Selective Forces Research Articles

Dissecting host-microbiome interaction effects on phytoplankton microbiome composition and diversity.

Phytoplankton and their associated microbiomes of heterotrophic bacteria are foundational to primary production, energy transfer, and biogeochemical cycling in aquatic systems. While it is known that these microbiomes are shaped by host-released dissolved organic matter (DOM), the extent to which dynamic phytoplankton-bacteria interactions shape bacterial community assembly remains to be examined. Here, we investigated the effects of two mechanisms in host-microbiome interactions on phytoplankton bacterial microbiome formation: (i) innate host selection and (ii) host-microbiome feedback. For the former, phytoplankton-produced DOM composition is based solely on the host's properties (species or physiological state); for the latter, the presence of the microbiome modifies host DOM production. The microbiome of Chlorella sorokiniana was extracted and exposed to six ratios of the two effects. We found that microbiome composition changed along with the six host-microbiome feedback versus innate host selection ratios, with the highest compositional distance between communities under the strongest and the weakest ratio of the two effects. This indicates that each mechanism selects for different bacterial species. In addition, our findings showed that when both selective forces were applied, it led to a higher community richness, while host-microbiome feedback alone reduces community evenness due to its strong species-specific selection.

Adaptive Evolution of Pseudomonas aeruginosa in Human Airways Shows Phenotypic Convergence Despite Diverse Patterns of Genomic Changes.

Selective forces in the environment drive bacterial adaptation to novel niches, choosing the fitter variants in the population. However, in dynamic and changing environments, the evolutionary processes controlling bacterial adaptation are difficult to monitor. Here, we follow 9 people with cystic fibrosis chronically infected with Pseudomonas aeruginosa, as a proxy for bacterial adaptation. We identify and describe the bacterial changes and evolution occurring between 15 and 35 yr of within-host evolution. We combine whole-genome sequencing, RNA sequencing, and metabolomics and compare the evolutionary trajectories directed by the adaptation of 4 different P. aeruginosa lineages to the lung. Our data suggest divergent evolution at the genomic level for most of the genes, with signs of convergent evolution with respect to the acquisition of mutations in regulatory genes, which drive the transcriptional and metabolomic program at late time of evolution. Metabolomics further confirmed convergent adaptive phenotypic evolution as documented by the reduction of the quorum-sensing molecules acyl-homoserine lactone, phenazines, and rhamnolipids (except for quinolones). The modulation of the quorum-sensing repertoire suggests that similar selective forces characterize at late times of evolution independent of the patient. Collectively, our data suggest that similar environments and similar P. aeruginosa populations in the patients at prolonged time of infection are associated with an overall reduction of virulence-associated features and phenotypic convergence.

Abstract PR006: Evolution of evolvability

Abstract The purpose of this work is to better understand how the rate of phenotypic adaptation of cells in a tumor affects its ability to survive treatment. Drug resistance is an ongoing problem for maintaining a sustained response in treating advanced cancers. Regardless of their lineage, heritable phenotypic adaptions may be beneficial for the tumor to survive stepwise changes in the environment during tumor growth. There may be further benefit for cells to develop the trait of being adaptable - to respond to large shifts in the microenvironment, survive metastasis to a new organ, and thrive when treatments are applied. Genomic instability and phenotypic redundancy may aid in adaptations, but there may be limits. With too much mutation and deviation from the parental phenotype, cells lose important regulatory and maintenance functions necessary to survive. So is there an optimal rate of evolvability? We use an off-lattice agent-based model to investigate how the rate of change through phenotypic trait space affects tumor growth and response to treatment. We assign cells with different combinations of proliferation rates and migration speeds and test how the variance from the parental cell on division affects the selection of trait combinations over time. During growth, heterogeneity is gained quickly and space matters less if evolvability is forced to continually increase, but there is more selection for proliferative phenotypes and slower evolvability if its rate is allowed to drift freely. We found that tradeoffs generally imposed a greater selection force leading to faster recurrence and the coexistence of proliferation or migration specialists. We compared responses to continuous, intermittent, and adaptive treatment schedules of an anti-proliferative drug. At some point with treatment, there is an optimal evolvability, as larger increases in diversity allows for cells to fall back into a sensitive state and be killed by treatment. We aim to design better treatment strategies that work for tumors with different levels of evolvability by understanding how the rate of tumor evolution affects growth and treatment response. Citation Format: Jill A. Gallaher, Maximilian Strobl, Jeffrey West, Mark Roberston-Tessi, Alexander R. A. Anderson. Evolution of evolvability [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr PR006.

Ecologically mediated differences in electric organ discharge drive evolution in a sodium channel gene in South American electric fishes.

Active electroreception-the ability to detect objects and communicate with conspecifics via the detection and generation of electric organ discharges (EODs)-has evolved convergently in several fish lineages. South American electric fishes (Gymnotiformes) are a highly species-rich group, possibly in part due to evolution of an electric organ (EO) that can produce diverse EODs. Neofunctionalization of a voltage-gated sodium channel gene accompanied the evolution of electrogenic tissue from muscle and resulted in a novel gene (scn4aa) uniquely expressed in the EO. Here, we investigate the link between variation in scn4aa and differences in EOD waveform. We combine gymnotiform scn4aa sequences encoding the C-terminus of the Nav1.4a protein, with biogeographic data and EOD recordings to test whether physiological transitions among EOD types accompany differential selection pressures on scn4aa. We found positive selection on scn4aa coincided with shifts in EOD types. Species that evolved in the absence of predators, which likely selected for reduced EOD complexity, exhibited increased scn4aa evolutionary rates. We model mutations in the protein that may underlie changes in protein function and discuss our findings in the context of gymnotiform signalling ecology. Together, this work sheds light on the selective forces underpinning major evolutionary transitions in electric signal production.

Thermal limits along tropical elevational gradients: Poison frog tadpoles show plasticity but maintain divergence across elevation

Temperature is arguably one of the most critical environmental factors impacting organisms at molecular, organismal, and ecological levels. Temperature variation across elevation may cause divergent selection in physiological critical thermal limits (CTMAX and CTMIN). Generally, high elevation populations are predicted to withstand lower environmental temperatures than low elevation populations. Organisms can also exhibit phenotypic plasticity when temperature varies, although theory and empirical evidence suggest that tropical ectotherms have relatively limited ability to acclimate. To study the effect of temperature variation along elevational transects on thermal limits, we measured CTMAX and CTMIN of 934 tadpoles of a poison frog species, Epipedobates anthonyi, along two elevational gradients (200–1700 m asl) in southwestern Ecuador to investigate their thermal tolerance across elevation. We also tested if tadpoles could plastically shift their critical thermal limits in response to exposure to different temperatures representing the range of temperatures they experience in nature (20 °C, 24 °C, and 28 °C). Overall, we found that CTMAX did not change across elevation. In contrast, CTMIN was lower at higher elevations, suggesting that elevational variation in temperature influences this thermal trait. Moreover, all populations shifted their CTMAX and CTMIN according to treatment temperatures, demonstrating an acclimation response. Overall, trends in CTMIN among high, mid, and low elevation populations were maintained despite plastic responses to treatment temperature. These results demonstrate that, for tadpoles of E. anthonyi across tropical elevational gradients, temperature acts as a selective force for CTMIN, even when populations show acclimation abilities in both, CTMAX and CTMIN. Our findings advance our understanding on how environmental variation affects organisms’ evolutionary trajectories and their abilities to persist in a changing climate in a tropical biodiversity hotspot.

Habitat complexity influences neuron number in six species of Puerto Rican Anolis.

Elucidating the selective forces shaping the diversity of vertebrate brains continues to be a major area of inquiry, particularly as it relates to cognition. Historically brain evolution was interpreted through the lens of relative brain size; however, recent evidence has challenged this approach. Investigating neuroanatomy at a finer scale, such as neuron number, can provide new insights into the forces shaping brain evolution in the context of information processing capacity. Ecological factors, such as the complexity of a species' habitat, place demands on cognition that could shape neuroanatomy. In this study, we investigate the relationship between neuron number and habitat complexity in three brain regions across six closely related anole species from Puerto Rico. After controlling for brain mass, we found that the number of neurons increased with habitat complexity across species in the telencephalon and 'rest of the brain,' but not in the cerebellum. Our results demonstrate that habitat complexity has shaped neuroanatomy in the Puerto Rican anole radiation and provide further evidence of the role of habitat complexity in vertebrate brain evolution.

Abstract A027: Detecting and modeling frequency-dependent evolution in serially passaged primary triple negative breast cancer patient derived xenografts

Abstract Tumor evolution is a contributing factor to most failed cancer treatments. The intratumor heterogeneity of cellular phenotypes found in the tumor microenvironment acts as an evolutionary substate for cancer cells during tumorigenesis, subsequent growth, and after the patient is in the clinic. Selective forces imposed by certain medications can cause the emergence of a tumor with a resistant phenotype. Chemotherapies that target rapidly dividing cells will select for slower dividing ones which are less sensitive to such agents. However, many selective pressures acting on the tumor microenvironment are yet to be elucidated. For example, the effect one cancer cell has on another’s growth through competitive (i.e., the struggle for resources) or cooperative (e.g., exchange of growth factors) interactions remains poorly understood. Our central hypothesis is that cancer cells with distinct karyotypes will have a varying growth rate influenced by the karyotype landscape of the entire tumor. That is, we expect the fitness of a cancer cell to be largely determined by its karyotype and the karyotypes of its neighbors. Thus, we predict that frequency-dependent selection has a significant impact on clonal evolution in cancer. To test this, we have developed two novel methods for respectively identifying likely instances of frequency-dependent selection and modeling the long-term evolutionary trajectory in such cases. To detect frequency-dependent effects, we investigate the relationship between the frequency of one clone and the growth rate of all others (including itself). If a statistically significant correlation can be found, we proceed to modeling clonal evolution. To do this, we use a penalized least squares method and find the best-fitting parameterization of the replicator equation to the clonally resolved frequency data. This provides us with a payoff matrix describing the intensity of competition between each pair of clones. Furthermore, it allows us to model the long-term evolutionary dynamics of the tumor and to make predictions regarding co-existence of clones or clonal sweeps. Recently, investigators serially passaged primary triple negative breast cancer (TNBC) patient derived xenograft (PDX) tumors in NRG mice for over a year, inferring clonal frequencies at multiple timepoints using single cell whole genome (scWGS) and RNA sequencing (scRNA-seq). From this data, we were able to detect statistically significant frequency-dependent effects in the majority of serially passaged PDX tumors. Of these, most are predicted to result in a clonal sweep. Three of the PDX tumors were treated with cisplatin which revealed clone-specific drug response. This presents an opportunity for adaptive therapy scheduling which takes advantage of fitness tradeoffs under different contexts. A greater understanding of the effects frequency-dependent selection has on tumor evolution will contribute to the design of therapies intended to preclude or delay the emergence of resistance to treatment. Citation Format: Thomas A. Veith, Richard Beck, Noemi Andor. Detecting and modeling frequency-dependent evolution in serially passaged primary triple negative breast cancer patient derived xenografts [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr A027.

Comammox and unknown ammonia oxidizers contribute to nitrite accumulation in an integrated A-B stage process that incorporates side-stream EBPR (S2EBPR)

A novel integrated pilot-scale A-stage high rate activated sludge, B-stage short-cut biological nitrogen removal and side-stream enhanced biological phosphorus removal (A/B-shortcut N-S2EBPR) process for treating municipal wastewater was demonstrated with the aim to achieve simultaneous and carbon- and energy-efficient N and P removal. In this studied period, an average of 7.62 ± 2.17 mg-N/L nitrite accumulation was achieved through atypical partial nitrification without canonical known NOB out-selection. Network analysis confirms the central hub of microbial community as Nitrospira, which was one to two orders of magnitude higher than canonical aerobic oxidizing bacteria (AOB) in a B-stage nitrification tank. The contribution of comammox Nitrospira as AOB was evidenced by the increased amoB/nxr ratio and higher ammonia oxidation activity. Furthermore, oligotyping analysis of Nitrospira revealed two dominant sub-clusters (microdiveristy) within the Nitrospira. The relative abundance of oligotype II, which is phylogenetically close to Nitrospira_midas_s_31566, exhibited a positive correlation with nitrite accumulation in the same operational period, suggesting its role as comammox Nitrospira. Additionally, the phylogenetic investigation suggested that heterotrophic organisms from the family Comamonadacea and the order Rhodocyclaceae embedding ammonia monooxygenase and hydroxylamine oxidase may function as heterotrophic nitrifiers. This is the first study that elucidated the impact of integrating the S2EBPR on nitrifying populations with implications on short-cut N removal. The unique conditions in the side-stream reactor, such as low ORP, favorable VFA concentrations and composition, seemed to exert different selective forces on nitrifying populations from those in conventional biological nutrient removal processes. The results provide new insights for integrating EBPR with short-cut N removal process for mainstream wastewater treatment.

Effects of selfing on the evolution of sexual reproduction.

Plants exhibit diverse breeding systems, with populations capable of outcrossing, selfing, and/or asexual reproduction. However, interactions between the three reproductive pathways remain not fully clear. Sexual reproduction introduces segregation and recombination, but incurs several costs. Selfing can affect the relative costs and benefits of sexual vs. asexual reproduction. Building population genetic models, I explore how selfing affects the evolution of a sexual reproduction rate modifier via (a) indirect selection due to segregation, (b) indirect selection from changes in recombination rates, and (c) selection from the cost of meiosis and mate limitation. The dominant selective force mediating the evolution of sex is found to vary with the rate of sexual reproduction and selfing, but selective force (a) and (c) are generally stronger than selective force (b). A modifier enhancing sexual reproduction tends to be favored by indirect selection generated by partially recessive, small-effect deleterious mutations, while hindered by highly recessive lethal mutations. Overall, evolution toward higher sexual reproduction is hindered at low sexual reproduction rates and intermediate selfing rates, but favored under high selfing rates. The results suggest that asexual reproduction may precede the evolution of selfing and offer insights into the evolution of mechanisms reducing geitonogamy in partially clonal populations.

Disentangling agglomeration economies from selection under policy distortions in China

ABSTRACT This paper explores the competing sources of productivity gains observed in China’s urban agglomerations focusing on three pillar industries: agro-food processing, textiles and electronics. The main results reveal that the higher aggregate productivity observed in denser Chinese cities is driven by both agglomeration and selection forces. Subsequent analysis shows that industrial support policies help to mitigate the selection penalty, but come at the expense of reducing agglomeration benefits. Complementing the city-level analysis, we estimate dynamic and distributive firm-level panel data models to explore the policy rationale of propping up inefficient firms, despite creating a less competitive environment. The micro-based results reveal that inefficient firms targeted by industrial support policies benefit from productivity spillovers in denser cities, mainly in the electronics industry, providing some policy rationale for keeping them in the market.

HIV Expression in Infected T Cell Clones.

The principal barrier to an HIV-1 cure is the persistence of infected cells harboring replication-competent proviruses despite antiretroviral therapy (ART). HIV-1 transcriptional suppression, referred to as viral latency, is foremost among persistence determinants, as it allows infected cells to evade the cytopathic effects of virion production and killing by cytotoxic T lymphocytes (CTL) and other immune factors. HIV-1 persistence is also governed by cellular proliferation, an innate and essential capacity of CD4+ T cells that both sustains cell populations over time and enables a robust directed response to immunological threats. However, when HIV-1 infects CD4+ T cells, this capacity for proliferation can enable surreptitious HIV-1 propagation without the deleterious effects of viral gene expression in latently infected cells. Over time on ART, the HIV-1 reservoir is shaped by both persistence determinants, with selective forces most often favoring clonally expanded infected cell populations harboring transcriptionally quiescent proviruses. Moreover, if HIV latency is incomplete or sporadically reversed in clonal infected cell populations that are replenished faster than they are depleted, such populations could both persist indefinitely and contribute to low-level persistent viremia during ART and viremic rebound if treatment is withdrawn. In this review, select genetic, epigenetic, cellular, and immunological determinants of viral transcriptional suppression and clonal expansion of HIV-1 reservoir T cells, interdependencies among these determinants, and implications for HIV-1 persistence will be presented and discussed.

Deterministic and stochastic processes generating alternative states of microbiomes.

The structure of microbiomes is often classified into discrete or semi-discrete types potentially differing in community-scale functional profiles. Elucidating the mechanisms that generate such "alternative states" of microbiome compositions has been one of the major challenges in ecology and microbiology. In a time-series analysis of experimental microbiomes, we here show that both deterministic and stochastic ecological processes drive divergence of alternative microbiome states. We introduced species-rich soil-derived microbiomes into eight types of culture media with 48 replicates, monitoring shifts in community compositions at six time points (8 media × 48 replicates × 6 time points = 2304 community samples). We then confirmed that microbial community structure diverged into a few state types in each of the eight medium conditions as predicted in the presence of both deterministic and stochastic community processes. In other words, microbiome structure was differentiated into a small number of reproducible compositions under the same environment. This fact indicates not only the presence of selective forces leading to specific equilibria of community-scale resource use but also the influence of demographic drift (fluctuations) on the microbiome assembly. A reference-genome-based analysis further suggested that the observed alternative states differed in ecosystem-level functions. These findings will help us examine how microbiome structure and functions can be controlled by changing the "stability landscapes" of ecological community compositions.

Body size shift in sympatric insects in response to distinct selective forces in fragmented urban environments

AbstractPhenotypic plasticity, which encompasses the diversification of both irreversible and reversible traits, has long been considered an adaptive response by animals to varying environmental conditions. However, the process by which irreversible and reversible traits are coordinated to form an adaptive response to the changing environment has yet to be clarified. Here, we investigated the variation in body size of two urban insect species in the context of habitat fragmentation. These species were the Chinese cricket Gryllus chinensis and the stove grasshopper Diestrammena japonica, which are sympatric in urban housing estates. Results indicated that both species changed in body size in patches of urban environment. However, their body size shifts showed opposite tendencies and were influenced by distinct selective forces: Chinese crickets increased their body size with the patch history and predation risk, whereas stove grasshoppers decreased their body size with the degree of fragmentation of the patches. Territorial and competitive Chinese crickets rarely experience resource scarcity during urban environment fragmentation. Thus, a larger body size was preferred in response to intraspecific competition among Chinese crickets. By contrast, stove grasshoppers are group‐living and scramble for resources as competitors, requiring a large territory to secure adequate food for supporting a group of individuals. Consequently, stove grasshoppers frequently experienced resource scarcity in the patchy habitat, favoring small body size to reduce individual requirements throughout the life cycle. Our findings indicate that the body size shift of sympatric insects may be subjected to distinct selective forces in fragmented habitats, depending primarily on their reversible traits.

Inter- and intraspecific female behavioral plasticity drive temporal niche segregation in two Tribolium species

Abstract Temporal niche segregation is a way to reduce competition over shared resources. Species with overlapping spatial niches often show plasticity and can use different activity times to minimize competition with and disturbance by other species. In many granivores, especially those living in their food resources, there is low competition over food, but other selective forces can drive distinct temporal activity times. Reproductive interference, that is, the interaction between individuals of different species during mate acquisition, can be such a driving force. Reproductive interference is a strong driving force for niche segregation between the co-occurring flour beetles Tribolium castaneum and Tribolium confusum (Coleoptera: Tenebrionidae). Nevertheless, most studies on Tribolium spp. evaluated other selective forces, such as resource competition, which are potentially weaker. Here, we aimed to characterize the species’ peak activity time and its plasticity when exposed to a possible reproductive interference cue. We used a synthetic aggregative pheromone, shared by both species, as a cue for potential reproductive interference. We compared temporal niche plasticity between the sexes because reproductive interference is known mainly to reduce the female’s fitness. We found that both species’ activity times were hard-wired to an endogenous clock and that the sexes differed in their peak activity time and activity level. However, once exposed to the aggregation pheromone, only females shifted their activity time to match that of conspecific males, hence expressing more plasticity than the males to reduce Reproductive interference. These findings suggest an important role of the aggregation pheromone in the process of niche segregation.

Do sympatric catfish radiations in Lake Tanganyika show eco-morphological diversification?

Abstract Adaptive radiation is characterized by eco-morphological differentiation, in which niche partitioning has been shown to be a central response to natural selection during the diversification of animal clades. This process is suggested to have generated the exceptional biodiversity in the East African rift lakes; however, aside from the cichlid fishes, the nature of the divergence, over time, or among species is less clear in the other radiations. To address this, we focus on two distantly related sympatric Lake Tanganyika catfish clades, the genus Synodontis, considered to be Müllerian mimics, and the subfamily Claroteinae. We investigate to what extent, if any, these radiations have undergone eco-morphological diversification. We place these radiations in a common phylogenetic context, and test for morphological divergence and trophic niche partitioning using novel trait data and stable isotope signatures. Diversification of both catfish clades was recent, with the Synodontis radiation synchronized in time with individual genera within the claroteine radiation, suggesting initial diversification was facilitated by lake basin dynamics and/or lake level fluctuations. There is evidence for eco-morphological diversification within the claroteine radiation, as inferred from observed morphological disparity and divergence in diet both between and within genera; however, several species show significant overlap in dietary isotopic signatures. In contrast, the Synodontis radiation has greater overlap between taxa both in morphology and in isotopic signatures potentially indicating niche conservatism, suggesting different selective forces may be driving these radiations.

Exploring Sexual Morphisms in Pigeon Breeds and Doves: Selection Forces and Ecological Significance

Exploring Sexual Morphisms in Pigeon Breeds and Doves: Selection Forces and Ecological Significance

Invasions eliminate the legacy effects of substrate history on microbial nitrogen cycling

AbstractChanges in substrate quality driven by climate, land use, or other forms of global change may represent a strong selective force on microbial communities. Invasion of new taxa into a community through dispersal, evolution, or recolonization could impact the outcome of this environmental selection. Here, we simulated substrate change with a trait‐based model of microbial litter decomposition (DEMENTpy) to assess the legacy effects of past substrate quality and the impact of selection by a new substrate on community decomposition activity. Simulations were run with different levels of invasion, including invasion from communities long‐adapted to the new substrate. Legacy effects were evident with substrate change for native communities differing in composition. Protein was the only substrate that exerted a strong enough selective force to affect community composition. Legacy effects disappeared when invaders came from substrates similar to the new substrate. Together, our simulations demonstrate that substrate quality changes associated with global change can lead to legacy effects on substrate degradation. In decomposing plant litter, such legacy effects can occur if substrate inputs shift to higher protein content and if invasion is low.

Bare parts in the Galliformes: the evolution of a multifunctional structure.

A morphological trait can have multiple functions shaped by varying selective forces. Bare parts in birds, such as wattles, casques and combs, are known to function in both signalling and thermoregulation. Studies have demonstrated such structures are targets of sexual selection via female choice in several species of Galliformes (junglefowl, turkeys and grouse), though other studies have shown some role in thermoregulation (guineafowl). Here, we tested fundamental hypotheses regarding the evolution and maintenance of bare parts in Galliformes. Using a phylogeny that included nearly 90% of species in the order, we evaluated the role of both sexual and natural selection in shaping the function of bare parts across different clades. We found a combination of both environmental and putative sexually selected traits strongly predicted the variation of bare parts for both males and females across Galliformes. When the analysis is restricted to the largest family, Phasianidae (pheasants, junglefowl and allies), sexually selected traits were the primary predictors of bare parts. Our results suggest that bare parts are important for both thermoregulation and sexual signalling across Galliformes but are primarily under strong sexual selection within the Phasianidae.

Revisiting the role of Acinetobacter spp. in side-stream enhanced biological phosphorus removal (S2EBPR) systems

We piloted the incorporation of side-stream enhanced biological phosphorus removal (S2EBPR) with A/B stage short-cut nitrogen removal processes to enable simultaneous carbon-energy-efficient nutrients removal. This unique configuration and system conditions exerted selective force on microbial populations distinct from those in conventional EBPR. Interestingly, effective P removal was achieved with the predominance of Acinetobacter (21.5 ± 0.1 %) with nearly negligible level of known conical PAOs (Ca. Accumulibacter and Tetrasphaera were 0.04 ± 0.10 % and 0.47 ± 0.32 %, respectively). Using a combination of techniques, such as fluorescence in situ hybridization (FISH) coupled with single cell Raman spectroscopy (SCRS), the metabolic tracing of Acinetobacter-like cells exerted PAO-like phenotypic profiling. In addition, comparative metagenomics analysis of the closely related Acinetobacter spp. revealed the EBPR relevant metabolic pathways. Further oligotyping analysis of 16s rRNA V4 region revealed sub-clusters (microdiversity) of the Acinetobacter and revealed that the sub-group (oligo type 1, identical (100 % alignment identity) hits from Acinetobacter_midas_s_49494, and Acinetobacter_midas_s_55652) correlated with EBPR activities parameters, provided strong evidence that the identified Acinetobacter most likely contributed to the overall P removal in our A/B-shortcut N-S2EBPR system. To the best of our knowledge, this is the first study to confirm the in situ EBPR activity of Acinetobacter using combined genomics and SCRS Raman techniques. Further research is needed to identify the specific taxon, and phenotype of the Acinetobacter that are responsible for the P-removal.

Two distinct Fusarium graminearum populations colonized European wheat in the past two decades.

Fusarium graminearum is the main causal agent of Fusarium head blight (FHB) disease in wheat in Europe. To reveal population structure and to pinpoint genetic targets of selection we studied genomes of 96 strains of F. graminearum using population genomics. Bayesian and phylogenomic analyses indicated that the F. graminearum emergence in Europe could be linked to two independently evolving populations termed here as East European (EE) and West European (WE) population. The EE strains are primarily prevalent in Eastern Europe, but to a lesser extent also in western and southern areas. In contrast, the WE population appears to be endemic to Western Europe. Both populations evolved in response to population-specific selection forces, resulting in distinct localized adaptations that allowed them to migrate into their environmental niche. The detection of positive selection in genes with protein/zinc ion binding domains, transcription factors and in genes encoding proteins involved in transmembrane transport highlights their important role in driving evolutionary novelty that allow F. graminearum to increase adaptation to the host and/or environment. F. graminearum also maintained distinct sets of accessory genes showing population-specific conservation. Among them, genes involved in host invasion and virulence such as those encoding proteins with high homology to tannase/feruloyl esterase and genes encoding proteins with functions related to oxidation-reduction were mostly found in the WE population. Our findings shed light on genetic features related to microevolutionary divergence of F. graminearum and reveal relevant genes for further functional research aiming at better control of this pathogen.