Biodiversity and ecosystem function in soil

1. Soils are one of the last great frontiers for biodiversity research and are home to an extraordinary range of microbial and animal groups. Biological activities in soils drive many of the key ecosystem processes that govern the global system, especially in the cycling of elements such as carbon, nitrogen and phosphorus. 2. We cannot currently make firm statements about the scale of biodiversity in soils, or about the roles played by soil organisms in the transformations of organic materials that underlie those cycles. The recent UK Soil Biodiversity Programme (SBP) has brought a unique concentration of researchers to bear on a single soil in Scotland, and has generated a large amount of data concerning biodiversity, carbon flux and resilience in the soil ecosystem. 3. One of the key discoveries of the SBP was the extreme diversity of small organisms: researchers in the programme identified over 100 species of bacteria, 350 protozoa, 140 nematodes and 24 distinct types of arbuscular mycorrhizal fungi. Statistical analysis of these results suggests a much greater 'hidden diversity'. In contrast, there was no unusual richness in other organisms, such as higher fungi, mites, collembola and annelids. 4. Stable-isotope (C-13) technology was used to measure carbon fluxes and map the path of carbon through the food web. A novel finding was the rapidity with which carbon moves through the soil biota, revealing an extraordinarily dynamic soil ecosystem. 5. The combination of taxonomic diversity and rapid carbon flux makes the soil ecosystem highly resistant to perturbation through either changing soil structure or removing selected groups of organisms

Constraining Absolute Plate Motions Since the Triassic

The absolute motion of tectonic plates since Pangea can be derived from observations of hotspot trails, paleomagnetism, or seismic tomography. However, fitting observations is typically carried out in isolation without consideration for the fit to unused data or whether the resulting plate motions are geodynamically plausible. Through the joint evaluation of global hotspot track observations (for times <80 Ma), first‐order estimates of net lithospheric rotation (NLR), and parameter estimation for paleo–trench migration (TM), we present a suite of geodynamically consistent, data‐optimized global absolute reference frames from 220 Ma to the present. Each absolute plate motion (APM) model was evaluated against six published APM models, together incorporating the full range of primary data constraints. Model performance for published and new models was quantified through a standard statistical analyses using three key diagnostic global metrics: root‐mean square plate velocities, NLR characteristics, and TM behavior. Additionally, models were assessed for consistency with published global paleomagnetic data and for ages <80 Ma for predicted relative hotspot motion, track geometry, and time dependence. Optimized APM models demonstrated significantly improved global fit with geological and geophysical observations while performing consistently with geodynamic constraints. Critically, APM models derived by limiting average rates of NLR to ~0.05°/Myr and absolute TM velocities to ~27‐mm/year fit geological observations including hotspot tracks. This suggests that this range of NLR and TM estimates may be appropriate for Earth over the last 220 Myr, providing a key step toward the practical integration of numerical geodynamics into plate tectonic reconstructions

Evaluating the Application of Microbial Induced Calcite Precipitation Technique to Stabilize Expansive Soils

Expansive soils, also known as swell-shrink soils have been a problem for civil infrastructures including roads and foundations from ancient times. The use of chemical additives such as cement and lime to stabilize expansive soils is a common practice among geotechnical engineers, especially for lightly loaded structures. However, several occurrences of subgrade failures have been observed after stabilizing with chemical additives. Hence, engineers are in search of sustainable stabilization alternatives. Microbial Induced Calcite Precipitation (MICP) is gaining attention as an environmentally friendly soil improvement technique. Several researchers have successfully tested its feasibility in mitigating liquefaction-induced problems in sandy soils. In this research, the authors are evaluating its effectiveness in stabilizing expansive soils. For this purpose two natural expansive soils with high and low plasticity properties were subjected to MICP treatments. The soil samples were first augmented with bacterium Sporosarcina Pasteurii and then treated with Calcium Chloride and Urea. Variables such as microbial concentrations and curing times were studied in this research. Geotechnical testing including Atterberg limits and unconfined compression strength were performed to evaluate the efficacy of MICP treatments. Preliminary results indicate that there is a reduction in plasticity and swelling characteristics of the soils and increase in the unconfined compression strength

Darkness visible: reflections on underground ecology

1 Soil science and ecology have developed independently, making it difficult for ecologists to contribute to urgent current debates on the destruction of the global soil resource and its key role in the global carbon cycle. Soils are believed to be exceptionally biodiverse parts of ecosystems, a view confirmed by recent data from the UK Soil Biodiversity Programme at Sourhope, Scotland, where high diversity was a characteristic of small organisms, but not of larger ones. Explaining this difference requires knowledge that we currently lack about the basic biology and biogeography of micro-organisms. 2 It seems inherently plausible that the high levels of biological diversity in soil play some part in determining the ability of soils to undertake ecosystem-level processes, such as carbon and mineral cycling. However, we lack conceptual models to address this issue, and debate about the role of biodiversity in ecosystem processes has centred around the concept of functional redundancy, and has consequently been largely semantic. More precise construction of our experimental questions is needed to advance understanding. 3 These issues are well illustrated by the fungi that form arbuscular mycorrhizas, the Glomeromycota. This ancient symbiosis of plants and fungi is responsible for phosphate uptake in most land plants, and the phylum is generally held to be species-poor and non-specific, with most members readily colonizing any plant species. Molecular techniques have shown both those assumptions to be unsafe, raising questions about what factors have promoted diversification in these fungi. One source of this genetic diversity may be functional diversity. 4 Specificity of the mycorrhizal interaction between plants and fungi would have important ecosystem consequences. One example would be in the control of invasiveness in introduced plant species: surprisingly, naturalized plant species in Britain are disproportionately from mycorrhizal families, suggesting that these fungi may play a role in assisting invasion. 5 What emerges from an attempt to relate biodiversity and ecosystem processes in soil is our extraordinary ignorance about the organisms involved. There are fundamental questions that are now answerable with new techniques and sufficient will, such as how biodiverse are natural soils? Do microbes have biogeography? Are there rare or even endangered microbes

Сучасний стан і проблеми управління залізничним транспортом України

Проаналізовано стан і тенденції розвитку залізничного транспорту. Розглянуті основні завдання державного регулювання галузі.Проанализировано состояние и тенденции развития железнодорожного транспорта. Рассмотренны основные задания государственного регулирования отрасли.The condition and trends of railway transport has been anilized. The main tasks of state regulation of railway transport has been considereted

Robust estimation of microbial diversity in theory and in practice

Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic studies. Here, we consider what the diversity observed in a sample tells us about the diversity of the community being sampled. First, we argue that one cannot reliably estimate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions. The reason for this is that sample data do not contain information about the number of rare species in the tail of species abundance distributions. We illustrate the difficulty in comparing species richness estimates by applying Chao's estimator of species richness to a set of in silico communities: they are ranked incorrectly in the presence of large numbers of rare species. Next, we extend our analysis to a general family of diversity metrics ("Hill diversities"), and construct lower and upper estimates of diversity values consistent with the sample data. The theory generalizes Chao's estimator, which we retrieve as the lower estimate of species richness. We show that Shannon and Simpson diversity can be robustly estimated for the in silico communities. We analyze nine metagenomic data sets from a wide range of environments, and show that our findings are relevant for empirically-sampled communities. Hence, we recommend the use of Shannon and Simpson diversity rather than species richness in efforts to quantify and compare microbial diversity.Comment: To be published in The ISME Journal. Main text: 16 pages, 5 figures. Supplement: 16 pages, 4 figure

Physical Activity Among Adolescent Cancer Survivors: The PACCS Study

OBJECTIVES Physical activity (PA) may modify risks of late effects after cancer. We aimed to examine levels of PA and sedentary time (ST) in a large, international sample of adolescent childhood cancer survivors in relation to sociodemographic and cancer-related factors and compare levels of PA and ST to reference cohorts. METHODS Survivors from any cancer diagnosis who had completed cancer treatment ≥1 year ago, aged 9 to 16 years, were eligible for the multicenter Physical Activity in Childhood Cancer Survivors study. PA and ST were measured by ActiGraph GT3X+ accelerometers. We performed linear regression analyses to assess factors associated with moderate-to-vigorous PA (MVPA) and ST, and compared marginal means of total PA, MVPA, and ST in 432 survivors to sex- and age-stratified references (2-year intervals) using immediate t-tests for aggregated data. RESULTS Among survivors, 34% fulfilled the World Health Organization's PA recommendation of ≥60 min of daily MVPA on average and their ST was 8.7 hours per day. Being female, older, overweight, a survivor of central nervous system tumor, or having experienced relapse were associated with lower MVPA and/or higher ST. Generally, male survivors spent less time in MVPA compared with references, whereas female survivors had similar levels. Both male and female survivors had higher ST than references in nearly all age groups. CONCLUSIONS The low PA and high ST in this large sample of adolescent childhood cancer survivors is worrisome. Combined, our results call for targeted interventions addressing both PA and ST in follow-up care after childhood cancer

New Detection Systems of Bacteria Using Highly Selective Media Designed by SMART: Selective Medium-Design Algorithm Restricted by Two Constraints

Culturing is an indispensable technique in microbiological research, and culturing with selective media has played a crucial role in the detection of pathogenic microorganisms and the isolation of commercially useful microorganisms from environmental samples. Although numerous selective media have been developed in empirical studies, unintended microorganisms often grow on such media probably due to the enormous numbers of microorganisms in the environment. Here, we present a novel strategy for designing highly selective media based on two selective agents, a carbon source and antimicrobials. We named our strategy SMART for highly Selective Medium-design Algorithm Restricted by Two constraints. To test whether the SMART method is applicable to a wide range of microorganisms, we developed selective media for Burkholderia glumae, Acidovorax avenae, Pectobacterium carotovorum, Ralstonia solanacearum, and Xanthomonas campestris. The series of media developed by SMART specifically allowed growth of the targeted bacteria. Because these selective media exhibited high specificity for growth of the target bacteria compared to established selective media, we applied three notable detection technologies: paper-based, flow cytometry-based, and color change-based detection systems for target bacteria species. SMART facilitates not only the development of novel techniques for detecting specific bacteria, but also our understanding of the ecology and epidemiology of the targeted bacteria

Study protocol for a randomized controlled trial of supportive parents – coping kids (SPARCK)—a transdiagnostic and personalized parent training intervention to prevent childhood mental health problems

Background: To meet the scientific and political call for effective prevention of child and youth mental health problems and associated long-term consequences, we have co-created, tested, and optimized a transdiagnostic preventive parent-training intervention, Supportive parents – coping kids (SPARCK), together with and for the municipal preventive frontline services. The target group of SPARCK is parents of children between 4 and 12 years who display symptoms of anxiety, depression, and/or behavioral problems, that is, indicated prevention. The intervention consists of components from various empirically supported interventions representing different theorical models on parent–child interactions and child behavior and psychopathology (i.e., behavioral management interventions, attachment theory, emotion socialization theory, cognitive-behavioral therapy, and family accommodation intervention). The content and target strategies of SPARCK are tailored to the needs of the families and children, and the manual suggests how the target strategies may be personalized and combined throughout the maximum 12 sessions of the intervention. The aim of this project is to investigate the effectiveness of SPARCK on child symptoms, parenting practices, and parent and child stress hormone levels, in addition to later use of specialized services compared with usual care (UC; eg. active comparison group). Methods: We describe a randomized controlled effectiveness trial in the frontline services of child welfare, health, school health and school psychological counselling services in 24 Norwegian municipalities. It is a two-armed parallel group randomized controlled effectiveness and superiority trial with 252 families randomly allocated to SPARCK or UC. Assessment of key variables will be conducted at pre-, post-, and six-month follow-up. Discussion: The current study will contribute with knowledge on potential effects of a preventive transdiagnostic parent-training intervention when compared with UC. Our primary objective is to innovate frontline services with a usable, flexible, and effective intervention for prevention of childhood mental health problems to promote equity in access to care for families and children across a heterogeneous service landscape characterized by variations in available resources, personnel, and end user symptomatology. Trial registration: ClinicalTrials.gov ID: NTCT0580052

Bacterial activity in cystic fibrosis lung infections

BACKGROUND: Chronic lung infections are the primary cause of morbidity and mortality in Cystic Fibrosis (CF) patients. Recent molecular biological based studies have identified a surprisingly wide range of hitherto unreported bacterial species in the lungs of CF patients. The aim of this study was to determine whether the species present were active and, as such, worthy of further investigation as potential pathogens. METHODS: Terminal Restriction Fragment Length Polymorphism (T-RFLP) profiles were generated from PCR products amplified from 16S rDNA and Reverse Transcription Terminal Restriction Fragment Length Polymorphism (RT-T-RFLP) profiles, a marker of metabolic activity, were generated from PCR products amplified from 16S rRNA, both extracted from the same CF sputum sample. To test the level of activity of these bacteria, T-RFLP profiles were compared to RT-T-RFLP profiles. RESULTS: Samples from 17 individuals were studied. Parallel analyses identified a total of 706 individual T-RF and RT-T-RF bands in this sample set. 323 bands were detected by T-RFLP and 383 bands were detected by RT-T-RFLP (statistically significant; P ≤ 0.001). For the group as a whole, 145 bands were detected in a T-RFLP profile alone, suggesting metabolically inactive bacteria. 205 bands were detected in an RT-T-RFLP profile alone and 178 bands were detected in both, suggesting a significant degree of metabolic activity. Although Pseudomonas aeruginosa was present and active in many patients, a low occurrence of other species traditionally considered to be key CF pathogens was detected. T-RFLP profiles obtained for induced sputum samples provided by healthy individuals without CF formed a separate cluster indicating a low level of similarity to those from CF patients. CONCLUSION: These results indicate that a high proportion of the bacterial species detected in the sputum from all of the CF patients in the study are active. The widespread activity of bacterial species in these samples emphasizes the potential importance of these previously unrecognized species within the CF lung