Leveraging microbiome rediversification for the ecological rescue of soil function.

BACKGROUND: Global biodiversity losses threaten ecosystem services and can impact important functional insurance in a changing world. Microbial diversity and function can become depleted in agricultural systems and attempts to rediversify agricultural soils rely on either targeted microbial introductions or retaining natural lands as biodiversity reservoirs. As many soil functions are provided by a combination of microbial taxa, rather than outsized impacts by single taxa, such functions may benefit more from diverse microbiome additions than additions of individual commercial strains. In this study, we measured the impact of soil microbial diversity loss and rediversification (i.e. rescue) on nitrification by quantifying ammonium and nitrate pools. We manipulated microbial assemblages in two distinct soil types, an agricultural and a forest soil, with a dilution-to-extinction approach and performed a microbiome rediversification experiment by re-introducing microorganisms lost from the dilution. A microbiome water control was included to act as a reference point. We assessed disruption and potential restoration of (1) nitrification, (2) bacterial and fungal composition through 16S rRNA gene and fungal ITS amplicon sequencing and (3) functional genes through shotgun metagenomic sequencing on a subset of samples. RESULTS: Disruption of nitrification corresponded with diversity loss, but nitrification was successfully rescued in the rediversification experiment when high diversity inocula were introduced. Bacterial composition clustered into groups based on high and low diversity inocula. Metagenomic data showed that genes responsible for the conversion of nitrite to nitrate and taxa associated with nitrogen metabolism were absent in the low diversity inocula microcosms but were rescued with high diversity introductions. CONCLUSIONS: In contrast to some previous work, our data suggest that soil functions can be rescued by diverse microbiome additions, but that the concentration of the microbial inoculum is important. By understanding how microbial rediversification impacts soil microbiome performance, we can further our toolkit for microbial management in human-controlled systems in order to restore depleted microbial functions.

Farm-scale differentiation of active microbial colonizers.

Microbial movement is important for replenishing lost soil microbial biodiversity and driving plant root colonization, particularly in managed agricultural soils, where microbial diversity and composition can be disrupted. Despite abundant survey-type microbiome data in soils, which are obscured by legacy DNA and microbial dormancy, we do not know how active microbial pools are shaped by local soil properties, agricultural management, and at differing spatial scales. To determine how active microbial colonizers are shaped by spatial scale and environmental conditions, we deployed microbial traps (i.e. sterile soil enclosed by small pore membranes) containing two distinct soil types (forest; agricultural), in three neighboring locations, assessing colonization through 16S rRNA gene and fungal ITS amplicon sequencing. Location had a greater impact on fungal colonizers (R2 = 0.31 vs. 0.26), while the soil type within the microbial traps influenced bacterial colonizers more (R2 = 0.09 vs. 0.02). Bacterial colonizers showed greater colonization consistency (within-group similarity) among replicate communities. Relative to bacterial colonizers, fungal colonizers shared a greater compositional overlap to sequences from the surrounding local bulk soil (R2 = 0.08 vs. 0.29), suggesting that these groups respond to distinct environmental constraints and that their in-field management may differ. Understanding how environmental constraints and spatial scales impact microbial recolonization dynamics and community assembly are essential for identifying how soil management can be used to shape agricultural microbiomes.

Soil salinization accelerates microbiome stabilization in iterative selections for plant performance.

Climate change-related soil salinization increases plant stress and decreases productivity. Soil microorganisms are thought to reduce salt stress through multiple mechanisms, so diverse assemblages could improve plant growth under such conditions. Previous studies have shown that microbiome selection can promote desired plant phenotypes, but with high variability. We hypothesized that microbiome selection would be more consistent in saline soils by increasing potential benefits to the plants. In both salt-amended and untreated soils, we transferred forward Brassica rapa root microbiomes (from high-biomass or randomly selected pots) across six planting generations while assessing bacterial (16S rRNA) and fungal (ITS) composition in detail. Uniquely, we included an add-back control (re-adding initial frozen soil microbiome) as a within-generation reference for microbiome and plant phenotype selection. We observed inconsistent effects of microbiome selection on plant biomass across generations, but microbial composition consistently diverged from the add-back control. Although salt amendment strongly impacted microbial composition, it did not increase the predictability of microbiome effects on plant phenotype, but it did increase the rate at which microbiome selection plateaued. These data highlight a disconnect in the trajectories of microbiomes and plant phenotypes during microbiome selection, emphasizing the role of standard controls to explain microbiome selection outcomes.

Abiotic conditions outweigh microbial origin during bacterial assembly in soils.

Understanding the processes guiding microbial community assembly in soils is essential for predicting microbiome structure and function following soil disturbance events like agricultural soil fumigation. However, assembly outcomes are complex and variable, being affected by both selective abiotic forces and by the history of colonizing microorganisms. To untangle the interactions between these factors, we conducted a controlled microcosm study tracking bacterial assembly in cleared soils over 7 weeks. We used mesh bags to connect five unsterilized source soils, differing in land use history (forested, agricultural, or fallow), with four sterile recipient soil treatments, differing in abiotic conditions (no soil additives, salt addition, urea addition, or mixed salt/urea addition). We found that 59%-96% of bacterial colonizers after 1 week were Firmicutes, but by 7 weeks Actinobacteria and Bacteroidetes were also dominant. Salt and nitrogen additions reshaped bacterial assembly by constraining alpha diversity by up to half and biomass accumulation by up to an order of magnitude. Within-treatment dispersion was significantly lower for salt and nutrient addition microcosms, suggesting deterministic selective pressures. In contrast, source soil origin had little impact on assembly trajectories. These results suggest that abiotic conditions can overshadow microbial source history in shaping community assembly outcomes.

Whole-Genome Sequences of Salmonella Isolates from an Ecological Wastewater Treatment System.

Twenty-seven Salmonella isolates were collected from four locations within an ecological wastewater treatment system located at The Pennsylvania State University and were subjected to whole-genome sequencing. The sequences obtained were used for in silico characterization, including serotyping and phylogenetic relatedness analysis.

Factoring Ecological, Societal, and Economic Considerations into Inoculant Development.

There are many paths toward effective microbial inoculants for agriculture. Considering what is practical for the present day technological and farming landscape should not limit our creativity in developing innovative technologies. However, factors including production costs, practicality of implementation, and technology adoption by farmers will drive the success of new management approaches.

Knowledge and practice of harm-reduction behaviours for alcohol and other illicit substance use in adolescents with type 1 diabetes.

OBJECTIVE: To survey adolescents with type 1 diabetes mellitus (T1DM) about their knowledge and application of harm-reduction recommendations when they engage in alcohol and other illicit substance use. METHODS: Cross-sectional survey and chart review of adolescents with T1DM aged 13 to 18 years. RESULTS: One hundred and ninety patients were approached and 164 were included in the analysis. Mean age was 15.6 years (standard deviation [SD]=1.5). Fifty-one per cent were male. Of those who reported consuming alcohol, 95% knew that they should have a friend or parent check their blood glucose in the middle of the night after drinking but only 62% reported actually doing this in practice. Similarly, 98% reported knowing that they should wear a medic alert identification but only 79% reported actually doing this. Of those who reported consuming cannabis, 14% reported forgetting to check blood glucose and 14% reported forgetting insulin when using cannabis. From the chart review, a significantly lower proportion of adolescents reported substance use during their clinic visits (alcohol 26%, tobacco 19%, illicit substance 25%) compared to the self report in the survey (alcohol 55%, tobacco 30%, illicit substance 32%). CONCLUSIONS: Adolescents' knowledge of harm-reduction practices for the use of alcohol and other illicit substances is not always put to practice. Motivating adolescents to use their knowledge in practice is an important area to improve in diabetes self-management. Those who reported engaging in substance use in the survey had not always reported use during interactions with health care providers. This emphasizes the need for unbiased, universal education of all adolescents in the clinic.

The Inherent Conflicts in Developing Soil Microbial Inoculants.

Potentially beneficial microorganisms have been inoculated into agricultural soils for years. However, concurrent with sequencing advances and successful manipulation of host-associated microbiomes, industry and academia have recently boosted investments into microbial inoculants, convinced they can increase crop yield and reduce fertilizer and pesticide requirements. The efficacy of soil microbial inoculants remains unreliable, and unlike crop breeding, in which target traits (e.g., yield) have long been considered alongside environmental compatibility, microbial inoculant ecology is not sufficiently integrated into microbial selection and production. We propose a holistic temporal model of the shifting constraints on inoculants at five stages of product development and application, and highlight potential conflicts between stages. We question the feasibility of developing ideal soil microbial inoculants with current approaches.

Prevalence of alcohol, tobacco, cannabis and other illicit substance use in a population of Canadian adolescents with type 1 diabetes compared to a general adolescent population.

BACKGROUND: Youth with chronic conditions may engage in risky behaviour to the same, if not higher, degree as their healthy peers. OBJECTIVES: To determine the prevalence of alcohol, tobacco, cannabis and illicit substance use in adolescents with type 1 diabetes (T1DM) compared to a general adolescent population. METHODS: Cross-sectional survey of adolescents with T1DM (13 to 18 years). A published contemporary Canadian youth survey on use of alcohol, tobacco and illicit drugs was used as data representative of the general adolescent population. Outcome measures between the T1DM and general group were compared using Chi-square and Fisher's exact test where appropriate. RESULTS: One hundred and sixty-four adolescents with T1DM (mean 15.6 years [SD 1.5]; 51.3% male) were participated. The proportions of adolescents with T1DM who have tried substances were: alcohol 51.8%, tobacco 27.4%, cannabis 22.6% and other illicit substances 7.3%. Compared to the general population (n=3469), there were no significant differences in the proportion of adolescents that reported ever consuming alcohol, tobacco or cannabis. Reported illicit substance use was significantly lower in adolescents with T1DM compared to general population (7.3% versus 36.0%, P<0.0001). CONCLUSIONS: Proportions reporting having ever consumed alcohol, tobacco or cannabis were not significantly different between the two groups. However, the proportion of adolescents with T1DM who reported ever consuming an illicit substance was different from the comparison group. It is important to explore risky behaviours with adolescents with T1DM and focus on prevention and education during routine clinic visits.

The association between body mass index and physical activity, and body image, self esteem and social support in adolescents with type 1 diabetes.

OBJECTIVE: To examine the associations between body mass index (BMI) and physical activity with body image, self-esteem and social support in adolescents with type 1 diabetes compared to adolescents without health conditions. METHODS: We studied 46 adolescents with type 1 diabetes and 27 comparison adolescents who provided self-reports of height and weight, which were used to calculate BMI z-scores. Participants also completed validated questionnaires that assessed physical activity, body image, self-esteem and social support. RESULTS: No significant group differences were found between adolescents with type 1 diabetes and comparison adolescents in terms of BMI and physical activity. Examination of group and gender revealed that higher BMI was significantly associated with a less positive body image in girls with diabetes only. Higher BMI was associated with poorer self-esteem and lower levels of social support in adolescents with diabetes, particularly girls. Higher levels of physical activity were not associated with a more positive body image and no significant associations were found between physical activity and self-esteem or social support. CONCLUSIONS: BMI and physical activity levels of adolescents with type 1 diabetes do not differ from those of adolescents without diabetes. Higher BMI is associated with a less positive body image and poorer psychosocial outcomes, particularly in girls with diabetes. As body image concerns and various psychosocial factors could be precursors to the development of eating-disorder symptoms, future research in adolescents with diabetes with higher BMIs should examine the associations among these variables. Further, it is essential that research on body image take into account gender differences.

Psychological correlates of eating disorder symptoms and body image in adolescents with type 1 diabetes.

OBJECTIVE: To examine eating disorder symptoms and body image in adolescents with type 1 diabetes and to investigate the associations among social support, self-esteem, health locus of control, eating disorder symptoms and body image. METHODS: Forty-six adolescents with type 1 diabetes and 27 healthy comparison adolescents completed questionnaires. RESULTS: No significant differences were identified in eating disorder symptoms and body image between adolescents with type 1 diabetes and healthy comparison adolescents. Regression analyses were completed with the full sample of adolescents with type 1 diabetes and healthy comparison adolescents. Higher levels of social support and being male were associated with a more positive body image, less body dissatisfaction and a lower drive for thinness. A belief by the adolescents that parents or healthcare providers (i.e. external powerful others locus of control) were in control of their health was associated with a more positive body image and less body dissatisfaction. Higher self-esteem was associated with a greater drive for thinness and a higher level of body dissatisfaction. CONCLUSIONS: Social support, health locus of control and self-esteem appear to be important correlates of eating disorder symptoms and body image in adolescents with diabetes and their typically developing peers.

Self-concept, attitude toward illness and family functioning in adolescents with type 1 diabetes.

OBJECTIVES: The primary objective of the present study was to assess self-concept in adolescents with type 1 diabetes, and to determine whether this is associated with attitudes toward having chronic disease, family functioning or severity of diabetes. The secondary objective was to assess the impact of family income, sex, age and age at diagnosis on adolescent self-concept. METHODS: A cross-sectional, self-report survey of 48 adolescents with type 1 diabetes (22 boys and 26 girls; mean +/- SD age at time of study 15.2+/-1.7 years [range 12.2 to 18.0 years]; mean age at diagnosis 9.2+/-3.3 years [range 1.3 to 14.9 years]) was performed using the Piers-Harris Children's Self-Concept (PHCSC) scale, second edition; the Child Attitude Toward Illness Scale; and the Family Assessment Measure scale, version III. Demographic information including net family income and a symptom inventory form to assess disease severity was collected. RESULTS: Adolescents' self-concept measured by the PHCSC scale was significantly positively correlated with a more positive attitude toward chronic illness as measured by the Child Attitude Toward Illness Scale. The PHCSC scale was found to have a significant negative correlation with the Family Assessment Measure scale score, indicating that a better self-concept was correlated with enhanced family functioning. Self-concept was not significantly correlated with disease severity, income of family, sex, age at diagnosis, age at time of study, episodes of diabetic ketoacidosis or episodes of hypoglycemia. CONCLUSIONS: Adolescents with better self-concept had more positive attitudes toward their chronic illness and enhanced family functioning. Although no correlation with diabetes disease severity was seen in the study population, interventions aimed at improving adolescent self-concept may have a positive impact on diabetes treatment by improving attitude toward living with type 1 diabetes.

Psychological correlates of depression in children with recurrent abdominal pain.

OBJECTIVE: To examine the associations between coping style, social support, self-efficacy, locus of control, maternal adjustment, and depressive symptoms in children with recurrent abdominal pain (RAP) of childhood. METHODS: Fifty children with RAP (8-18 years) and their mothers were recruited from a gastroenterology clinic (GI) and community medical practices. Participants completed questionnaires that assessed coping style, social support, self-efficacy, locus of control, maternal adjustment, and psychological adjustment. RESULTS: Passive coping strategies such as isolating oneself from others, catastrophizing, and behavioral disengagement were associated with more child-reported depressive symptoms. Higher levels of self-efficacy and greater social support from teachers and classmates were associated with fewer child-reported depressive symptoms. Higher levels of maternal adjustment problems, higher social support from parents, and lower social support from classmates were associated with maternal reports of more child internalizing symptoms. CONCLUSIONS: These findings suggest that coping style, self-efficacy, social support, and maternal adjustment are correlates of depressive symptoms in children with RAP.

Psychosocial adjustment in siblings of children with autism.

BACKGROUND: This study investigated psychosocial adjustment in siblings of children with autism compared to siblings of children with Down syndrome and siblings of normally developing children. In addition, the relationships between feelings of loneliness, social support and psychosocial adjustment, and the influence of gender and family size on psychological adjustment were examined. METHODS: Ninety siblings (30 per group) between the ages of 8 and 18 and one parent of each child participated in this study. RESULTS: Results indicated that siblings of children with autism, as well as comparison siblings, were well adjusted and reported low levels of loneliness. Siblings of children with autism also reported that they received high levels of social support in their lives. CONCLUSIONS: Large family size appears to facilitate healthy adjustment in siblings of children with autism.