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Roles of different ecological classes of algal exometabolites in regulating microbial community composition are not well understood. Here, we identify exometabolites from the model diatom Phaeodactylum tricornutum and demonstrate their potential to influence bacterial abundances. We profiled exometabolites across a time course of axenic algal growth using liquid chromatography-tandem mass spectrometry. We then investigated growth of 12 bacterial isolates on individual-identified exometabolites. Lastly, we compared responses of a P. tricornutum-adapted enrichment community to additions of two contrasting metabolites: selective growth substrate 4-hydroxybenzoic acid and putative signaling/facilitator molecule lumichrome. We identified 50 P. tricornutum metabolites and found distinct temporal accumulation patterns. Two exometabolites (of 12 tested) supported growth of distinct subsets of bacterial isolates. While algal exudates and algal presence drove similar changes in community composition compared with controls, exogenous 4-hydroxybenzoic acid addition promoted increased abundances of taxa that utilized it in isolation, and also revealed the importance of factors relating to algal presence in regulating community composition. This work demonstrates that secretion of selective bacterial growth substrates represents one mechanism by which algal exometabolites can influence bacterial community composition and illustrates how the algal exometabolome has the potential to modulate bacterial communities as a function of algal growth.

Abstract: Translocation programs for endangered mammalian carnivores face numerous challenges, including the potential for lethal interactions between releasees and resident conspecifics. Here we evaluate whether familiarizing residents with the scent of releasees might be an effective strategy for reducing aggression following Tasmanian devil (Sarcophilus harrisii) translocation. Tasmanian devils live in loose social networks in which residents have overlapping home ranges and use communal latrines. In a controlled ex situ experiment, we first found that devils readily distinguished between the feces of familiar and unfamiliar conspecifics. Next, we swapped feces between devils slated for release and wild resident devils, seeding a random half of communal latrines in the wild with the feces of releasee prior to their release, and used motion-activated video cameras to record devil visits. Wild resident devil visitation frequency and olfactory communication behaviors initially increased at experimental latrine sites where feces were deposited but not at control sites. After release, the translocated devils used both types of latrine sites and spent more time investigating experimental sites, but investigatory and scent-marking behaviors of the wild resident devils decreased, suggesting that they had become familiar with the releasees through scent. We further show that Tasmanian devil latrine sites are strongly associated with ecotones and the presence of shrubs. These findings contribute to our understanding of Tasmanian devil scent ecology and suggest that devil translocations conducted into existing populations would benefit from familiarization through latrine scent manipulation. More broadly, our results suggest an important role for scent ecology in carnivore translocation programs. Significance statement: A conservation management action that is being trialed for endangered Tasmanian devils is to breed devils in human care and reinforce dwindling small resident populations through translocation. However, with limited social interactions, unfamiliar devils may interact aggressively, increasing injury and reducing translocation success. Scent communication is nearly ubiquitous in mammals and may be a prerequisite for management of social aggression. Almost nothing is known about devil scent ecology. Our discovery that devils become familiarized with conspecifics through feces, combined with findings that wild devils that are exposed to translocated devil scent in advance of release show reduced interest in scent-seeded latrines, even after new devils are released, suggests that devils familiarized through scent in advance of relocation may exhibit reduced aggression. These results provide an avenue for improving the success of translocations for devils and other at-risk solitary mammalian carnivores.

Uterine artery (UA) hydrogen sulfide (H2S) production is augmented in pregnancy and, on stimulation by systemic/local vasodilators, contributes to pregnancy-dependent uterine vasodilation; however, how H2S exploits this role is largely unknown. S-sulfhydration converts free thiols to persulfides at reactive cysteine(s) on targeted proteins to affect the entire proteome posttranslationally, representing the main route for H2S to elicit its function. Here, we used Tag-Switch to quantify changes in sulfhydrated (SSH-) proteins (ie, sulfhydrome) in H2S-treated nonpregnant and pregnant human UA. We further used the low-pH quantitative thiol reactivity profiling platform by which paired sulfhydromes were subjected to liquid chromatography tandem mass spectrometry-based peptide sequencing to generate site (cysteine)-specific pregnancy-dependent H2S-responsive human UA sulfhydrome. Total levels of sulfhydrated proteins were significantly greater in pregnant vs nonpregnant human UA and further stimulated by treatment with sodium hydrosulfide. We identified a total of 360 and 1671 SSH-peptides from 480 and 1186 SSH-proteins in untreated and sodium hydrosulfide-treated human UA, respectively. Bioinformatics analyses identified pregnancy-dependent H2S-responsive human UA SSH peptides/proteins, which were categorized to various molecular functions, pathways, and biological processes, especially vascular smooth muscle contraction/relaxation. Pregnancy-dependent changes in these proteins were rectified by immunoblotting of the Tag-Switch labeled SSH proteins. Low-pH quantitative thiol reactivity profiling failed to identify low abundance SSH proteins such as KATP channels in human UA; however, immunoblotting of Tag-Switch-labeled SSH proteins identified pregnancy-dependent upregulation of SSH-KATP channels without altering their total proteins. Thus, comprehensive analyses of human UA sulfhydromes influenced by endogenous and exogenous H2S inform novel roles of protein sulfhydration in uterine hemodynamics regulation.

Natural products biosynthesized from biocontrol fungi in the rhizosphere can have both beneficial and deleterious effects on plants. Herein, we performed a comprehensive analysis of natural product biosynthetic gene clusters (BGCs) from the widely used biocontrol fungus Trichoderma afroharzianum T22 (ThT22). This fungus encodes at least 64 BGCs, yet only seven compounds and four BGCs were previously characterized or mined. We correlated 21 BGCs of ThT22 with known primary and secondary metabolites through homologous BGC comparison and characterized one unknown BGC involved in the biosynthesis of eujavanicol A using heterologous expression. In addition, we performed untargeted transcriptomics and metabolic analysis to demonstrate the activation of silent ThT22 BGCs via the "one strain many compound" (OSMAC) approach. Collectively, our analysis showcases the biosynthetic capacity of ThT22 and paves the way for fully exploring the roles of natural products of ThT22.

While traditionally considered important mainly in hypoxic roots during flooding, upregulation of fermentation pathways in plants has recently been described as an evolutionarily conserved drought survival strategy, with acetate signaling mediating reprograming of transcription and cellular carbon and energy metabolism from roots to leaves. The amount of acetate produced directly correlates with survival through potential mechanisms including defense gene activation, biosynthesis of primary and secondary metabolites, and aerobic respiration. Here, we review root ethanolic fermentation responses to hypoxia during saturated soil conditions and summarize studies highlighting acetate fermentation under aerobic conditions coupled with respiration during growth and drought responses. Recent work is discussed demonstrating long-distance transport of acetate via the transpiration stream as a respiratory substrate. While maintenance and growth respiration are often modeled separately in terrestrial models, here we propose the concept of 'Defense Respiration' fueled by acetate fermentation in which upregulation of acetate fermentation contributes acetate substrate for alternative energy production via aerobic respiration, biosynthesis of primary and secondary metabolites, and the acetylation of proteins involved in defense gene regulation. Finally, we highlight new frontiers in leaf-atmosphere emission measurements as a potential way to study acetate fermentation responses of individual leaves, branches, ecosystems, and regions.

We investigated the influence of seasonality and proximity to the forest canopy on nocturnal turbulence regimes in the roughness sublayer of a Central Amazon forest. Since convective systems of different scales are common in this region, we also analyzed the effect of extreme wind gusts (propagated from convective downdrafts) on the organization of the turbulence regimes, and their potential to cause the mortality of canopy trees. Our data include high-frequency winds, temperature and ozone concentration at different heights during the dry and wet seasons of 2014. In addition, we used critical wind-speed data derived from a tree-winching experiment and a modeling study conducted in the same study site. Two different turbulence regimes were identified at three heights above the canopy: a weakly stable (WS) and a very stable regime (VS). The threshold wind speeds that mark the transition between turbulence regimes were larger during the dry season and increased as a function of the height above the canopy. The turbulent fluxes of sensible heat and momentum during the WS accounted for 88% of the entire nighttime flux. Downdrafts occurred only in the WS and favored a fully coupled state of wind flow along the canopy profile. The destructive potential of winds was four times higher than on nights without downdrafts.

Environmental impact assessment (EIA) is a decision support tool that analyzes the environmental and social impacts of infrastructure projects. This paper focuses on the California Environmental Quality Act (CEQA), a law requiring EIA use in California, to examine where new infrastructure is proposed and whether EIA can shape infrastructure distribution and environmental justice through the review process. We analyze the temporal and spatial distribution of more than 7000 infrastructure projects and their environmental impacts as proposed under CEQA from 2011 to 2020. Using fixed-effects negative binomial regression to model the association between the number of initiated projects and existing socioeconomic and environmental conditions by census tract, and multinomial logistic regression to investigate determinants of a project's level of environmental review, we find an unequal distribution of infrastructure. We find that socio-economically vulnerable communities and those with greater burden of environmental pollution are less likely to be the site of newly proposed infrastructure, but that proposed projects tend to be beneficial, less-polluting infrastructure like parks or schools that could help redress past injustices. Moreover, projects proposed in vulnerable communities are less likely to receive the most stringent reviews or have their impacts mitigated. These findings suggest that CEQA interacts with distributive justice in contradictory ways. They also highlight the need to separately consider environmental amenities versus harms such that EIA processes do not stand as a barrier to constructing beneficial infrastructure in environmental justice communities.

No-till is often referred to as a climate change mitigation option, possibly with a stronger conviction, than as a practice to manage soil organic C (SOC) content. We conducted a global meta-analysis to evaluate the effect of no-till (NT) on SOC concentration (SOCc, g C kg−1 soil) and stock (SOCs, Mg C ha−1 land) across climate, soil texture, cropping systems, and no-till duration to appraise the priority-setting. Compared to conventional tillage, NT favoured a significant rise (ΔSOCc) of 38% in the 0–5 cm soil layer and a much lesser 6% increase in the 5–10 cm layer and no change beyond 10 cm. The temperate climate had nearly twice ΔSOCc in the 0–5 cm layer compared to other climates, while the tropical climate favoured sub-surface accumulation. Coarse- and medium-textured soils and the inclusion of legumes in crop rotation facilitated larger positive ΔSOCs under NT. The microbial biomass C was the most abundant C pool, with 61% and 23% increases under NT in 0–5 and 5–10 cm layers. A large ΔSOCc in aggregates also characterized the top 0–5 cm layer. The difference in SOCs was realized to a maximum 30 cm depth (5.4 Mg ha−1 or 14%) in favour of NT, although varying with the duration of its adoption. The contribution of NT in mitigating global anthropogenic greenhouse gas emissions is meagre, although it can substantially offset emissions from agriculture (17–58%). The benefit of NT in improving SOC is primarily restricted to the surface layer, which is potentially exposed, and therefore an increase could be short-lived. Nevertheless, a short-term gain in SOC is likely to enhance soil quality and crop productivity. Thus, NT may be promoted as a sustainable agricultural management practice rather than emphasizing its role as a potential climate change mitigation option.

The slow-fast continuum is a commonly used framework to describe variation in life-history strategies across species. Individual life histories have also been assumed to follow a similar pattern, especially in the pace-of-life syndrome literature. However, whether a slow-fast continuum commonly explains life-history variation among individuals within a population remains unclear. Here, we formally tested for the presence of a slow-fast continuum of life histories both within populations and across species using detailed long-term individual-based demographic data for 17 bird and mammal species with markedly different life histories. We estimated adult lifespan, age at first reproduction, annual breeding frequency, and annual fecundity, and identified the main axes of life-history variation using principal component analyses. Across species, we retrieved the slow-fast continuum as the main axis of life-history variation. However, within populations, the patterns of individual life-history variation did not align with a slow-fast continuum in any species. Thus, a continuum ranking individuals from slow to fast living is unlikely to shape individual differences in life histories within populations. Rather, individual life-history variation is likely idiosyncratic across species, potentially because of processes such as stochasticity, density dependence, and individual differences in resource acquisition that affect species differently and generate non-generalizable patterns across species.

Emerging technology has immense potential to increase the scale and efficiency of marine conservation. One such technology is large-area imaging (LAI), which relies on structure-from-motion photogrammetry to create composite products, including 3-dimensional (3-D) environmental models, that are larger in spatial extent than the individual images used to create them. Use of LAI has become widespread in certain fields of marine science, primarily to measure the 3D structure of benthic ecosystems and track change over time. However, the use of LAI in the field of marine conservation appears limited. We conducted a review of the coral reef literature on the use of LAI to identify research themes and regional trends in applications of this technology. We also surveyed 135 coral reef scientists and conservation practitioners to determine community familiarity with LAI, evaluate barriers practitioners face in using LAI, and identify applications of LAI believed to be most exciting or relevant to coral conservation. Adoption of LAI was limited primarily to researchers at institutions based in advanced economies and was applied infrequently to conservation, although conservation practitioners and survey respondents from emerging economies indicated they expect to use LAI in the future. Our results revealed disconnect between current LAI research topics and conservation priorities identified by practitioners, highlighting the need for more diverse, conservation-relevant research using LAI. We provide recommendations for how early adopters of LAI (typically Global North scientists from well-resourced institutions) can facilitate access to this conservation technology. These recommendations include developing training resources, creating partnerships for data storage and analysis, publishing standard operating procedures for LAI workflows, standardizing methods, developing tools for efficient data extraction from LAI products, and conducting conservation-relevant research using LAI.

The morphological diversity of the inflorescence determines flower and seed production, which is critical for plant adaptation. Hall's panicgrass (Panicum hallii, P. hallii) is a wild perennial grass that has been developed as a model to study perennial grass biology and adaptive evolution. Highly divergent inflorescences have evolved between the 2 major ecotypes in P. hallii, the upland ecotype (P. hallii var hallii, HAL2 genotype) with compact inflorescence and large seed and the lowland ecotype (P. hallii var filipes, FIL2 genotype) with an open inflorescence and small seed. Here we conducted a comparative analysis of the transcriptome and DNA methylome, an epigenetic mark that influences gene expression regulation, across different stages of inflorescence development using genomic references for each ecotype. Global transcriptome analysis of differentially expressed genes (DEGs) and co-expression modules underlying the inflorescence divergence revealed the potential role of cytokinin signaling in heterochronic changes. Comparing DNA methylome profiles revealed a remarkable level of differential DNA methylation associated with the evolution of P. hallii inflorescence. We found that a large proportion of differentially methylated regions (DMRs) were located in the flanking regulatory regions of genes. Intriguingly, we observed a substantial bias of CHH hypermethylation in the promoters of FIL2 genes. The integration of DEGs, DMRs, and Ka/Ks ratio results characterized the evolutionary features of DMR-associated DEGs that contribute to the divergence of the P. hallii inflorescence. This study provides insights into the transcriptome and epigenetic landscape of inflorescence divergence in P. hallii and a genomic resource for perennial grass biology.

The circadian oscillator allows organisms to synchronize their cellular and physiological activities with diurnal environmental changes. In plants, the circadian clock is primarily composed of multiple transcriptional-translational feedback loops. Regulators of post-transcriptional events, such as precursor messenger RNAs (pre-mRNA) splicing factors, are also involved in controlling the pace of the clock. However, in most cases the underlying mechanisms remain unclear. We have previously identified XAP5 CIRCADIAN TIMEKEEPER (XCT) as an Arabidopsis thaliana circadian clock regulator with uncharacterized molecular functions. Here, we report that XCT physically interacts with components of the spliceosome, including members of the Nineteen Complex (NTC). PacBio Iso-Seq data show that xct mutants have transcriptome-wide pre-mRNA splicing defects, predominantly aberrant 3' splice site selection. Expression of a genomic copy of XCT fully rescues those splicing defects, demonstrating that functional XCT is important for splicing. Dawn-expressed genes are significantly enriched among those aberrantly spliced in xct mutants, suggesting that the splicing activity of XCT may be circadian regulated. Furthermore, we show that loss-of-function mutations in PRP19A or PRP19B, 2 homologous core NTC components, suppress the short circadian period phenotype of xct-2. However, we do not see rescue of the splicing defects of core clock genes in prp19 xct mutants. Therefore, our results suggest that XCT may regulate splicing and the clock function through genetically separable pathways.

Permafrost-affected ecosystems are subject to warming and thawing, which can increase the availability of subsurface nitrogen (N) with consequences in otherwise N-limited tundra and alpine vegetation. Here, we quantify the extent of warming and permafrost thawing and the corresponding effects on nitrogen availability and plant growth based on a 20-year survey across 14 sites on the Tibetan Plateau. The survey showed that most sites have been subject to warming and thawing and that the upper permafrost zone across all sites was rich in inorganic N, mainly as ammonium. We further explore the efficiency of plants to utilize 15N-labelled inorganic N over five years following 15N addition at the permafrost table far below the main root zone. The 15N experiment showed that deep-rooted plant species were able to utilize the labelled N. A SEM model suggests that changes in vegetation can be explained by both active layer warming and permafrost thawing and the associated changes in inorganic nitrogen availability. Our results highlight a feedback mechanism of climate warming, in which released plant-available N may favour deep-rooted plants. This can explain important changes in plant composition and growth across the sites on the Tibetan Plateau.

Stream restorations are increasingly critical for managing and recovering freshwater biodiversity in human-dominated landscapes. However, few studies have quantified how rehabilitative actions promulgate through aquatic communities over decades. Here, a long-term dataset is analyzed for fish assemblage change, incorporating data pre- and post-restoration periods, and testing the extent to which native assemblage stability has increased over time. In the late 1950s, a large capacity dam was installed on Putah Creek (Solano County, CA, USA), which altered the natural flow regime, channel structure, geomorphic processes, and overall ecological function. Notably, downstream flows were reduced (especially during summer months) resulting in an aquatic assemblage dominated by warm-water nonnative species, while endemic native species subsisted at low levels as subordinates. A court-mediated Accord was ratified in 2000, providing a more natural flow regime, specifically for native and anadromous fishes in the stream. The richness of nonnative species decreased at every site following the Accord, while the richness of native species increased or stayed constant. At the three most upstream sites, native species richness increased over time and ultimately exceeded nonnative richness. Native assemblage recovery was strongest upriver, closer to flow releases and habitat restoration activities, and decreased longitudinally downstream. Rank-abundance curves through time revealed that, while species evenness was low throughout the study, dominance shifted from nonnative to native species in the upstream sites coincident with rehabilitation efforts. Mean rank shifts decreased following flow rehabilitation; thus the assemblage became increasingly stable over time following flow rehabilitation. Putah Creek's rehabilitation may represent a model for others interested in improving endemic freshwater communities in degraded ecosystems.

Soil viral ecology is a growing research field; however, the state of knowledge still lags behind that of aquatic systems. Therefore, to facilitate progress, the first Soil Viral Workshop was held to encourage international scientific discussion and collaboration, suggest guidelines for future research, and establish soil viral research as a concrete research area. The workshop took place at Søminestationen, Denmark, between 15 and 17th of June 2022. The meeting was primarily held in person, but the sessions were also streamed online. The workshop was attended by 23 researchers from ten different countries and from a wide range of subfields and career stages. Eleven talks were presented, followed by discussions revolving around three major topics: viral genomics, virus-host interactions, and viruses in the soil food web. The main take-home messages and suggestions from the discussions are summarized in this report.

Abstract: Many studies of community assembly focus on a single ontogenetic stage (typically adults) when trying to infer assembly processes from patterns of biodiversity. This focus ignores the finding that assembly mechanisms may strongly differ between life‐stages, and the role of ontogenetic dependency: the mechanisms by which one life stage directly affects the composition of another life stage. Within a 4‐ha forest dynamics plot in California USA, we explored how the relative importance of multiple assembly processes shifts across life stages and assessed ontogenetic dependency of seedlings on adults in woody plant communities. To assess variation in assembly processes across life stages, we examined how β‐diversity of adult and seedling communities were each influenced by space and 13 environmental variables (soils, topography) using distance‐based redundancy analysis and variation partitioning. We then assessed the ontogenetic dependency of seedlings on adults by including adult composition as a predictor in the seedling community variation partitioning. We found differences between adult and seedling composition. For the adults, we found 18 species including pines, oaks and manzanitas characteristic of this mid‐elevation forest. For seedlings, we found 11 species, and that oaks made up 75% of all seedlings while only making up 45% of all adults. Adult β‐diversity was primarily explained by space (44.0%) with environment only explaining 18.6% and 37.4% unexplained. In contrast, most of the explained variation in seedling β‐diversity was due to ontogenetic dependency alone (13.6% explained by adult composition) with 1.6% explained by space and the environment jointly, and 62.8% unexplained. Synthesis: Here, we describe a conceptual framework for integrating ontogeny more explicitly into community assembly research and demonstrate how different assembly processes structured adult and seedling β‐diversity in a temperate dry forest. While adult β‐diversity was largely driven by spatial processes, seedling β‐diversity was largely unexplained, with ontogenetic dependency comprising most of the explained variation. These patterns suggest that future assembly research should consider how assembly processes and their underlying mechanisms may shift with ontogeny, and that interactions between ontogenetic stages (ontogenetic dependency) are critical to consider when assessing variation in assembly processes.

Questions remain regarding the effect of baseline host and exposure factors on vaccine efficacy (VE) across pathogens and vaccine platforms. We report placebo-controlled data from four Phase 3 COVID-19 trials during the early period of the pandemic. This was a cross-protocol analysis of four randomized, placebo-controlled efficacy trials (Moderna/mRNA1273, AstraZeneca/AZD1222, Janssen/Ad26.COV2.S, and Novavax/NVX-CoV2373) using a harmonized design. Trials were conducted in the United States and international sites in adults ≥ 18 years of age. VE was assessed for symptomatic and severe COVID-19. We analyzed 114,480 participants from both placebo and vaccine arms, enrolled July 2020 to February 2021, with follow up through July 2021. VE against symptomatic COVID-19 showed little heterogeneity across baseline socio-demographic, clinical or exposure characteristics, in either univariate or multivariate analysis, regardless of vaccine platform. Similarly, VE against severe COVID-19 in the single trial (Janssen) with sufficient endpoints for analysis showed little evidence of heterogeneity. COVID-19 VE is not influenced by baseline host or exposure characteristics across efficacy trials of different vaccine platforms and countries when well matched to circulating virus strains. This supports use of these vaccines, regardless of platform type, as effective tools in the near term for reducing symptomatic and severe COVID-19, particularly for older individuals and those with common co-morbidities during major variant shifts. Clinical trial registration numbers: NCT04470427, NCT04516746, NCT04505722, and NCT04611802.

Spatial dynamics can promote persistence of strongly interacting predators and prey. Theory predicts that spatial predator-prey systems are prone to long transients, meaning that the dynamics leading to persistence or extinction manifest over hundreds of generations. Furthermore, the form and duration of transients may be altered by spatial network structure. Few empirical studies have examined the importance of transients in spatial food webs, especially in a network context, due to the difficulty in collecting the large scale and long-term data required. We examined predator-prey dynamics in protist microcosms using three experimental spatial structures: isolated, river-like dendritic networks and regular lattice networks. Densities and patterns of occupancy were followed for both predators and prey over a time scale that equates to >100 predator and >500 prey generations. We found that predators persisted in dendritic and lattice networks whereas they went extinct in the isolated treatment. The dynamics leading to predator persistence played out over long transients with three distinct phases. The transient phases showed differences between dendritic and lattice structures, as did underlying patterns of occupancy. Spatial dynamics differed among organisms in different trophic positions. Predators showed higher local persistence in more connected bottles while prey showed this in more spatially isolated ones. Predictions based on spatial patterns of connectivity derived from metapopulation theory explained predator occupancy, while prey occupancy was better explained by predator occupancy. Our results strongly support the hypothesized role of spatial dynamics in promoting persistence in food webs, but that the dynamics ultimately leading to persistence may occur with long transients which in turn may be influenced by spatial network structure and trophic interactions.

Fire-induced turbulence and the feedback into the fire, following ambient changes, differ for forested (sub-canopy) and grassland environments. Here, we synthesize observations from multiple experimental surface fires: two sub-canopy backing fires, one sub-canopy heading fire, and a grassland heading fire. We identify and compare the most essential coherent structures and processes of each case from the turbulent momentum fluxes and turbulent kinetic energy (TKE) budget terms. In the sub-canopy burns, turbulent eddies are strongest near the canopy top: high streamwise turbulent flux accompanies low cross-stream turbulent flux and vice versa. In the grassland fire, both streamwise and cross-stream eddies strengthen simultaneously until a certain height, informing a vertical length scale for the fire-influence. Moreover, the forward sweep from streamwise eddies assists in the fire spread by pushing hot gases towards unburnt fuel. In the sub-canopy fires, shear production and buoyancy production are more substantial near the canopy top for more intense fires, while their magnitudes decrease with decreasing fire intensity. At mid-canopy-height scales, buoyancy production dominates shear production, becoming the key mechanism for vertical transport of TKE. In the grassland fire, shear production dominates buoyancy production near the surface and is insignificant beyond a certain height relative to the flame length, while buoyancy production increases with height, becoming substantial further away from the surface. Turbulent transport terms are also active in both environments. For intense sub-canopy fires, there is a loss in TKE due to its expulsion to the boundary layer aloft via the transport term, compensated by a reversal process: TKE influx via the transport term. In the grassland fire, the transport term mimics this behavior until a certain height. The insights into the relative significance of the respective turbulent fluxes and TKE budget terms in each environment can help simplify the complex system of equations governing fire physics.

HIV reservoirs persist in anatomic compartments despite antiretroviral therapy (ART). Characterizing archival HIV DNA in the central nervous system (CNS) and other tissues is crucial to inform cure strategies. We evaluated paired autopsy brain-frontal cortex (FC), occipital cortex (OCC), and basal ganglia (BG)-and peripheral lymphoid tissues from 63 people with HIV. Participants passed away while virally suppressed on ART at the last visit and without evidence of CNS opportunistic disease. We quantified total HIV DNA in all participants and obtained full-length HIV-envelope (FL HIV-env) sequences from a subset of 14 participants. We detected HIV DNA (gag) in most brain (65.1%) and all lymphoid tissues. Lymphoid tissues had higher HIV DNA levels than the brain (P  0.2), while OCC had the lowest levels (P = 0.01). Females had higher HIV DNA levels in tissues than males (gag, P = 0.03; 2-LTR, P = 0.05), suggesting possible sex-associated mechanisms for HIV reservoir persistence. Most FL HIV-env sequences (n = 143) were intact, while 42 were defective. Clonal sequences were found in 8 out of 14 participants, and 1 participant had clonal defective sequences in the brain and spleen, suggestive of cell migration. From 10 donors with paired brain and lymphoid sequences, we observed evidence of compartmentalized sequences in 2 donors. Our data further the idea that the brain is a site for archival HIV DNA during ART where compartmentalized provirus may occur in a subset of people. Future studies assessing FL HIV-provirus and replication competence are needed to further evaluate the HIV reservoirs in tissues. IMPORTANCE HIV infection of the brain is associated with adverse neuropsychiatric outcomes, despite efficient antiretroviral treatment. HIV may persist in reservoirs in the brain and other tissues, which can seed virus replication if treatment is interrupted, representing a major challenge to cure HIV. We evaluated reservoirs and genetic features in postmortem brain and lymphoid tissues from people with HIV who passed away during suppressed HIV replication. We found a differential distribution of HIV reservoirs across brain regions which was lower than that in lymphoid tissues. We observed that most HIV reservoirs in tissues had intact envelope sequences, suggesting they could potentially generate replicative viruses. We found that women had higher HIV reservoir levels in brain and lymphoid tissues than men, suggesting possible sex-based mechanisms of maintenance of HIV reservoirs in tissues, warranting further investigation. Characterizing the archival HIV DNA in tissues is important to inform future HIV cure strategies.

Most flowering plants require animal pollination and are visited by multiple pollinator species. Historically, the effects of pollinators on plant fitness have been compared using the number of pollen grains they deposit, and the number of seeds or fruits produced following a visit to a virgin flower. While useful, these methods fail to consider differences in pollen quality and the fitness of zygotes resulting from pollination by different floral visitors. Here we show that, for three common native self-compatible plants in Southern California, super-abundant, non-native honeybees (Apis mellifera L.) visit more flowers on an individual before moving to the next plant compared with the suite of native insect visitors. This probably increases the transfer of self-pollen. Offspring produced after honeybee pollination have similar fitness to those resulting from hand self-pollination and both are far less fit than those produced after pollination by native insects or by cross-pollination. Because honeybees often forage methodically, visiting many flowers on each plant, low offspring fitness may commonly result from honeybee pollination of self-compatible plants. To our knowledge, this is the first study to directly compare the fitness of offspring resulting from honeybee pollination to that of other floral visitors.

Diurnal biting flies are strongly attracted to blue objects. This behaviour is widely exploited for fly control, but its functional significance is debated. It is hypothesized that blue objects resemble animal hosts; blue surfaces resemble shaded resting places; and blue attraction is a by-product of attraction to polarized light. We computed the fly photoreceptor signals elicited by a large sample of leaf and animal integument reflectance spectra, viewed under open/cloudy illumination and under woodland shade. We then trained artificial neural networks (ANNs) to distinguish animals from leaf backgrounds, and shaded from unshaded surfaces, in order to find the optimal means of doing so based upon the sensory information available to a fly. After training, we challenged ANNs to classify blue objects used in fly control. Trained ANNs could make both discriminations with high accuracy. They discriminated animals from leaves based upon blue-green photoreceptor opponency and commonly misclassified blue objects as animals. Meanwhile, they discriminated shaded from unshaded stimuli using achromatic cues and never misclassified blue objects as shaded. We conclude that blue-green opponency is the most effective means of discriminating animals from leaf backgrounds using a fly's sensory information, and that blue objects resemble animal hosts through such mechanisms.

BackgroundAbnormal or undesired mare behaviours are often assumed to be associated with ovarian abnormalities.ObjectivesWe aimed to determine the incidence of abnormal behaviours and their association with concentrations of one or more ovarian hormones associated with a granulosa cell tumour (GCT).Study designRetrospective descriptive.MethodsA total of 2914 hormonal profile samples submitted with the words behave, behaviour, or behaving in the submission history were analysed. The association between reported abnormal behaviours and concentrations of testosterone, anti-Müllerian hormone (AMH), inhibins and inhibin-B were assessed. Statistical analysis was performed using a Chi-squared test of association.ResultsOf the 2914 cases that were submitted due to behaviour issues, 2506 (86%) did not have any of the measured hormones reach GCT-like concentrations. The remaining 408 cases had either one (63%), two (25.5%), or three (11.5%) hormones with concentrations consistent with those from confirmed GCT cases. Testosterone had the lowest percent of GCT-like values among the cases (7.7%), compared with AMH (9.4%), inhibins (9.6%) and inhibin B (8.7%). Stallion-like behaviour was significantly associated with increased concentrations of all four hormones. In contrast, aggression, oestrous and other abnormal behaviours were significantly less likely to be associated with increased concentrations of the hormones.Main limitationsRetrospective study, using sample submission history.ConclusionOverall, the abnormal behaviours among mares, except the stallion-like behaviour, were not associated with increased ovarian hormones. These results highlight the common misassumption about the involvement of the ovaries in 'abnormal behaviours' or 'undesirable behaviours' of mares.

Salmonella invades host cells and replicates inside acidified, remodeled vacuoles that are exposed to reactive oxygen species (ROS) generated by the innate immune response. Oxidative products of the phagocyte NADPH oxidase mediate antimicrobial activity, in part, by collapsing the ΔpH of intracellular Salmonella. Given the role of arginine in bacterial resistance to acidic pH, we screened a library of 54 single-gene mutants in Salmonella that are each involved in, but do not entirely block, arginine metabolism. We identified several mutants that affected Salmonella virulence in mice. The triple mutant ΔargCBH, which is deficient in arginine biosynthesis, was attenuated in immunocompetent mice, but recovered virulence in phagocyte NADPH oxidase deficient Cybb-/- mice. Furthermore, ΔargCBH Salmonella was profoundly susceptible to the bacteriostatic and bactericidal effects of hydrogen peroxide. Peroxide stress led to a larger collapse of the ΔpH in ΔargCBH mutants than occurred in wild-type Salmonella. The addition of exogenous arginine rescued ΔargCBH Salmonella from peroxide-induced ΔpH collapse and killing. Combined, these observations suggest that arginine metabolism is a hitherto unknown determinant of virulence that contributes to the antioxidant defenses of Salmonella by preserving pH homeostasis. In the absence of phagocyte NADPH oxidase-produced ROS, host cell-derived l-arginine appears to satisfy the needs of intracellular Salmonella. However, under oxidative stress, Salmonella must additionally rely on de novo biosynthesis to maintain full virulence.

Coloration facilitates evolutionary investigations in nature because the interaction between genotype, phenotype and environment is relatively accessible. In a landmark set of studies, Endler addressed this complexity by demonstrating that the evolution of male Trinidadian guppy coloration is shaped by the local balance between selection for mate attractiveness versus crypsis. This became a textbook paradigm for how antagonistic selective pressures may determine evolutionary trajectories in nature. However, recent studies have challenged the generality of this paradigm. Here, we respond to these challenges by reviewing five important yet underappreciated factors that contribute to colour pattern evolution: (i) among-population variation in female preference and correlated variation in male coloration, (ii) differences in how predators versus conspecifics view males, (iii) biased assessment of pigmentary versus structural coloration, (iv) the importance of accounting for multi-species predator communities, and (v) the importance of considering the multivariate genetic architecture and multivariate context of selection and how sexual selection encourages polymorphic divergence. We elaborate these issues using two challenging papers. Our purpose is not to criticize but to point out the potential pitfalls in colour research and to emphasize the depth of consideration necessary for testing evolutionary hypotheses using complex multi-trait phenotypes such as guppy colour patterns.

1. Biodiversity is an important component of natural ecosystems, with higher species richness often correlating with an increase in ecosystem productivity. Yet, this relationship varies substantially across environments, typically becoming less pronounced at high levels of species richness. However, species richness alone cannot reflect all important properties of a community, including community evenness, which may mediate the relationship between biodiversity and productivity. If the evenness of a community correlates negatively with richness across forests globally, then a greater number of species may not always increase overall diversity and productivity of the system. Theoretical work and local empirical studies have shown that the effect of evenness on ecosystem functioning may be especially strong at high richness levels, yet the consistency of this remains untested at a global scale. 2. Here, we used a dataset of forests from across the globe, which includes composition, biomass accumulation and net primary productivity, to explore whether productivity correlates with community evenness and richness in a way that evenness appears to buffer the effect of richness. Specifically, we evaluated whether low levels of evenness in speciose communities correlate with the attenuation of the richness–productivity relationship. 3. We found that tree species richness and evenness are negatively correlated across forests globally, with highly speciose forests typically comprising a few dominant and many rare species. Furthermore, we found that the correlation between diversity and productivity changes with evenness: at low richness, uneven communities are more productive, while at high richness, even communities are more productive. 4. Synthesis. Collectively, these results demonstrate that evenness is an integral component of the relationship between biodiversity and productivity, and that the attenuating effect of richness on forest productivity might be partly explained by low evenness in speciose communities. Productivity generally increases with species richness, until reduced evenness limits the overall increases in community diversity. Our research suggests that evenness is a fundamental component of biodiversity–ecosystem function relationships, and is of critical importance for guiding conservation and sustainable ecosystem management decisions.

In practice, cows are fed by pen, but a diet is formulated to the nutrient requirements of a single cow. If the DM intake (DMI) of a pen were equal for all cows, this approach would have no error, but cows are grouped into pens on pregnancy and other management factors creating a distribution of DMI. The goal of precision feeding is to meet the requirements of individual animals to increase efficiency and reduce environmental impact but is not achieved when a group is fed as if the individuals have uniform requirements and the DMI distribution is not normal. The hypothesis of this work is that the DMI of cow pens are not normally distributed and the total DMI from the best-fit distribution shape for a cow pen will have lower percentage error to the observed DMI than a prediction of a single DMI that is fed at a uniform level and assumes a normal distribution. Our objective was to describe the distribution shape of DMI by week of lactation, and for different pen types. Pens were generated by randomly assorting cows by the week of lactation from a database into different categories of pen for size and lactation period. These pens were fitted to the best distribution type, and its parameters were used to randomly generate distribution plots that predict the total DMI for each pen. A second predictive model estimated the DMI of each pen using an empirical equation of DMI that was multiplied by the number of cows in the pen to represent feeding of a uniform DMI quantity. The percentage error for the distribution shape model was significantly lower than the empirical model with pen errors being less than 1%. The beta distribution type was the most common distribution to best represent the data of pen DMI. Describing the distribution and using it to predict a total pen DMI provides accurate estimates of feed quantity for a group. Reducing error by using the distribution of DMI for feed formulation, instead of the nutrient requirements of an individual animal can provide a precision nutrition approach to group feeding.

Integrated phenotypes, that is, correlated suites of traits, can impact both evolutionary and ecological processes. Similarly, phenotypic plasticity, or the ability of one genotype to generate multiple phenotypes, can act as both a facilitator and constraint on evolutionary processes. While there has been an increasing focus on correlated behavioural means (i.e. behavioural syndromes), less attention has been paid to how plasticity in different behavioural traits may be correlated. Such correlated behavioural plasticities are likely to affect evolution and ecology, although possibly in different ways. Here, we review key insights from three research fields, behavioural syndromes, phenotypic plasticity and integrated phenotypes to provide a conceptual framework to understand why, how and when plasticities of different behavioural traits may become correlated. In particular, the conditions under which plasticity and behavioural syndromes are predicted to be important are also where correlated behavioural plasticities are likely to have the strongest impacts. In this review, we define correlated behavioural plasticities, summarize the conditions that are likely to give rise to them and highlight testable predictions in an effort to spark targeted research into this important phenomenon. We also provide a worked example to highlight how studying correlated plasticity can yield important new insights.

Linking science with action affords a prime opportunity to leverage greater societal impact from research and increase the use of evidence in decision-making. Success in these areas depends critically upon processes of producing and mobilizing knowledge, as well as supporting and making decisions. For decades, scholars have idealized and described these social processes in different ways, resulting in numerous assumptions that now variously guide engagements at the interface of science and society. We systematically catalog these assumptions based on prior research on the science-policy interface, and further distill them into a set of 26 claims. We then elicit expert perspectives (n = 16) about these claims to assess the extent to which they are accurate or merit further examination. Out of this process, we construct a research agenda to motivate future scientific research on actionable knowledge, prioritizing areas that experts identified as critical gaps in understanding of the science-society interface. The resulting agenda focuses on how to define success, support intermediaries, build trust, and evaluate the importance of consensus and its alternatives – all in the diverse contexts of science-society-decision-making interactions. We further raise questions about the centrality of knowledge in these interactions, discussing how a governance lens might be generative of efforts to support more equitable processes and outcomes. We offer these suggestions with hopes of furthering the science of actionable knowledge as a transdisciplinary area of inquiry.

Geometric modelling of river channel topography is a method of design synthesis wherein specific 2D geometric elements of river topography, such as the bed profile, cross-sectional shape and channel planform contours, are expressed mathematically in isolation and then combined to produce a 3D heightmap. We utilized the geometric modelling framework to synthesize channel terrains that reveal flow–form–function linkages to investigate what roles variability in bed roughness, thalweg elevation and channel width play in defining hydraulic and ecohydraulic conditions of a channel reach from baseflow to bankfull discharge. To achieve a robust inquiry for a range of settings, this study developed four distinct synthetic channel terrain models for each of three stream reaches of different channel types in the South Fork Eel River in northern coastal California, USA. To test the process-based effects of these diverse terrain synthesis options, we compared the resulting hydraulic patterns and preferred habitat availability for fry/juvenile steelhead trout and coho salmon over a range of discharges. Among thalweg bed undulation, width variation and bed roughness, we found thalweg bed undulation was the key factor affecting the channel ecohydraulic response at baseflow condition. At bankfull condition, thalweg bed elevation had the largest effect in high-order mainstem streams identified by gravel-cobble dominated high width-to-depth, riffle-pool sequences, width variation had the largest effect in mid-order confined channels with gravel-cobble, high width-to-depth ratio with expansions/contractions and bed roughness in low-order streams with low width-to-depth ratio, high-gradient, cobble-boulder and step-pool/cascade channels.

Brucella spp. are facultatively intracellular bacteria that can infect, survive, and multiply in various host cell types in vivo and/or in vitro. The genus Brucella has markedly expanded in recent years with the identification of novel species and hosts, which has revealed additional information about the cell and tissue tropism of these pathogens. Classically, Brucella spp. are considered to have tropism for organs that contain large populations of phagocytes such as lymph nodes, spleen, and liver, as well as for organs of the genital system, including the uterus, epididymis, testis, and placenta. However, experimental infections of several different cultured cell types indicate that Brucella may actually have a broader cell tropism than previously thought. Indeed, recent studies indicate that certain Brucella species in particular hosts may display a pantropic distribution in vivo. This review discusses the available knowledge on cell and tissue tropism of Brucella spp. in natural infections of various host species, as well as in experimental animal models and cultured cells.

Methods to diagnose and monitor equine pregnancy continue to advance with improved instrumentation enabling the development of novel, non-invasive approaches to assess fetal well-being and viability using ultrasound and endocrine testing. From early embryonic loss to placentitis, that is typically encountered later in gestation, fetal viability and development as well as placental function can be evaluated using two fundamentally different, structural and functional, approaches. Ultrasound provides structural information on embryonic and fetal growth using such parameters as combined thickness of the uterus and placenta (CTUP), visual assessment of fetal fluids, activity, heart rate and multiple biometrics involving the fetal head and eyes, limbs and joints among many others, depending on the stage of gestation. Endocrine profiles that include progesterone and 5α-dihydroprogesterone, other metabolites, androgens and estrogens can be evaluated simultaneously using liquid chromatography-tandem mass spectrometry (LC-MS/MS) providing more functional information on fetal and placental competence and development. Endocrine information can be used in making clinical decisions including the need for progestin supplementation or when it can cease, and even estimating gestational stage in mares that cannot be easily palpated or scanned, as with mini-breeds or rancorous animals most notably. When used together, monitoring gestation by ultrasound and hormonal analysis provides unusual insight into feto-placental well-being and the progress of pregnancy, helping to identify problems needing therapeutic intervention.

Key messageThe diploid wheat recessive stem rust resistance gene SrTm4 was fine-mapped to a 754-kb region on chromosome arm 2AmL and potential candidate genes were identified. Race Ug99 of Puccinia graminis f. sp. tritici (Pgt), the causal agent of wheat stem (or black) rust is one of the most serious threats to global wheat production. The identification, mapping, and deployment of effective stem rust resistance (Sr) genes are critical to reduce this threat. In this study, we generated SrTm4 monogenic lines and found that this gene confers resistance to North American and Chinese Pgt races. Using a large mapping population (9522 gametes), we mapped SrTm4 within a 0.06 cM interval flanked by marker loci CS4211 and 130K1519, which corresponds to a 1.0-Mb region in the Chinese Spring reference genome v2.1. A physical map of the SrTm4 region was constructed with 11 overlapping BACs from the resistant Triticum monococcum PI 306540. Comparison of the 754-kb physical map with the genomic sequence of Chinese Spring and a discontinuous BAC sequence of DV92 revealed a 593-kb chromosomal inversion in PI 306540. Within the candidate region, we identified an L-type lectin-domain containing receptor kinase (LLK1), which was disrupted by the proximal inversion breakpoint, as a potential candidate gene. Two diagnostic dominant markers were developed to detect the inversion breakpoints. In a survey of T. monococcum accessions, we identified 10 domesticated T. monococcum subsp. monococcum genotypes, mainly from the Balkans, carrying the inversion and showing similar mesothetic resistant infection types against Pgt races. The high-density map and tightly linked molecular markers developed in this study are useful tools to accelerate the deployment of SrTm4-mediated resistance in wheat breeding programs.

Hydatid disease is a neglected zoonotic parasitic disease caused by cysts of the tapeworm Echinococcus granulosus. Canids, especially domestic dogs, are definitive hosts of the parasite and are the most pragmatic targets for control programs. A governmental dog deworming campaign was established in 1979 to control hydatidosis in southern Chile, which succeeded in reducing the prevalence of canine echinococcosis in Tierra del Fuego province from 68.4% (in 1978) to 1.2% (in 2002). In 2004, however, the program was dismantled to reduce costs, and since then, no follow-up echinococcosis monitoring has been conducted. We surveyed 356 domestic dogs and interviewed owners or workers at 45 ranches in Chilean Tierra del Fuego during the summer of 2015-2016. Faecal flotation was employed to detect Taeniidae eggs, and PCR was used to test faecal samples for Echinococcus granulosus. Taeniidae eggs and Echinococcus sp. DNA were detected in the faeces of 45.4% (147/324) and 6.9% (23/331) of dogs, respectively. Infrequent dog deworming and the presence of culpeo foxes (Lycalopex culpaeus) were significant predictors of the prevalence of Echinococcus sp. DNA and Taeniidae eggs. Furthermore, the presence of introduced chilla foxes (Lycalopex griseus), the municipality, and several operational characteristics of ranches (number of sheep, frequency of sheep slaughter, number of dogs, frequency of removal of dog faeces, feeding of dogs with sheep viscera) were also predictive of the prevalence of Taeniidae eggs. Our findings reveal an ongoing risk of echinococcosis with pathogen maintenance in ranch dogs in Chilean Tierra del Fuego, and in the absence of adequate control programmes, there is a tangible risk of re-emergence of hydatid disease as a public health concern.

Early-stage pedogenic processes and formation rates on completely obliterated volcanic landscapes, such as the super explosive 1815 Mount Tambora eruption, have not previously been robustly explored. The objectives of this study were to determine (i) the mineralogical composition of the sand fraction, selected physical and chemical soil properties and potential nutrient reserves after 200 years of pedogenesis, and (ii) chemical weathering indices, rate of soil formation, and rates of C and N accretion. Soil formation was examined for five soil profiles on stable plain/foot slope positions representing the diversity of soils in these landscape positions, which are important for agricultural production. Results showed that the soil mineralogical composition of the sand fraction was dominated by easily weatherable minerals (e.g., labradorite and augite volcanic glass) indicating high potential nutrient reserves (e.g., Ca2+, Mg2+, K+, P) as confirmed by X-ray fluorescence (XRF) analyses. Allophanic material formation was minimal ( B horizons (45.4 ± 2.4) > C horizons (43.8 ± 4.2) ≈ tephra/lava (43.1), indicating accumulation of Al oxides and depletion of base cations in the upper horizons. Similarly, the base depletion index (BDI) showed a trend of A horizons (1.13 ± 0.18) < B horizons (1.25 ± 0.09) < C horizons (1.34 ± 0.20) ≈ tephra/lava (1.35), indicating depletion of base cations (Ca2+, Mg2+, K+, Na+) from the soil surface to C horizons. Based on solum depths (A + B horizons) and 200 years of post-eruption soil development, the solum formation rate ranged from 1.2 to 5.3 mm yr−1. Appreciable stocks of SOC (2.3–12.8 kg C m−2) and SON (0.21–0.77 kg m−2) accumulated over the 200 year period. Eruption materials from the Mt. Tambora eruption with a precisely known timescale contributed new pedological insights documenting rapid soil formation rates from pyroclastic materials leading to a rapid recovery of soil functions to support agricultural production.

Variation in decay rates across woody species is a key uncertainty in predicting the fate of carbon stored in deadwood, especially in the tropics. Quantifying the relative contributions of biotic decay agents, particularly microbes and termites, under different climates and across species with diverse wood traits could help explain this variation. To fill this knowledge gap, we deployed woody stems from 16 plant species native to either rainforest (n = 10) or savanna (n = 6) in northeast Australia, with and without termite access. For comparison, we also deployed standardized, non-native pine blocks at both sites. We hypothesized that termites would increase rates of deadwood decay under conditions that limit microbial activity. Specifically, termite contributions to wood decay should be greater under dry conditions and in wood species with traits that constrain microbial decomposers. Termite discovery of stems was surprisingly low with only 17.6% and 22.6% of accessible native stems discovered in the rainforest and savanna respectively. Contrary to our hypothesis, stems discovered by termites decomposed faster only in the rainforest. Termites discovered and decayed pine blocks at higher rates than native stems in both the rainforest and savanna. We found significant variation in termite discovery and microbial decay rates across native wood species within the same site. Although wood traits explained 85% of the variation in microbial decay, they did not explain termite-driven decay. For stems undiscovered by termites, decay rates were greater in species with higher wood nutrient concentrations and syringyl:guiacyl lignin ratios but lower carbon concentrations and wood densities. Synthesis. Ecosystem-scale predictions of deadwood turnover and carbon storage should account for the impact of wood traits on decomposer communities. In tropical Australia, termite-driven decay was lower than expected for native wood on the ground. Even if termites are present, they may not always increase decomposition rates of fallen native wood in tropical forests. Our study shows how the drivers of wood decay differ between Australian tropical rainforest and savanna; further research should test whether such differences apply world-wide.

Tree-removal treatments have been broadly applied across piñon-juniper ecosystems of the western United States to reduce tree cover, stimulate understory plant production, and promote habitat for shrub- and grassland-obligate wildlife species. Mastication treatments have become an increasingly common approach, yet the efficacy of these treatments can vary on the basis of a variety of factors, including soil characteristics, woodland structure, and grazing pressures. Here, we assessed vegetation responses to mastication treatments across three dominant soil types in two-needle piñon (Pinus edulis Engelm. [Pinaceae])−one-seed juniper (Juniperus monosperma [Engelm.] Sarg.) woodlands in southeast Colorado, United States, a region characterized by monsoonal precipitation, limited presence of introduced plant species, and relatively high grazing intensity by cattle and wildlife. We found that mastication treatments were effective at increasing herbaceous plant cover and species diversity (by 1.2 × and 1.5 ×) and at reducing the amount of exposed soil (60% reduction) 3 yr following treatment. This was mainly due to increases in native perennial grasses. Further, there were limited (and insignificant) increases in cover of annual plants and low abundance of introduced species in treated plots. Understory plant responses to treatment were similar across soils with a range of available water capacities. The increase in understory plant cover and richness paired with the low abundance of introduced species suggests that mastication treatments increase forage production for cattle and wild ungulates. In addition, the lack of soil type differences in treatment response suggests that mastication treatment placement does not need to prioritize soil type and can instead focus on other key areas of importance, such as wildlife habitat connectivity, historic woodland structure, and treatment feasibility.

Acute and chronic viral infections result in the differentiation of effector and exhausted T cells with functional and phenotypic differences that dictate whether the infection is cleared or progresses to chronicity. High CD38 expression has been observed on CD8+ T cells across various viral infections and tumors in patients, suggesting an important regulatory function for CD38 on responding T cells. Here, we show that CD38 expression was increased and sustained on exhausted CD8+ T cells following chronic lymphocytic choriomeningitis virus (LCMV) infection, with lower levels observed on T cells from acute LCMV infection. We uncovered a cell-intrinsic role for CD38 expression in regulating the survival of effector and exhausted CD8+ T cells. We observed increased proliferation and function of Cd38-/- CD8+ progenitor exhausted T cells compared to those of wild-type (WT) cells. Furthermore, decreased oxidative phosphorylation and glycolytic potential were observed in Cd38-/- CD8+ T cells during chronic but not acute LCMV infection. Our studies reveal that CD38 has a dual cell-intrinsic function in CD8+ T cells, where it decreases proliferation and function yet supports their survival and metabolism. These findings show that CD38 is not only a marker of T cell activation but also has regulatory functions on effector and exhausted CD8+ T cells. IMPORTANCE Our study shows how CD38 expression is regulated on CD8+ T cells responding during acute and chronic viral infection. We observed higher CD38 levels on CD8+ T cells during chronic viral infection compared to levels during acute viral infection. Deleting CD38 had an important cell-intrinsic function in ensuring the survival of virus-specific CD8+ T cells throughout the course of viral infection. We found defective metabolism in Cd38-/- CD8+ T cells arising during chronic infection and changes in their progenitor T cell phenotype. Our studies revealed a dual cell-intrinsic role for CD38 in limiting proliferation and granzyme B production in virus-specific exhausted T cells while also promoting their survival. These data highlight new avenues for research into the mechanisms through which CD38 regulates the survival and metabolism of CD8+ T cell responses to viral infections.

HIV can establish a long-lived latent infection in cells harboring integrated non-expressing proviruses. Latency reversing agents (LRAs), including protein kinase C (PKC) modulators, can induce expression of latent HIV, thereby reducing the latent reservoir in animal models. However, PKC modulators such as bryostatin-1 also cause cytokine upregulation in peripheral blood mononuclear cells (PBMCs), including cytokines that might independently reverse HIV latency. To determine whether cytokines induced by PKC modulators contribute to latency reversal, primary human PBMCs were treated with bryostatin-1 or the bryostatin analog SUW133, a superior LRA, and supernatant was collected. As anticipated, LRA-treated cell supernatant contained increased levels of cytokines compared to untreated cell supernatant. However, exposure of latently-infected cells with this supernatant did not result in latency reactivation. These results indicate that PKC modulators do not have significant indirect effects on HIV latency reversal in vitro and thus are targeted in their latency reversing ability.

Acid tropical soils may become more productive when treated with agricultural lime, but optimal lime rates have yet to be determined in many tropical regions. In these regions, lime rates can be estimated with lime requirement models based on widely available soil data. We reviewed seven of these models and introduced a new model (LiTAS). We evaluated the models' ability to predict the amount of lime needed to reach a target change in soil chemical properties with data from four soil incubation studies covering 31 soil types. Two foundational models, one targeting acidity saturation and the other targeting base saturation, were more accurate than the five models that were derived from them, while the LiTAS model was the most accurate. The models were used to estimate lime requirements for 303 African soil samples. We found large differences in the estimated lime rates depending on the target soil chemical property of the model. Therefore, an important first step in formulating liming recommendations is to clearly identify the soil property of interest and the target value that needs to be reached. While the LiTAS model can be useful for strategic research, more information on acidity-related problems other than aluminum toxicity is needed to comprehensively assess the benefits of liming.

Key messageHere, we provide an updated set of guidelines for naming genes in wheat that has been endorsed by the wheat research community. The last decade has seen a proliferation in genomic resources for wheat, including reference- and pan-genome assemblies with gene annotations, which provide new opportunities to detect, characterise, and describe genes that influence traits of interest. The expansion of genetic information has supported growth of the wheat research community and catalysed strong interest in the genes that control agronomically important traits, such as yield, pathogen resistance, grain quality, and abiotic stress tolerance. To accommodate these developments, we present an updated set of guidelines for gene nomenclature in wheat. These guidelines can be used to describe loci identified based on morphological or phenotypic features or to name genes based on sequence information, such as similarity to genes characterised in other species or the biochemical properties of the encoded protein. The updated guidelines provide a flexible system that is not overly prescriptive but provides structure and a common framework for naming genes in wheat, which may be extended to related cereal species. We propose these guidelines be used henceforth by the wheat research community to facilitate integration of data from independent studies and allow broader and more efficient use of text and data mining approaches, which will ultimately help further accelerate wheat research and breeding.

Demographic factors are fundamental in shaping infectious disease dynamics. Aspects of populations that create structure, like age and sex, can affect patterns of transmission, infection intensity and population outcomes. However, studies rarely link these processes from individual to population-scale effects. Moreover, the mechanisms underlying demographic differences in disease are frequently unclear. Here, we explore sex-biased infections for a multi-host fungal disease of bats, white-nose syndrome, and link disease-associated mortality between sexes, the distortion of sex ratios and the potential mechanisms underlying sex differences in infection. We collected data on host traits, infection intensity and survival of five bat species at 42 sites across seven years. We found females were more infected than males for all five species. Females also had lower apparent survival over winter and accounted for a smaller proportion of populations over time. Notably, female-biased infections were evident by early hibernation and likely driven by sex-based differences in autumn mating behaviour. Male bats were more active during autumn which likely reduced replication of the cool-growing fungus. Higher disease impacts in female bats may have cascading effects on bat populations beyond the hibernation season by limiting recruitment and increasing the risk of Allee effects.

While the goal of universal drug susceptibility testing has been a key component of the WHO End TB Strategy, in practice, this remains inaccessible to many. Rapid molecular tests for tuberculosis (TB) and antituberculosis drug resistance could significantly improve access to testing. In this study, we evaluated the accuracy of the Akonni Biosystems XDR-TB (extensively drug-resistant TB) TruArray and lateral-flow-cell (XDR-LFC) assay (Akonni Biosystems, Inc., Frederick, MD, USA), a novel assay that detects mutations in seven genes associated with resistance to antituberculosis drugs: katG, the inhA promoter, and the ahpC promoter for isoniazid; rpoB for rifampin; gyrA for fluoroquinolones; rrs and the eis promoter for kanamycin; and rrs for capreomycin and amikacin. We evaluated assay performance using direct sputum samples from 566 participants recruited in a prospective cohort in Moldova over 2 years. The sensitivity and specificity against the phenotypic reference were both 100% for isoniazid, 99.2% and 97.9% for rifampin, 84.8% and 99.1% for fluoroquinolones, 87.0% and 84.1% for kanamycin, 54.3% and 100% for capreomycin, and 79.2% and 100% for amikacin, respectively. Whole-genome sequencing data for a subsample of 272 isolates showed 95 to 99% concordance with the XDR-LFC-reported suspected mutations. The XDR-LFC assay demonstrated a high level of accuracy for multiple drugs and met the WHO's minimum target product profile criteria for isoniazid and rifampin, while the sensitivity for fluoroquinolones and amikacin fell below target thresholds, likely due to the absence of a gyrB target in the assay. With optimization, the XDR-LFC shows promise as a novel near-patient technology to rapidly diagnose drug-resistant tuberculosis.

Deciduous woody plants like poplar (Populus spp.) have seasonal bud dormancy. It has been challenging to simultaneously delay the onset of bud dormancy in the fall and advance bud break in the spring, as bud dormancy, and bud break were thought to be controlled by different genetic factors. Here, we demonstrate that heterologous expression of the REVEILLE1 gene (named AaRVE1) from Agave (Agave americana) not only delays the onset of bud dormancy but also accelerates bud break in poplar in field trials. AaRVE1 heterologous expression increases poplar biomass yield by 166% in the greenhouse. Furthermore, we reveal that heterologous expression of AaRVE1 increases cytokinin contents, represses multiple dormancy-related genes, and up-regulates bud break-related genes, and that AaRVE1 functions as a transcriptional repressor and regulates the activity of the DORMANCY-ASSOCIATED PROTEIN 1 (DRM1) promoter. Our findings demonstrate that AaRVE1 appears to function as a regulator of bud dormancy and bud break, which has important implications for extending the growing season of deciduous trees in frost-free temperate and subtropical regions to increase crop yield.

Research on the ecology and conservation of Lepidoptera (and other species) has historically neglected tropical diversity – but the Lepidoptera of tropical Africa have been particularly understudied. Central Africa represents a major centre of biodiversity for butterflies, moths and other taxa but major threats including habitat loss, habitat degradation/ disturbance and climate change are threatening their persistence. Additionally, a range of obstacles to research and conservation are apparent in Central Africa, including major socioeconomic disparity, persistent armed conflicts, corruption, and a lack of local resources (e.g., funding and museums). Here we outline the history of research on the butterflies of Central Africa and highlight the importance of further conservation efforts in maintaining the biodiversity of Lepidoptera and other understudied insects in the region. Proactive measures acknowledging the prevailing regional challenges must be taken immediately. Among the major recommendations, we suggest: 1) enhancing museum collections, 2) facilitating strong scientific collaboration that enhances local capacity, 3) ensuring that funded projects are not disrupted by corruption, and 4) working to advance the socioeconomic status of local communities. Potential for scientific and community advancement in the region is substantial if investment and research efforts are targeted effectively.

Dynamic energy budget (DEB) theory has been applied to model a wide range of organisms, including microbes. In the standard DEB model, biomass is partitioned into reserve and structural compartments, where reserve biomass is mobilized in a pseudolinear manner (while the reserve biomass density, defined as the ratio between reserve and structural biomass, decays linearly) to drive maintenance and the growth of structural biomass (and extracellular enzyme production if it is considered). However, the linear dynamics of the reserve biomass density makes the standard DEB model incapable of explaining the slowdown of microbial growth at high reserve density that is caused by macromolecular crowding effect which reduces biochemical reaction rates (a typical situation occurs when microbes are experiencing severe moisture stress) and is inconsistent with the observation that intracellular enzymatic reactions generally follow non-linear kinetics. By partitioning biomass into reserve, kinetic, and structural compartments, we show here that the Equilibrium Chemistry Approximation (ECA) kinetics can be used to represent enzymatically catalyzed reserve biomass mobilization that can then drive the kinetic and structural biomass synthesis. This revised DEB model better represents the tradeoff in ribosome allocation for structural growth and internal enzyme production, is structurally compatible with metabolic models of cell individuals, and includes the standard DEB model and the popular compromise model as special cases for representing population growth. We then applied the revised DEB model to interpret components of bacterial respiration, their dependence on substrate availability, and emergent microbial carbon use efficiency dynamics for an exponentially growing population. We found that the revised DEB model enables a better understanding of bacterial substrates use (carbon in our examples) than that can be derived from a few other models in the literature. In particular, the revised DEB model explains why carbon use efficiency may first increase, then plateau, and finally decrease with growth rate (and substrate uptake rate), as a function of proteomics. Additionally, the revised DEB model explains why the kinetic biomass compartment needs to be divided to reasonably incorporate proteomic control of microbial growth.