and combined with S. rhizophila, M. oxydans and P. amylolyticus in dual-species biofilms with three respective replicates. At last, we combined all four species in a multispecies biofilm with five replicates and conducted a RNA seq based comparative gene expression study utilizing the Illumina sequencing technology. Please note that the 'prodigal_all_new.txt' contains gene names (which are listed in the matrix_sum.txt) and their position in the genomes, which are included in the file 'all_contigs_500.fasta'.
2016-07-22 | E-GEOD-80267 | biostudies-arrayexpress
Project description:Interspecific mutualisms are often vulnerable to instability because low benefit : cost ratios can rapidly lead to extinction or to the conversion of mutualism to parasite-host or predator-prey interactions. We hypothesize that the evolutionary stability of mutualism can depend on how benefits and costs to one mutualist vary with the population density of its partner, and that stability can be maintained if a mutualist can influence demographic rates and regulate the population density of its partner. We test this hypothesis in a model of mutualism with key features of senita cactus (Pachycereus schottii)-senita moth (Upiga virescens) interactions, in which benefits of pollination and costs of larval seed consumption to plant fitness depend on pollinator density. We show that plants can maximize their fitness by allocating resources to the production of excess flowers at the expense of fruit. Fruit abortion resulting from excess flower production reduces pre-adult survival of the pollinating seed-consumer, and maintains its density beneath a threshold that would destabilize the mutualism. Such a strategy of excess flower production and fruit abortion is convergent and evolutionarily stable against invasion by cheater plants that produce few flowers and abort few to no fruit. This novel mechanism of achieving evolutionarily stable mutualism, namely interspecific population regulation, is qualitatively different from other mechanisms invoking partner choice or selective rewards, and may be a general process that helps to preserve mutualistic interactions in nature.
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Project description:According to apparent competition theory, sharing a predator should cause indirect interactions among prey that can affect the structure and the dynamics of natural communities. Though shifts in prey dominance and predator resource use along environmental gradients are rather common, empirical evidence on the role of indirect prey-prey interactions through shared predation particularly with increasing productivity, is still scarce. In an 8-week lake mesocosm experiment, we manipulated both the addition of inorganic nutrients and the presence of generalist fish predators (crucian carp, Carassius carassius L.), to test for the effects of indirect interactions through shared predation along a productivity gradient. We found that apparent mutualism (indirect positive interaction) between benthic and pelagic prey strongly affected short-term responses of aquatic food webs to increasing productivity in the presence of a generalist fish. Increasing productivity favoured the relative abundance of benthic prey, following trends in natural productive lake systems. This led to a shift in fish selectivity from pelagic to benthic prey driven by changes in fish behaviour, which resulted in apparent mutualism due to the lower and delayed top-down control of pelagic prey at increasing productivity. Our results show empirical evidence that the coupling of multiple production pathways can lead to strong indirect interactions through shared predation, whereby prey dynamics on short time-scales are highly dependent on the foraging behaviour of generalist predators. This mechanism may play an important role in short-term responses of food webs across environmental gradients.
| S-EPMC8048462 | biostudies-literature
Project description:Mutualistic interactions are taxonomically and functionally diverse. Despite their ubiquity, however, the basic ecological and evolutionary processes underlying their origin and maintenance are poorly understood. A major reason for this is the lack of an experimentally tractable model system. We examine the evolution of an experimentally imposed obligate mutualism between sulfate-reducing and methanogenic microorganisms that have no known history of previous interaction. Twenty-four independent pairings (cocultures) of the bacterium Desulfovibrio vulgaris and the archaeon Methanococcus maripaludis were established and followed for 300 community doublings in two environments, one allowing for the development of a heterogeneous distribution of resources and the other not. Evolved cocultures grew up to 80% faster and were up to 30% more productive (biomass yield per mole of substrate) than the ancestors. The evolutionary process was marked by periods of significant instability leading to extinction of two of the cocultures, but it resulted in more stable, efficient, and productive mutualisms for most replicated pairings. Comparisons of evolved cocultures with those assembled from one evolved mutualist and one ancestral mutualist showed that evolution of both species contributed to improved productivity. Surprisingly, however, overall improvements in growth rate and yield were less than the sum of the individual contributions, suggesting antagonistic interactions between mutations from the coevolved populations. Physical constraints on the transfer of metabolites in the evolution environment affected the evolution of M. maripaludis, but not of D. vulgaris. Together, these results demonstrate that challenges can imperil nascent obligate mutualisms and demonstrate the evolutionary responses that enable their persistence and future evolution.
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Project description:It is well known that bacteria often exist in naturally formed multispecies biofilms. Within these biofilms, interspecies interactions seem to play an important role in ecological processes. Little is known about the effects of interspecies interactions on gene expression in these multispecies biofilms. This study presents a comparative gene expression analysis of the Xanthomonas retroflexus transcriptome when grown in a single-species biofilm and in dual- and four-species consortia with Stenotrophomonas rhizophila, Microbacterium oxydans and Paenibacillus amylolyticus. The results revealed complex interdependent interaction patterns in the multispecies biofilms. Many of the regulated functions are related to interactions with the external environment and suggest a high phenotypic plasticity in response to coexistence with other species. Furthermore, the changed expression of genes involved in aromatic and branched chain amino acid biosynthesis suggests nutrient cross feeding as an contribution factor for the observed synergistic biofilm production when these four species coexists in a biofilm.
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Project description:Gibel carp (Carassius gibelio) is a cyprinid fish that originated in eastern Eurasia and is considered as invasive in European freshwater ecosystems. The populations of gibel carp in Europe are mostly composed of asexually reproducing triploid females (i.e., reproducing by gynogenesis) and sexually reproducing diploid females and males. Although some cases of coexisting sexual and asexual reproductive forms are known in vertebrates, the molecular mechanisms maintaining such coexistence are still in question. Both reproduction modes are supposed to exhibit evolutionary and ecological advantages and disadvantages. To better understand the coexistence of these two reproduction strategies, we performed transcriptome profile analysis of gonad tissues (ovaries), and studied the differentially expressed reproduction-associated genes in sexual and asexual females. We used high-throughput RNA sequencing to generate transcriptomic profiles of gonadal tissues of triploid asexual females and males, diploid sexual males and females of gibel carp, as well as diploid individuals from two closely-related species, C. auratus and Cyprinus carpio. Using SNP clustering, we showed the close similarity of C. gibelio and C. auratus with a basal position of C. carpio to both Carassius species. Using transcriptome profile analyses, we showed that many genes and pathways are involved in both gynogenetic and sexual reproduction in C. gibelio; however, we also found that 1500 genes, including 100 genes involved in cell cycle control, meiosis, oogenesis, embryogenesis, fertilization, steroid hormone signaling and biosynthesis were differently expressed in the ovaries of asexual and sexual females. We suggest that the overall downregulation of reproduction-associated pathways in asexual females, and their maintenance in sexual ones, allow for their stable coexistence, integrating the evolutionary and ecological advantages and disadvantages of the two reproductive forms. However, we showed that many sexual-reproduction-related genes are maintained and expressed in asexual females, suggesting that gynogenetic gibel carp retains the genetic toolkits for meiosis and sexual reproduction. These findings shed new light on the evolution of this asexual and sexual complex.
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