Marker-gene and metagenomic sequencing have profoundly expanded our ability to measure biological communities. But the measurements they provide differ from the truth, often dramatically, because ...these experiments are biased toward detecting some taxa over others. This experimental bias makes the taxon or gene abundances measured by different protocols quantitatively incomparable and can lead to spurious biological conclusions. We propose a mathematical model for how bias distorts community measurements based on the properties of real experiments. We validate this model with 16S rRNA gene and shotgun metagenomics data from defined bacterial communities. Our model better fits the experimental data despite being simpler than previous models. We illustrate how our model can be used to evaluate protocols, to understand the effect of bias on downstream statistical analyses, and to measure and correct bias given suitable calibration controls. These results illuminate new avenues toward truly quantitative and reproducible metagenomics measurements.
We review evidence that supports the conclusion that people can and do learn in two distinct ways – one associative, the other propositional. No one disputes that we solve problems by testing ...hypotheses and inducing underlying rules, so the issue amounts to deciding whether there is evidence that we (and other animals) also rely on a simpler, associative system, that detects the frequency of occurrence of different events in our environment and the contingencies between them. There is neuroscientific evidence that associative learning occurs in at least some animals (e.g., Aplysia californica), so it must be the case that associative learning has evolved. Since both associative and propositional theories can in principle account for many instances of successful learning, the problem is then to show that there are at least some cases where the two classes of theory predict different outcomes. We offer a demonstration of cue competition effects in humans under incidental conditions as evidence against the argument that all such effects are based on cognitive inference. The latter supposition would imply that if the necessary information is unavailable to inference then no cue competition should occur. We then discuss the case of unblocking by reinforcer omission, where associative theory predicts an irrational solution to the problem, and consider the phenomenon of the Perruchet effect, in which conscious expectancy and conditioned response dissociate. Further discussion makes use of evidence that people will sometimes provide one solution to a problem when it is presented to them in summary form, and another when they are presented in rapid succession with trial-by trial information. We also demonstrate that people trained on a discrimination may show a peak shift (predicted by associative theory), but given the time and opportunity to detect the relationships between S+ and S−, show rule-based behavior instead. Finally, we conclude by presenting evidence that research on individual differences suggests that variation in intelligence and explicit problem solving ability are quite unrelated to variation in implicit (associative) learning, and briefly consider the computational implications of our argument, by asking how both associative and propositional processes can be accommodated within a single framework for cognition.
Clostridioides difficile is a bacterial pathogen that causes a range of clinical disease from mild to moderate diarrhea, pseudomembranous colitis, and toxic megacolon. Typically, C. difficile ...infections (CDIs) occur after antibiotic treatment, which alters the gut microbiota, decreasing colonization resistance against C. difficile. Disease is mediated by two large toxins and the expression of their genes is induced upon nutrient depletion via the alternative sigma factor TcdR. Here, we use tcdR mutants in two strains of C. difficile and omics to investigate how toxin-induced inflammation alters C. difficile metabolism, tissue gene expression and the gut microbiota, and to determine how inflammation by the host may be beneficial to C. difficile. We show that C. difficile metabolism is significantly different in the face of inflammation, with changes in many carbohydrate and amino acid uptake and utilization pathways. Host gene expression signatures suggest that degradation of collagen and other components of the extracellular matrix by matrix metalloproteinases is a major source of peptides and amino acids that supports C. difficile growth in vivo. Lastly, the inflammation induced by C. difficile toxin activity alters the gut microbiota, excluding members from the genus Bacteroides that are able to utilize the same essential nutrients released from collagen degradation.
Rapid arctic vegetation change as a result of global warming includes an increase in the cover and biomass of deciduous shrubs. Increases in shrub abundance will result in a proportional increase of ...shrub litter in the litter community, potentially affecting carbon turnover rates in arctic ecosystems. We investigated the effects of leaf and root litter of a deciduous shrub, Betula nana, on decomposition, by examining species-specific decomposition patterns, as well as effects of Betula litter on the decomposition of other species. We conducted a 2-yr decomposition experiment in moist acidic tundra in northern Alaska, where we decomposed three tundra species (Vaccinium vitis-idaea, Rhododendron palustre, and Eriophorum vaginatum) alone and in combination with Betula litter. Decomposition patterns for leaf and root litter were determined using three different measures of decomposition (mass loss, respiration, extracellular enzyme activity). We report faster decomposition of Betula leaf litter compared to other species, with support for species differences coming from all three measures of decomposition. Mixing effects were less consistent among the measures, with negative mixing effects shown only for mass loss. In contrast, there were few species differences or mixing effects for root decomposition. Overall, we attribute longer-term litter mass loss patterns to patterns created by early decomposition processes in the first winter. We note numerous differences for species patterns between leaf and root decomposition, indicating that conclusions from leaf litter experiments should not be extrapolated to below-ground decomposition. The high decomposition rates of Betula leaf litter aboveground, and relatively similar decomposition rates of multiple species below, suggest a potential for increases in turnover in the fast-decomposing carbon pool of leaves and fine roots as the dominance of deciduous shrubs in the Arctic increases, but this outcome may be tempered by negative litter mixing effects during the early stages of encroachment.
1. Ecosystem properties may be determined by the number of different species or groups of species in a community, the identity of those groups, and their relative abundance. The mass ratio theory ...predicts that the effect of species or groups of species on ecosystem properties will be dependent on their proportional abundance in a community. 2. Single plant functional groups (graminoids, legumes, non-leguminous forbs) were removed from a natural grassland in northern Canada to examine the role of group identity in determining both ecosystem properties and biomass compensation by remaining species. Removals were conducted across two different environmental treatments (fertilization and fungicide) to examine the context dependency of functional group identity effects. 3. The degree of biomass compensation in the first 4 years after removal was influenced by the identity of the functional group removed and also of those remaining. When graminoids were removed, none of the remaining functional groups compensated for the loss of biomass. Graminoids partially compensated for the removal of forbs or legumes, with the degree of compensation depending on environmental treatments. 4. Light interception, soil moisture and soil nutrients were all influenced by functional group identity, with graminoids having a greater impact than expected based on their biomass contribution to the community. Legumes, in contrast, had very little effect on any of the ecosystem properties measured. 5. For most ecosystem properties measured, the role of plant functional groups was not context dependent; functional groups had the same effect on ecosystem properties regardless of fertilization or fungicide treatments. 6. Synthesis. We have shown that the effects of losing a functional group do not solely depend on the group's dominance. In this northern grassland, there are greater effects of losing graminoids than one would predict based on their biomass contributions to the community, and functional group identity plays a critical role in determining the effects of diversity loss.
To understand SARS-Co-V-2 infection and transmission in UK nursing homes in order to develop preventive strategies for protecting the frail elderly residents.
An outbreak investigation involving 394 ...residents and 70 staff, was carried out in 4 nursing homes affected by COVID-19 outbreaks in central London. Two point-prevalence surveys were performed one week apart where residents underwent SARS-CoV-2 testing and had relevant symptoms documented. Asymptomatic staff from three of the four homes were also offered SARS-CoV-2 testing.
Overall, 26% (95% CI 22–31) of residents died over the two-month period. All-cause mortality increased by 203% (95% CI 70–336) compared with previous years. Systematic testing identified 40% (95% CI 35–46) of residents as positive for SARS-CoV-2, and of these 43% (95% CI 34–52) were asymptomatic and 18% (95% CI 11–24) had only atypical symptoms; 4% (95% CI −1 to 9) of asymptomatic staff also tested positive.
The SARS-CoV-2 outbreak in four UK nursing homes was associated with very high infection and mortality rates. Many residents developed either atypical or had no discernible symptoms. A number of asymptomatic staff members also tested positive, suggesting a role for regular screening of both residents and staff in mitigating future outbreaks.
Although the negative consequences of increased nitrogen (N) supply for plant communities and soil chemistry are well known, most studies have focused on mesic grasslands, and the fate of added N in ...arid and semi-arid ecosystems remains unclear. To study the impacts of long-term increased N deposition on ecosystem N pools, we sampled a 26-year-long fertilization (10 g N m−2 yr−1) experiment in the northern Chihuahuan Desert at the Sevilleta National Wildlife Refuge (SNWR) in New Mexico. To determine the fate of the added N, we measured multiple soil, microbial, and plant N pools in shallow soils at three time points across the 2020 growing season. We found small but significant increases with fertilization in soil-available NO3--N and NH4+-N, yet the soil microbial and plant communities do not appear to be taking advantage of the increased N availability, with no changes in biomass or N content in either community. However, there were increases in total soil N with fertilization, suggesting increases in microbial or plant N earlier in the experiment. Ultimately, the majority of the N added in this multi-decadal experiment was not found in the shallow soil or the microbial or plant community and is likely to have been lost from the ecosystem entirely.
Phosphorus (P) limits or co‐limits plant and microbial life in multiple ecosystems, including the arctic tundra. Although current global carbon (C) models focus on the coupling between soil nitrogen ...(N) and C, ecosystem P response to climate warming may also influence the global C cycle. Permafrost soils may see enhanced or reduced P availability under climate warming through multiple mechanisms including changing litter inputs through plant community change, changing plant–microbial dynamics, altered rates of mineralization of soil organic P through increased microbial activity, and newly exposed mineral‐bound P via deeper thaw. We investigated the effect of long‐term warming on plant leaf, multiple soil and microbial C, N, and P pools, and microbial extracellular enzyme activities, in Alaskan tundra plots underlain by permafrost. Here, we show that 25 yr of experimental summer warming increases community‐level plant leaf P through changing community composition to favour relatively P‐rich plant species. However, despite associated increases in P‐rich litter inputs, we found only a few responses in the belowground pools of P available for plant and microbial uptake, including a weak positive response for citric acid–extractable PO4 in the surface soil, a decrease in microbial biomass P, and no change in soil P (or C or N) stocks. This weak, neutral, or negative belowground P response to warming despite enhanced litter P inputs is consistent with a growing number of studies in the arctic tundra that find no long‐term response of soil C and N stocks to warming.
Global change in the Arctic promotes deeper soil thaw and enhanced soil microbial activity, increasing nitrogen (N) and phosphorus (P) availability to plants and microbes in strongly nutrient‐limited ...ecosystems. This critical, positive climate feedback has been examined through fertilization experiments that describe short‐term (<10 yr) above‐ or belowground responses to combined NP additions, with evidence of enhanced shrub growth, nutrient availability, and soil organic matter decomposition. There has been less opportunity for long‐term comparisons of both above‐ and belowground responses with factorial N and P additions in different systems, despite broad awareness that ecosystem response can shift with time, and the potential for decoupled above‐ vs. belowground or N vs. P responses, currently and with further predicted global change. We examined the response of the plants, soil microbes, and soil nutrients, to factorial N and P additions in the moist acidic tundra (MAT; 26 yr of nutrient additions) and moist non‐acidic tundra (MNT; 16 yr). Aboveground, the MAT plant community continues to change as predicted by earlier studies: Functional groups responded independently to N and P, but NDVI‐biomass, especially of Betula nana, only increased with N addition. Unlike shorter‐term MNT studies, the MNT vegetation, which does not include B. nana, shows few new fertilization responses. Belowground responses were not predicted by aboveground responses in either MAT or MNT. In contrast to the N response aboveground, MAT microbial biomass responded positively and microbial phosphatase activity negatively to P additions, implying possible release from microbial P limitation. Critically, earlier published results of declines in soil total carbon (C) with combined NP addition in the MAT are not present in the long term. We make two conclusions: (1) Arctic ecosystems are not universally N‐limited but also exhibit complex responses to P alone or in combination with N; and (2) the presence or absence of key vegetation species can cascade from aboveground to belowground and restrict the extrapolation of responses of nutrient addition in a single arctic ecosystem to other arctic ecosystems, the short‐term to the long term, or aboveground to belowground.
Reliable characterization of particles freshly emitted from the ocean surface requires a sampling method that is able to isolate those particles and prevent them from interacting with ambient gases ...and particles. Here we report measurements of particles directly emitted from the ocean using a newly developed in situ particle generator (Sea Sweep). The Sea Sweep was deployed alongside R/V Atlantis off the coast of California during May of 2010. Bubbles were generated 0.75 m below the ocean surface with stainless steel frits and swept into a hood/vacuum hose to feed a suite of aerosol instrumentation on board the ship. The number size distribution of the directly emitted, nascent particles had a dominant mode at 55–60 nm (dry diameter) and secondary modes at 30–40 nm and 200–300 nm. The nascent aerosol was not volatile at 230°C and was not enriched in SO4=, Ca++, K+, or Mg++above that found in surface seawater. The organic component of the nascent aerosol (7% of the dry submicrometer mass) volatilized at a temperature between 230 and 600°C. The submicrometer organic aerosol characterized by mass spectrometry was dominated by non‐oxygenated hydrocarbons. The nascent aerosol at 50, 100, and 145 nm dry diameter behaved hygroscopically like an internal mixture of sea salt with a small organic component. The CCN/CN activation ratio for 60 nm Sea Sweep particles was near 1 for all supersaturations of 0.3 and higher indicating that all of the particles took up water and grew to cloud drop size. The nascent organic aerosol mass fraction did not increase in regions of higher surface seawater chlorophyll but did show a positive correlation with seawater dimethylsulfide (DMS).
Key Points
The ocean is a source of sub 100nm particles to the atmosphere
Hygroscopically the particles behave like an internal mixture of sea salt/organic
Organic mass fraction did not correlate with chlorophyll
PDF
