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While work in temperate forests suggests that there are consistent differences in plant–soil feedback (PSF) between plants with arbuscular and ectomycorrhizal associations, it is unclear whether these differences exist in tropical rainforests. We tested the effects of mycorrhizal type, phylogenetic relationships to overstory species, and soil fertility on the growth of tree seedlings in a tropical Bornean rainforest with a high diversity of both ectomycorrhizal and arbuscular mycorrhizal trees. We found that ectomycorrhizal tree seedlings had higher growth in soils conditioned by close relatives and that this was associated with higher mycorrhizal colonization. By contrast, arbuscular mycorrhizal tree seedlings generally grew more poorly in soils conditioned by close relatives. For ectomycorrhizal species, the phylogenetic trend was insensitive to soil fertility. For arbuscular mycorrhizal seedlings, however, the effect of growing in soils conditioned by close relatives became increasingly negative as soil fertility increased. Our results demonstrate consistent effects of mycorrhizal type on plant–soil feedbacks across forest biomes. The positive effects of ectomycorrhizal symbiosis may help explain biogeographic variation across tropical forests, such as familial dominance of the Dipterocarpaceae in southeast Asia. However, positive feedbacks also raise questions about the role of PSFs in maintaining tropical diversity.

Global climate change is driving species poleward and upward in high-latitude regions, but the extent to which the biodiverse tropics are similarly affected is poorly known due to a scarcity of historical records. In 1802, Alexander von Humboldt ascended the Chimborazo volcano in Ecuador. He recorded the distribution of plant species and vegetation zones along its slopes and in surrounding parts of the Andes. We revisited Chimborazo in 2012, precisely 210 y after Humboldt’s expedition. We documented upward shifts in the distribution of vegetation zones as well as increases in maximum elevation limits of individual plant taxa of >500 m on average. These range shifts are consistent with increased temperatures and glacier retreat on Chimborazo since Humboldt’s study. Our findings provide evidence that global warming is strongly reshaping tropical plant distributions, consistent with Humboldt’s proposal that climate is the primary control on the altitudinal distribution of vegetation.

Interrupting transmission events is critical to tuberculosis control. Cough-generated aerosol cultures predict tuberculosis transmission better than microbiological or clinical markers. We hypothesize that highly infectious individuals with pulmonary tuberculosis (positive for cough aerosol cultures) have elevated inflammatory markers and unique transcriptional profiles compared to less infectious individuals. We performed a prospective, longitudinal study using cough aerosol sampling system. We enrolled 142 participants with treatment-naïve pulmonary tuberculosis in Kenya and assessed the association of clinical, microbiologic, and immunologic characteristics with Mycobacterium tuberculosis aerosolization and transmission in 129 household members. Contacts of the forty-three aerosol culture-positive participants (30%) are more likely to have a positive interferon-gamma release assay (85% vs 53%, P = 0.006) and higher median IFNγ level (P < 0.001, 4.28 IU/ml (1.77-5.91) vs. 0.71 (0.01-3.56)) compared to aerosol culture-negative individuals. We find that higher bacillary burden, younger age, larger mean upper arm circumference, and host inflammatory profiles, including elevated serum C-reactive protein and lower plasma TNF levels, associate with positive cough aerosol cultures. Notably, we find pre-treatment whole blood transcriptional profiles associate with aerosol culture status, independent of bacillary load. These findings suggest that tuberculosis infectiousness is associated with epidemiologic characteristics and inflammatory signatures and that these features may identify highly infectious persons. Using cough-generated aerosol cultures, authors probe the inflammatory markers and epidemiological characteristics of individuals with pulmonary tuberculosis, in association with infection state.

Plant species leave a chemical signature in the soils below them, generating fine-scale spatial variation that drives ecological processes. Since the publication of a seminal paper on plant-mediated soil heterogeneity by Paul Zinke in 1962, a robust literature has developed examining effects of individual plants on their local environments (individual plant effects). Here, we synthesize this work using meta-analysis to show that plant effects are strong and pervasive across ecosystems on six continents. Overall, soil properties beneath individual plants differ from those of neighbours by an average of 41%. Although the magnitudes of individual plant effects exhibit weak relationships with climate and latitude, they are significantly stronger in deserts and tundra than forests, and weaker in intensively managed ecosystems. The ubiquitous effects of plant individuals and species on local soil properties imply that individual plant effects have a role in plant–soil feedbacks, linking individual plants with biogeochemical processes at the ecosystem scale.

Despite heavy exposure to Mycobacterium tuberculosis (Mtb), some individuals are resistant to TST and IGRA conversion (RSTRs). The functional and immunological mechanisms governing resistance are poorly understood. We hypothesized that RSTR and LTBI alveolar macrophages (AMs) respond differently to Mtb infection with transcriptional programs that are distinct from peripheral blood monocytes. We examined media and Mtb-infected AMs from bronchoalveolar lavage fluid collected from a RSTR cohort in Uganda with over 10 years of clinical follow-up. With transcriptional profiles of BAL cells analyzed immediately after collection, gene set enrichment analysis (GSEA) revealed 13 differentially expressed gene sets between RSTR ( n  = 19) and LTBI ( n  = 26) groups, including one (Hallmark E2F targets) which was positively enriched in the RSTR group (FDR < 0.3). In a subset of this cohort ( n  = 7 RSTR and 8 LTBI), AMs were examined with and without Mtb infection. When comparing the RSTR and LTBI groups, we identified 52 DEGs including 22 in the media condition, 15 with Mtb stimulation, and 11 with the interaction term (FDR < 0.2, Log 2-fold change > 1/<-1). Notably, RSTR AMs appear to upregulate inflammation more strongly than LTBI counterparts, including Hallmark inflammatory response (FDR < 0.2), IFNγ response (FDR < 0.1), and IFNα response (FDR < 0.1) while existing in a more non-inflammatory state at baseline (Hallmark TNF signaling via NF-kB (down, FDR < 0.1), inflammatory response (down, FDR < 0.1). In a comparison of peripheral blood monocyte gene expression profiles from the same cohort, there were both shared and AM-specific RSTR profiles detected. Together, these results suggest that RSTR and LTBI AMs have different basal and Mtb-induced transcriptional profiles, including some that differ from peripheral blood monocytes.

A mechanistic understanding of uncommon immune outcomes such as resistance to infection has led to the development of novel therapies. Using gene level analytic methods, we previously found distinct monocyte transcriptional responses associated with resistance to Mycobacterium tuberculosis (Mtb) infection defined as persistently negative tuberculin skin test (TST) and interferon gamma release assay (IGRA) reactivity among highly exposed contacts (RSTR phenotype). Using transcript isoform analyses, we aimed to identify novel RSTR-associated genes hypothesizing that previous gene-level differential expression analysis obscures isoform-specific differences that contribute to phenotype. Monocytes from 49 RSTR versus 52 subjects with latent Mtb infection (LTBI) were infected with M. tuberculosis (H37Rv) or left unstimulated (media) prior to RNA isolation and sequencing. RSTR-associated gene expression was then identified using differential transcript isoform analysis. We identified 81 differentially expressed transcripts (DETs) in 70 genes (FDR <0.05) comparing RSTR and LTBI phenotypes with the majority (n = 79 DETs) identified under Mtb-stimulated conditions. Seventeen of these genes were previously identified with gene-level bulk RNAseq analyses including genes in the IFNγ response that had increased expression among LTBI subjects, findings consistent with a clinical phenotype based on IGRA reactivity. Among the subset of 23 genes with positive differential expression among Mtb-infected RSTR monocytes, 13 were not previously identified. These novel DET genes included PDE4A and ZEB2, which each had multiple DETs with higher expression among RSTR subjects, and ACSL4 and GAPDH that each had a single transcript isoform associated with RSTR. Transcript isoform-specific analyses identify transcriptional associations, such as those associated with resistance to TST/IGRA conversion, that are obscured when using gene-level approaches. These findings should be validated with additional RSTR cohorts and whether the newly identified candidate resistance genes directly influence the monocyte Mtb response requires functional study.

Mepolizumab (anti-IL5 therapy) reduces asthma exacerbations in urban children with exacerbation-prone eosinophilic asthma. We previously utilized nasal transcriptomics to identify inflammatory pathways (gene co-expression modules) associated with asthma exacerbations despite this therapy. In this study, we applied differential gene correlation analysis on these targeted gene co-expression modules to gain better insight into the treatment effects on correlation structure within gene networks. Mepolizumab treatment resulted in loss of correlation amongst eosinophil-specific genes but conservation and even strengthening of correlation amongst mast cell-specific genes, T2 cytokines, and airway epithelial inflammatory genes. Notably, mepolizumab induced significant gain in correlation of genes associated with multiple aspects of airway epithelial inflammation including those related to extracellular matrix production and nitric oxide synthesis, and this change was associated with a poor clinical response to mepolizumab. These findings highlight that using differential gene correlation analysis offers insight into the molecular regulatory effects of treatment on gene interactions and may lead to better understanding of disease mechanisms and therapeutic responses. ClinicalTrials.gov ID: NCT03292588. Mepolizumab (anti-IL-5 therapy) has been shown to reduce type 2 inflammation in asthma. Here the authors use bulk transcriptomics from nasal samples before and after mepolizumab treatment to assess the changes and associations with treatment outcomes.

Seedling recruitment can be strongly affected by the composition of nearby plant species. At the neighborhood scale (on the order of tens of meters), adult conspecifics can modify soil chemistry and the presence of host microbes (pathogens and mutualists) across their combined canopy area or rooting zones. At local or small spatial scales (on the order of one to few meters), conspecific seed or seedling density can influence the strength of intraspecific light and resource competition and also modify the density‐dependent spread of natural enemies such as pathogens or invertebrate predators. Intrinsic correlation between proximity to adult conspecifics (i.e., recruitment neighborhood) and local seedling density, arising from dispersal, makes it difficult to separate the independent and interactive factors that contribute to recruitment success. Here, we present a field experiment in which we manipulated both the recruitment neighborhood and seedling density to explore how they interact to influence the growth and survival of Dryobalanops aromatica, a dominant ectomycorrhizal tree species in a Bornean tropical rainforest. First, we found that both local seedling density and recruitment neighborhood had effects on performance of D. aromatica seedlings, though the nature of these impacts varied between growth and survival. Second, we did not find strong evidence that the effect of density on seedling survival is dependent on the presence of conspecific adult trees. However, accumulation of mutualistic fungi beneath conspecifics adults does facilitate establishment of D. aromatica seedlings. In total, our results suggest that recruitment near adult conspecifics was not associated with a performance cost and may have weakly benefitted recruiting seedlings. Positive effects of conspecifics may be a factor facilitating the regional hyperabundance of this species. Synthesis: Our results provide support for the idea that dominant species in diverse forests may escape the localized recruitment suppression that limits abundance in rarer species. We present a rare‐field experiment in which we manipulated both the recruitment neighborhood (whether or not seedlings recruited in proximity to adult conspecifics) and seedling density to explore how they interact to influence the growth and survival of a dominant ectomycorrhizal tree species in a Bornean tropical rainforest. Our results provide support for the idea that dominant species in diverse forests may escape the localized recruitment suppression that limits abundance in rarer species and that ectomycorrhizal fungi play an important role in reducing CNDD for some tropical trees.