A communal catalogue reveals Earth's multiscale microbial diversity.

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.

Financial stress and debt in clinical psychology doctoral students.

INTRODUTION: Few studies examine the financial burden of clinical psychology doctoral programs and its impact on achievements, stress, and mental health. OBJECTIVES: The current study sought to better understand students' financial stress and debt, and how financial stress may impact their mental health and the attainment of personal and professional milestones. METHOD: Students (N = 912) completed an online survey assessing demographics, sources of income and expenditures, mental health, and milestones. RESULTS: After accounting for yearly inflation, stipends have not kept pace with the average cost of living in the United States. Over one-third of students indicated that they had no expendable pretax income after paying for their education and typical living expenses. Additionally, over 80% reported acquiring additional debt in graduate school to offset their living expenses. Financial concerns were associated with delays in major life milestones (e.g., buying a car/house, getting married/starting a family, having children), as well as avoiding medical (34.2%) or mental (41.4%) health care, with 17.5% of participants experiencing a health crisis they could not afford while in graduate school. Financial stress was associated with an increase in time spent thinking about finances, higher rates of depression and anxiety symptoms, and decreased sleep. CONCLUSION: Many clinical psychology doctoral students experience financial stress and are often unable to afford basic educational, personal living, and health care expenses, likely worsening mental health. Academic programs and leadership are encouraged to increase student stipends, improve financial transparency, provide access to health care, and alleviate financial stress and debt.

Pregnancy options counseling.

PURPOSE OF REVIEW: This article reviews key aspects of pregnancy options counseling, and highlights how inappropriate counseling can create barriers to timely and safe abortion care. RECENT FINDINGS: Access to safe abortion services in the United States is increasingly constrained. One way to combat this hostile environment is to ensure that individuals presenting for care early in pregnancy have access to comprehensive and unbiased pregnancy options counseling. There are unfortunately many barriers to individuals receiving adequate pregnancy options counseling, and marginalized groups experience disproportionate effects of inappropriate counseling. Research shows that individuals desire appropriate pregnancy options counseling when seeking early pregnancy care, and that providers often serve as a barrier to this care. Provider miseducation and opposition to pregnancy options counseling, particularly as it concerns abortion care, creates challenges and delays for people seeking abortion services. Crisis Pregnancy Centers use misinformation to further these barriers to appropriate care. SUMMARY: Nondirective and patient-centered pregnancy options counseling is standard of care. People seeking pregnancy options counseling desire and deserve comprehensive and accurate information. Providers must not serve as barriers to safe and appropriate care. Increasing nondirective pregnancy options counseling research, education, and training is crucial to ensuring access to safe and appropriate abortion care.

Advances in Research on Adolescent Suicide and a High Priority Agenda for Future Research.

Suicide is the second leading cause of death for adolescents in the United States, yet remarkably little is known regarding risk factors for suicidal thoughts and behaviors (STBs), relatively few federal grants and scientific publications focus on STBs, and few evidence-based approaches to prevent or treat STBs are available. This "decade in review" article discusses five domains of recent empirical findings that span biological, environmental, and contextual systems and can guide future research in this high priority area: (1) the role of the central nervous system; (2) physiological risk factors, including the peripheral nervous system; (3) proximal acute stress responses; (4) novel behavioral and psychological risk factors; and (5) broader societal factors impacting diverse populations and several additional nascent areas worthy of further investigation.

Linking post-stressor interpersonal processes in adolescent girls' close friendships with acute HPA stress responses.

INTRODUCTION: For adolescent girls, close friendships may facilitate stress management and mitigate risk for internalizing psychopathology. However, little is known about how friendship processes may buffer (or potentially exacerbate) acute psychobiological responses to interpersonal stressors in ways that affect risk. METHODS: In a sample of 220 girls (ages 12-17 years) with a history of internalizing symptoms, this study investigated friendship dynamics following the Trier Social Stress Test (TSST) to evaluate associations between post-stressor friendship behaviors (expressions of vulnerability by the stressed teen; support offered by their close friend) and hypothalamic-pituitary-adrenal (HPA) axis stress responses. RESULTS: Multilevel regression modeling revealed that girls who displayed more pronounced cortisol reactivity expressed greater vulnerability to, and received greater support from, their close friend. Expressed vulnerability was associated with more efficient cortisol recovery. Close friend support was not significantly associated with cortisol recovery, nor did it influence the connection between expressed vulnerability and cortisol recovery. CONCLUSIONS: Findings suggest that HPA reactivity may prompt expressions of vulnerability to girls' close friends, and in this context, promote more efficient HPA recovery. Findings highlight the role friendship dynamics may play in HPA-related risk for internalizing symptoms and point to expressed vulnerability in adolescent girls' close friendships as a potential consideration for interpersonally-centered therapeutic approaches.

Mental health concerns and barriers to care among future clinical psychologists.

Few studies have examined the mental health of clinical psychology doctoral students, a unique group given their education and training in psychopathology, assessment, and intervention. Students (N = 912) completed an online survey assessing demographics, mental health, mental healthcare utilization, and barriers to care during graduate school. Nearly 25% of participants reported moderate to severe symptoms of anxiety, 20% reported moderate to severe symptoms of depression or suicidal intent (SI), and more than 10% reported a high risk of alcohol abuse or moderate to severe drug use during graduate school. In comparison to peers, ethnic minority and lesbian, gay, bisexual, transgender, and queer (LGBTQ+) participants reported more symptoms of depression and SI. LGBTQ+ participants reported more nonsuicidal self-injury and drug use. Participants also experienced significant barriers to receiving mental healthcare (e.g., financial difficulties, limited availability, insufficient time). Leadership is encouraged to prioritize the mental health of clinical psychology doctoral students, which may have implications on their service provision.

Clinical psychology PhD students' admission experiences: Implications for recruiting racial/ethnic minority and LGBTQ students.

AIM: The purpose of this study was to explore differences in the clinical psychology PhD program admissions experience (i.e., interviewing and decision-making) by race/ethnicity and lesbian, gay, bisexual, transgender, and queer (LGBTQ) identity. METHODS: Participants were 803 students (24% racial/ethnic minority; 19% LGBTQ) enrolled in US clinical psychology PhD programs. Two-group comparisons tested for differences in admission experiences by race/ethnicity and LGBTQ identity. RESULTS: Racial/ethnic minority and LGBTQ students considered a programmatic commitment to diversity as more important in application decisions compared to non-Hispanic White and cisgender heterosexual students, respectively. LGBTQ students were more likely to be advised to not discuss personal information (e.g., sexual orientation) than cisgender heterosexual students. Racial/ethnic minority and LGBTQ students identified financial considerations and program outcomes as more important in their decision-making compared with non-Hispanic White and cisgender heterosexual students, respectively. CONCLUSION: Increasing funding and fostering authentic training environments should be prioritized in institutional conversations around recruiting racial/ethnic minority and LGBTQ trainees.

Differential effects of the menstrual cycle on reactive and proactive aggression in borderline personality disorder.

Borderline personality disorder (BPD) is characterized by rapidly shifting symptoms, including intense anger and aggressive behavior. Understanding how fluctuations in ovarian hormones across the menstrual cycle may contribute to symptom instability is key for accurate assessment of BPD symptoms and effective interventions. Reactive and proactive aggression, as well as anger-in and anger-out, were assessed daily in 15 physically healthy, unmedicated naturally cycling female individuals meeting criteria for BPD across 35 days. Urine luteinizing hormone surge and salivary progesterone were used to confirm ovulation and verify the cycle phase. Multilevel models evaluated cyclical differences of symptoms between cycle phases. Both forms of aggressive behavior demonstrated marked cycle effects, with reactive aggression highest during the midluteal cycle phase, co-occurring with initial increases in anger and irritability and followed by perimenstrual peaks in anger and anger-in. In contrast, highest levels of proactive aggression were observed during the follicular and ovulatory phases, when emotional symptoms and anger were otherwise at lowest levels. These findings highlight the importance of identifying the function of aggression when considering potential psychological and biological influences. Naturally cycling individuals with BPD may be at elevated risk for luteal worsening of a range of interpersonally reactive symptoms, including reactive aggression, whereas proactive aggression may occur more in phases characterized by less emotional and cognitive vulnerability and greater reward sensitivity. Research on aggression in this population should consider cycle effects. Cycling individuals with BPD attempting to reduce aggressive behavior may benefit from cycle-tracking to increase awareness of these effects and to develop appropriate strategies.

Perimenstrual exacerbation of symptoms in borderline personality disorder: evidence from multilevel models and the Carolina Premenstrual Assessment Scoring System.

BACKGROUND: Individuals with a borderline personality disorder (BPD) suffer from a constellation of rapidly shifting emotional, interpersonal, and behavioral symptoms. The menstrual cycle may contribute to symptom instability among females with this disorder. METHODS: Fifteen healthy, unmedicated females with BPD and without dysmenorrhea reported daily symptoms across 35 days. Urine luteinizing hormone and salivary progesterone (P4) were used to confirm ovulation and cycle phase. Cyclical worsening of symptoms was evaluated using (1) phase contrasts in multilevel models and (2) the Carolina Premenstrual Assessment Scoring System (C-PASS), a protocol for evaluating clinically significant cycle effects on symptoms. RESULTS: Most symptoms demonstrated midluteal worsening, a perimenstrual peak, and resolution of symptoms in the follicular or ovulatory phase. Post-hoc correlations with person-centered progesterone revealed negative correlations with most symptoms. Depressive symptoms showed an unexpected delayed pattern in which baseline levels of symptoms were observed in the ovulatory and midluteal phases, and exacerbations were observed during both the perimenstrual and follicular phases. The majority of participants met C-PASS criteria for clinically significant (⩾30%) symptom exacerbation. All participants met the emotional instability criterion of BPD, and no participant met DSM-5 criteria for premenstrual dysphoric disorder (PMDD). CONCLUSIONS: Females with BPD may be at elevated risk for perimenstrual worsening of emotional symptoms. Longitudinal studies with fine-grained hormonal measurement as well as hormonal experiments are needed to determine the pathophysiology of perimenstrual exacerbation in BPD.

Suicide Risk and the Menstrual Cycle: a Review of Candidate RDoC Mechanisms.

PURPOSE OF REVIEW: Risk for suicidal behavior may fluctuate across the menstrual cycle. Here, we use the RDoC framework to review potential mechanisms by which the cycle may increase acute suicide risk. RECENT FINDINGS: The menstrual cycle impacts the majority of RDoC constructs linked to suicide risk, particularly among hormone-sensitive women, such as those with premenstrual dysphoric disorder or premenstrual exacerbation of a psychiatric disorder. Despite this, there are no published studies examining suicidal ideation, planning, or behavior longitudinally across the cycle. More work is needed to understand how hormone sensitivity may relate to both trait and state suicide risk. Intensive multilevel investigations of cyclical hormone effects on suicide risk through specific RDoC mechanisms are suggested. This is a fertile research area and may provide key insights regarding the mechanisms of acute suicide risk.

Disfluencies signal reference to novel objects for adults but not children.

Speech disfluencies can guide the ways in which listeners interpret spoken language. Here, we examined whether three-year-olds, five-year-olds, and adults use filled pauses to anticipate that a speaker is likely to refer to a novel object. Across three experiments, participants were presented with pairs of novel and familiar objects and heard a speaker refer to one of the objects using a fluent ("Look at the ball/lep!") or disfluent ("Look at thee uh ball/lep!") expression. The salience of the speaker's unfamiliarity with the novel referents, and the way in which the speaker referred to the novel referents (i.e., a noun vs. a description) varied across experiments. Three- and five-year-olds successfully identified familiar and novel targets, but only adults' looking patterns reflected increased looks to novel objects in the presence of a disfluency. Together, these findings demonstrate that adults, but not young children, use filled pauses to anticipate reference to novel objects.

Size, Composition, and Source Profiles of Inhalable Bioaerosols from Colorado Dairies.

Particulate matter emissions from agricultural livestock operations contain both chemical and biological constituents that represent a potential human health hazard. The size and composition of these dusts, however, have not been well described. We evaluated the full size distribution (from 0 to 100 µm in aerodynamic diameter) and chemical/biological composition of inhalable dusts inside several Colorado dairy parlors. Four aerodynamic size fractions (<3, 3-10, 10-30, and >30 µm) were collected and analyzed using a combination of physiochemical techniques to understand the structure of bacterial communities and chemical constituents. Airborne particulate mass followed a bimodal size distribution (one mode at 3 µm and a second above 30 µm), which also correlated with the relative concentrations of the following microbiological markers: bacterial endotoxin, 3-hydroxy fatty acids, and muramic acid. Sequencing of the 16S-rRNA components of this aerosol revealed a microbiome derived predominantly from animal sources. Bacterial genera included Staphlyococcus, Pseudomonas, and Streptococcus, all of which have proinflammatory and pathogenic capacity. Our results suggest that the size distribution of bioaerosols emitted by dairy operations extends well above 10 µm in diameter and contains a diverse mixture of potentially hazardous constituents and opportunistic pathogens. These findings should inform the development of more effective emissions control strategies.

Spatial scale drives patterns in soil bacterial diversity.

Soil microbial communities are essential for ecosystem function, but linking community composition to biogeochemical processes is challenging because of high microbial diversity and large spatial variability of most soil characteristics. We investigated soil bacterial community structure in a switchgrass stand planted on soil with a history of grassland vegetation at high spatial resolution to determine whether biogeographic trends occurred at the centimeter scale. Moreover, we tested whether such heterogeneity, if present, influenced community structure within or among ecosystems. Pronounced heterogeneity was observed at centimeter scales, with abrupt changes in relative abundance of phyla from sample to sample. At the ecosystem scale (> 10 m), however, bacterial community composition and structure were subtly, but significantly, altered by fertilization, with higher alpha diversity in fertilized plots. Moreover, by comparing these data with data from 1772 soils from the Earth Microbiome Project, it was found that 20% of bacterial taxa were shared between their site and diverse globally sourced soil samples, while grassland soils shared approximately 40% of their operational taxonomic units with the current study. By spanning several orders of magnitude, the analysis suggested that extreme patchiness characterized community structure at smaller scales but that coherent patterns emerged at larger length scales.

Language Delays and Child Depressive Symptoms: the Role of Early Stimulation in the Home.

The present study investigated the role of early stimulation in the home and child language delays in the emergence of depressive symptoms. Data were from a longitudinal study of at-risk children in Hawaii (n = 587). Low learning stimulation in the home at age 3 and language delays in first grade both significantly increased risk for child depressive symptoms in third grade. Structural equation modeling supported the hypothesized path models from home learning environment at age 3 to depressive symptoms in third grade controlling for a host of correlated constructs (maternal depression, child temperament, and child internalizing symptoms). Total language skills in the first grade mediated the effect of home learning environment on depressive symptoms. The study and findings fit well with a nurturing environment perspective. Implications for understanding the etiology of child depression and for designing interventions and prevention strategies are discussed.

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes.

For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions for soil microbial communities despite soil microbes being the dominant engines of biogeochemical cycles and a major pool of living biomass in terrestrial ecosystems. We used metagenomic sequencing to compare the composition and functional attributes of 16 soil microbial communities collected from cold deserts, hot deserts, forests, grasslands, and tundra. Those communities found in plant-free cold desert soils typically had the lowest levels of functional diversity (diversity of protein-coding gene categories) and the lowest levels of phylogenetic and taxonomic diversity. Across all soils, functional beta diversity was strongly correlated with taxonomic and phylogenetic beta diversity; the desert microbial communities were clearly distinct from the nondesert communities regardless of the metric used. The desert communities had higher relative abundances of genes associated with osmoregulation and dormancy, but lower relative abundances of genes associated with nutrient cycling and the catabolism of plant-derived organic compounds. Antibiotic resistance genes were consistently threefold less abundant in the desert soils than in the nondesert soils, suggesting that abiotic conditions, not competitive interactions, are more important in shaping the desert microbial communities. As the most comprehensive survey of soil taxonomic, phylogenetic, and functional diversity to date, this study demonstrates that metagenomic approaches can be used to build a predictive understanding of how microbial diversity and function vary across terrestrial biomes.

Dinitrogen fixation associated with shoots of aquatic carnivorous plants: is it ecologically important?

BACKGROUND AND AIMS: Rootless carnivorous plants of the genus Utricularia are important components of many standing waters worldwide, as well as suitable model organisms for studying plant-microbe interactions. In this study, an investigation was made of the importance of microbial dinitrogen (N2) fixation in the N acquisition of four aquatic Utricularia species and another aquatic carnivorous plant, Aldrovanda vesiculosa. METHODS: 16S rRNA amplicon sequencing was used to assess the presence of micro-organisms with known ability to fix N2. Next-generation sequencing provided information on the expression of N2 fixation-associated genes. N2 fixation rates were measured following (15)N2-labelling and were used to calculate the plant assimilation rate of microbially fixed N2. KEY RESULTS: Utricularia traps were confirmed as primary sites of N2 fixation, with up to 16 % of the plant-associated microbial community consisting of bacteria capable of fixing N2. Of these, rhizobia were the most abundant group. Nitrogen fixation rates increased with increasing shoot age, but never exceeded 1·3 µmol N g(-1) d. mass d(-1). Plant assimilation rates of fixed N2 were detectable and significant, but this fraction formed less than 1 % of daily plant N gain. Although trap fluid provides conditions favourable for microbial N2 fixation, levels of nif gene transcription comprised <0·01 % of the total prokaryotic transcripts. CONCLUSIONS: It is hypothesized that the reason for limited N2 fixation in aquatic Utricularia, despite the large potential capacity, is the high concentration of NH4-N (2·0-4·3 mg L(-1)) in the trap fluid. Resulting from fast turnover of organic detritus, it probably inhibits N2 fixation in most of the microorganisms present. Nitrogen fixation is not expected to contribute significantly to N nutrition of aquatic carnivorous plants under their typical growth conditions; however, on an annual basis the plant-microbe system can supply nitrogen in the order of hundreds of mg m(-2) into the nutrient-limited littoral zone, where it may thus represent an important N source.

Using low volume eDNA methods to sample pelagic marine animal assemblages.

Environmental DNA (eDNA) is an increasingly useful method for detecting pelagic animals in the ocean but typically requires large water volumes to sample diverse assemblages. Ship-based pelagic sampling programs that could implement eDNA methods generally have restrictive water budgets. Studies that quantify how eDNA methods perform on low water volumes in the ocean are limited, especially in deep-sea habitats with low animal biomass and poorly described species assemblages. Using 12S rRNA and COI gene primers, we quantified assemblages comprised of micronekton, coastal forage fishes, and zooplankton from low volume eDNA seawater samples (n = 436, 380-1800 mL) collected at depths of 0-2200 m in the southern California Current. We compared diversity in eDNA samples to concurrently collected pelagic trawl samples (n = 27), detecting a higher diversity of vertebrate and invertebrate groups in the eDNA samples. Differences in assemblage composition could be explained by variability in size-selectivity among methods and DNA primer suitability across taxonomic groups. The number of reads and amplicon sequences variants (ASVs) did not vary substantially among shallow (<200 m) and deep samples (>600 m), but the proportion of invertebrate ASVs that could be assigned a species-level identification decreased with sampling depth. Using hierarchical clustering, we resolved horizontal and vertical variability in marine animal assemblages from samples characterized by a relatively low diversity of ecologically important species. Low volume eDNA samples will quantify greater taxonomic diversity as reference libraries, especially for deep-dwelling invertebrate species, continue to expand.

A modeling pipeline to relate municipal wastewater surveillance and regional public health data.

As COVID-19 becomes endemic, public health departments benefit from improved passive indicators, which are independent of voluntary testing data, to estimate the prevalence of COVID-19 in local communities. Quantification of SARS-CoV-2 RNA from wastewater has the potential to be a powerful passive indicator. However, connecting measured SARS-CoV-2 RNA to community prevalence is challenging due to the high noise typical of environmental samples. We have developed a generalized pipeline using in- and out-of-sample model selection to test the ability of different correction models to reduce the variance in wastewater measurements and applied it to data collected from treatment plants in the Chicago area. We built and compared a set of multi-linear regression models, which incorporate pepper mild mottle virus (PMMoV) as a population biomarker, Bovine coronavirus (BCoV) as a recovery control, and wastewater system flow rate into a corrected estimate for SARS-CoV-2 RNA concentration. For our data, models with BCoV performed better than those with PMMoV, but the pipeline should be used to reevaluate any new data set as the sources of variance may change across locations, lab methods, and disease states. Using our best-fit model, we investigated the utility of RNA measurements in wastewater as a leading indicator of COVID-19 trends. We did this in a rolling manner for corrected wastewater data and for other prevalence indicators and statistically compared the temporal relationship between new increases in the wastewater data and those in other prevalence indicators. We found that wastewater trends often lead other COVID-19 indicators in predicting new surges.

Asymmetric functional divergence of young, dispersed gene duplicates in Arabidopsis thaliana.

One prediction of the classic Ohno model of gene duplication predicts that new genes form from the asymmetric functional divergence of a newly arisen, redundant duplicate locus. In order to understand the mechanisms which give rise to functional divergence of newly formed dispersed duplicates, we assessed the expression and molecular evolutionary divergence of a suite of 19 highly similar dispersed duplicates in Arabidopsis thaliana. These duplicates have a K sil equal to or less than 5 % and are specific to the A. thaliana lineage; thus, they predictably represent some of the youngest duplicates in the A. thaliana genome. We found that the majority of young duplicate loci exhibit asymmetric expression patterns, with the daughter locus exhibiting reduced expression across all tissues analyzed relative to the progenitor locus or simply not expressed. Furthermore, daughter loci, on the whole, have significantly more nonsynonymous substitutions than the progenitor loci. We also identified four pairs of loci which exhibit significant (P < 0.05) evolutionary rate asymmetry, three of which exhibit elevated dN/dS in the duplicate copy. We suggest, based on these data, that functional diversification initially takes the form of asymmetric regulatory divergence that can be a direct consequence of the mode of duplication. The reduced and/or absence of expression in the daughter copy relaxes functional constraint on its protein coding sequence leading to the asymmetric accumulation of nonsynonymous mutations. Thus, our data both affirm Ohno's prediction while explaining the mechanism by which functional divergence initially occurs following duplication for dispersed gene duplicates.