The keystone zooplankton Daphnia magna has recently been used as a model system for understanding host-microbiota interactions. However, the bacterial species present and functions associated with ...their genomes are not well understood. In order to understand potential functions of these species, we combined 16S rRNA sequencing and shotgun metagenomics to characterize the whole-organism microbiota of Daphnia magna. We assembled five potentially novel metagenome-assembled genomes (MAGs) of core bacteria in Daphnia magna. Genes involved in host colonization and immune system evasion were detected across the MAGs. Some metabolic pathways were specific to some MAGs, including sulfur oxidation, nitrate reduction, and flagellar assembly. Amino acid exporters were identified in MAGs identified as important for host fitness, and pathways for key vitamin biosynthesis and export were identified across MAGs. In total, our examination of functions in these MAGs shows a diversity of nutrient acquisition and metabolism pathways present that may benefit the host, as well as genomic signatures of host association and immune system evasion.
Host-associated microbial communities are impacted by external and within-host factors, i.e., diet and feeding behavior. For organisms known to have a circadian rhythm in feeding behavior, microbiome ...composition is likely impacted by the different rates of microbe introduction and removal across a daily cycle, in addition to any diet-induced changes in microbial interactions. Here, we measured feeding behavior and used 16S rRNA sequencing to compare the microbial community across a diel cycle in two distantly related species of Daphnia, that differ in their life history traits, to assess how daily feeding patterns impact microbiome composition. We find that Daphnia species reared under similar laboratory conditions have significantly different microbial communities. Additionally, we reveal that Daphnia have daily differences in their microbial composition that correspond with feeding behavior, such that there is greater microbiome diversity at night during the host's active feeding phase. These results highlight that zooplankton microbiomes are relatively distinct and are likely influenced by host phylogeny.
Abstract
Chronic antibiotic exposure impacts host health through changes to the microbiome. The detrimental effects of antibiotic perturbation on microbiome structure and function after one host ...generation of exposure have been well-studied, but less is understood about multigenerational effects of antibiotic exposure and subsequent recovery. In this study, we examined microbiome composition and host fitness across five generations of exposure to antibiotics in the model zooplankton host Daphnia magna. By utilizing a split-brood design where half of the offspring from antibiotic-exposed parents were allowed to recover and half were maintained in antibiotics, we examined recovery and resilience of the microbiome. Unexpectedly, we discovered that isolation of single host individuals across generations exerted a strong effect on microbiome composition, with microbiome diversity decreasing over generations regardless of treatment, while host body size and cumulative reproduction increased across generations. Though antibiotics did cause substantial changes to microbiome composition within a generation, recovery generally occurred in one generation regardless of the number of prior generations spent in antibiotics. Our results demonstrate that isolation of individual hosts leads to stochastic extinction of less abundant taxa in the microbiome, suggesting that these taxa are likely maintained via transmission in host populations.
Multiple generations of isolation and antibiotic exposure both change host fitness and microbiome composition, with isolation unexpectedly benefitting several host fitness metrics.
The application of road deicing salts has led to the salinization of freshwater ecosystems in northern regions worldwide. Increased chloride concentrations in lakes, streams, ponds, and wetlands may ...negatively affect freshwater biota, potentially threatening ecosystem services. In an effort to reduce the effects of road salt, operators have increased the use of salt alternatives, yet we lack an understanding of how these deicers affect aquatic communities. We examined the direct and indirect effects of the most commonly used road salt (NaCl) and a proprietary salt mixture (NaCl, KCl, MgCl2), at three environmentally relevant concentrations (150, 470, and 780 mg Cl−/L) on freshwater wetland communities in combination with one of three biotic stressors (control, predator cues, and competitors). The communities contained periphyton, phytoplankton, zooplankton, and two tadpole species (American toads, Anaxyrus americanus; wood frogs, Lithobates sylvaticus). Overall, we found the two road salts did not interact with the natural stressors. Both salts decreased pH and reduced zooplankton abundance. The strong decrease in zooplankton abundance in the highest NaCl concentration caused a trophic cascade that resulted in increased phytoplankton abundance. The highest NaCl concentration also reduced toad activity. For the biotic stressors, predatory stress decreased whereas competitive stress increased the activity of both tadpole species. Wood frog survival, time to metamorphosis, and mass at metamorphosis all decreased under competitive stress whereas toad time to metamorphosis increased and mass at metamorphosis decreased. Road salts and biotic stressors can both affect freshwater communities, but their effects are not interactive.
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•Effects of road salts and biotic stressors were examined using aquatic communities.•Increased concentrations of both salt types reduced zooplankton abundance and pH.•High NaCl concentrations reduced American toad tadpole activity.•High NaCl concentrations caused a trophic cascade, resulting in more phytoplankton.•No interactive effects of road salts and biotic stressors were observed.
The direct and indirect effects of road salts reported are important for management and conservation efforts given the salinization of freshwater systems following winter road maintenance.
Host-associated microbes contribute to host fitness, but it is unclear whether these contributions are from rare keystone taxa, numerically abundant taxa, or interactions among community members. ...Experimental perturbation of the microbiota can highlight functionally important taxa; however, this approach is primarily applied in systems with complex communities where the perturbation affects hundreds of taxa, making it difficult to pinpoint contributions of key community members. Here, we use the ecological model organism
to examine the importance of rare and abundant taxa by perturbing its relatively simple microbiota with targeted antibiotics. We used sublethal antibiotic doses to target either rare or abundant members across two temperatures and then measured key host life history metrics and shifts in microbial community composition. We find that removal of abundant taxa had greater impacts on host fitness than did removal of rare taxa and that the abundances of nontarget taxa were impacted by antibiotic treatment, suggesting that no rare keystone taxa exist in the
microbiota but that microbe-microbe interactions may play a role in host fitness. We also find that microbial community composition was impacted by antibiotics differently across temperatures, indicating that ecological context shapes within-host microbial responses and effects on host fitness.
Understanding the contributions of rare and abundant taxa to host fitness is an outstanding question in host microbial ecology. In this study, we use the model zooplankton
and its relatively simple cohort of bacterial taxa to disentangle the roles of distinct taxa in host life history metrics, using a suite of antibiotics to selectively reduce the abundance of functionally important taxa. We also examine how environmental context shapes the importance of these bacterial taxa in host fitness.
ABSTRACT Host-associated microbes contribute to host fitness, but it is unclear whether these contributions are from rare keystone taxa, numerically abundant taxa, or interactions among community ...members. Experimental perturbation of the microbiota can highlight functionally important taxa; however, this approach is primarily applied in systems with complex communities where the perturbation affects hundreds of taxa, making it difficult to pinpoint contributions of key community members. Here, we use the ecological model organism Daphnia magna to examine the importance of rare and abundant taxa by perturbing its relatively simple microbiota with targeted antibiotics. We used sublethal antibiotic doses to target either rare or abundant members across two temperatures and then measured key host life history metrics and shifts in microbial community composition. We find that removal of abundant taxa had greater impacts on host fitness than did removal of rare taxa and that the abundances of nontarget taxa were impacted by antibiotic treatment, suggesting that no rare keystone taxa exist in the Daphnia magna microbiota but that microbe-microbe interactions may play a role in host fitness. We also find that microbial community composition was impacted by antibiotics differently across temperatures, indicating that ecological context shapes within-host microbial responses and effects on host fitness. IMPORTANCE Understanding the contributions of rare and abundant taxa to host fitness is an outstanding question in host microbial ecology. In this study, we use the model zooplankton Daphnia magna and its relatively simple cohort of bacterial taxa to disentangle the roles of distinct taxa in host life history metrics, using a suite of antibiotics to selectively reduce the abundance of functionally important taxa. We also examine how environmental context shapes the importance of these bacterial taxa in host fitness.
The microorganisms living on and in hosts, collectively known as the microbiome, significantly impact host life history through a wide range of functions. While it is often assumed that abundant taxa ...contribute more functional benefits to their hosts, rare keystone taxa can also have significant impacts on host fitness. In my research, I sought to understand the functional roles of abundant and rare taxa in the microbiome of the model zooplankton species Daphnia magna, as its simple microbiome and experimental tractability readily allowed for microbiome manipulation and characterization of functionally relevant taxa.To unravel the functions of Daphnia magna-associated bacteria, I first address how we understand transmission of beneficial host-associated taxa from colonized hosts to naïve hosts in Chapter 1, as transmission is a critical component of functional relationships among hosts and microbes. I then ask what species and functions were present in the Daphnia magna microbiome, using short-read metagenome sequencing to assemble and profile metagenome-assembled genomes of abundant and rare species (Chapter 2). Next, I manipulate the Daphnia magna microbiome with antibiotics to suppress different classes of the microbiome and measured host fitness outcomes (Chapter 3). In Chapter 4, I explore the impacts of 5 generations of antibiotic exposure and isolation on microbiome composition and host fitness. Finally, I expand the effect of isolation discovered in Chapter 4 to a 15-generation experiment in Chapter 5, asking what functions are lost as rare taxa and how host fitness is impacted by this loss. Overall, I find evidence of host-microbe and microbe-microbe interactions, with abundant species exerting beneficial effects on host fitness. I also find that rare taxa are likely beneficial in stressful contexts. Furthermore, I discovered 13 distinct metagenome-assembled genomes, revealing strain-level diversity in the Daphnia magna microbiome. My research demonstrates the tractability of Daphnia magna as a model organism for microbiome research and lays the groundwork for future research using multi-omics methods to understand multispecies interactions in this model system.
Fractures through the physis account for 18-30% of all paediatric fractures, leading to growth arrest in up to 5.5% of cases. We have limited knowledge to predict which physeal fractures result in ...growth arrest and subsequent deformity or limb length discrepancy. The purpose of this study is to identify factors associated with physeal growth arrest to improve patient outcomes.
This prospective cohort study was designed to develop a clinical prediction model for growth arrest after physeal injury. Patients ≤ 18 years old presenting within four weeks of injury were enrolled if they had open physes and sustained a physeal fracture of the humerus, radius, ulna, femur, tibia or fibula. Patients with prior history of same-site fracture or a condition known to alter bone growth or healing were excluded. Demographic data, potential prognostic indicators, and radiographic data were collected at baseline, during healing, and at one- and two-years post-injury.
A total of 332 patients had at least six months of follow-up or a diagnosis of growth arrest within six months of injury. In a comparison analysis, patients who developed growth arrest were more likely to be older (12.8 years vs. 9.4 years) and injured on the right side (53.0% vs. 45.7%). Initial displacement and angulation rates were higher in the growth arrest group (59.0% vs. 47.8% and 47.0% vs. 38.8%, respectively), but the amount of angulation was similar (27.0° vs. 28.4°). Rates of growth arrest were highest in distal femoral fractures (86%).
The incidence of growth arrest in this patient population appears higher than the past literature reports at 30.1%. However, there may be variances in diagnostic criteria for growth arrest, and the true incidence may be lower. A number of patients were approaching skeletal maturity, and any growth arrest is likely to have less clinical significance in these cases. Further prospective long-term follow-up is required to determine risk factors, incidence, and true clinical impact of growth arrest when it does occur.
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