Proprotein convertase subtilisin/kexin type 9 (PCSK9), platelet activation and interaction with the vascular endothelium: the impact of PCSK9 inhibition with evolocumab in acute coronary syndrome

Background/Introduction

Platelet activation and endothelial dysfunction may contribute to adverse outcomes in patients with acute myocardial infarction. Pre-clinical studies indicate PCSK9 enhances platelet activation.

Purpose

Our goals were (1) to examine the role of PCSK9 as a potential mediator of platelet activation in patients with acute coronary syndrome (ACS) and (2) to perform immunohistochemical studies of left internal mammary artery (LIMA) specimens to examine interactions among PCSK9, platelets, and endothelial cells in specimens obtained during coronary bypass surgery.

Methods

Participants from the Evolocumab in Acute Coronary Syndrome trials (EVACS; NCT03515304, NCT04082442), with a NSTEMI and a troponin-I of >5 ng/ml or a STEMI were randomized to placebo or to 420 mg SC of evolocumab, a monoclonal anti-PCSK9 antibody, within 24 hours of hospitalization. We performed serial ex vivo analysis of PF4, a marker of platelet activation, in serum samples obtained at baseline (prior to study drug administration) and at day 30. PF4 values were normalized to total platelet count. All of the participants were on guideline-directed therapies for ACS. Additionally, LIMA samples from patients undergoing coronary bypass surgery were immunostained with PCSK9, the endothelial cell transmembrane glycoprotein CD31 (platelet endothelial cell adhesion molecule-1) and the platelet surface marker CD61 (integrin beta-3). Outcome data were summarized using medians and interquartile ranges.

Results

Forty-six participants were randomized in a 1:1 fashion to placebo or to evolocumab. Mean (±SD) age of the cohort was 60±13 years, 48% were women and 22% were African American. Baseline PF4 levels (expressed as ng/1k platelets) were similar between the two groups (placebo: 9.3 [4–12] vs evolocumab 8.0 [4–12], p=0.8). In the placebo group, there was a significant increase in PF4 at 30 days to 13.1 [11–14], p<0.01 (baseline vs 30 days). In contrast, there was no significant change from baseline in the evolocumab group at 30 days (10.7 [6–13]), which was significantly lower than the placebo group (p=0.04). Furthermore, immunostaining of LIMA specimens obtained from patients during coronary artery bypass surgery revealed colocalization of PCSK9, CD31, and CD61 on the vascular endothelial cell surface (see Figure).

Conclusion

PCSK9 inhibition with evolocumab decreases platelet activation in ACS patients on dual anti-platelet therapy. PCSK9 is associated with platelets and endothelial cells at the vascular endothelium. PCSK9 is a potential mediator of the interaction between platelets and vascular endothelial cells in patients with coronary artery disease.

Funding Acknowledgement

Type of funding sources: Other. Main funding source(s): Amgen

Photogrammetric evaluation of corrective surgery for trigonocephaly

The aim of this study was to capture preoperative, postoperative, and follow-up head shapes of male trigonocephaly patients who underwent fronto-orbital remodelling (FOR), using three-dimensional (3D) photography. Fifty-seven male infants with metopic synostosis operated on using standardized FOR during a 5-year period were included. All measurements were compared with those of an age-matched healthy control cohort (n = 253 for early postoperative comparison, n = 43 for the 1-year follow-up comparison) to determine the effect of FOR at 14 days and at 1 year post-surgery. Intracranial volume, frontal angle, nasofrontal angle, interfrontoparietal-interparietal ratio, and inter-orbital distances were measured 1 day preoperatively, 14 days and 1 year postoperatively. Mean age at surgery was 9.7 ± 1.1 months. Prior to surgery, boys with metopic synostosis showed a reduced intracranial volume (-7.0%, P < 0.001), frontal angle (-10.2%, P < 0.001), interfrontoparietal-interparietal ratio (-4.9%, P < 0.01), and orbital distances (-6.5%, P < 0.001) compared to the reference group, but values did not differ significantly from the specific control group after surgery (all P> 0.05). This was consistent by the time of the follow-up examination. Corrective surgery should therefore aim to achieve volume expansion and correction of the deformity. Furthermore, 3D photogrammetry provides a valuable alternative to computed tomography scans in the diagnosis of metopic synostosis, significantly reducing the amount of radiation exposure to the brain.

An appraisal of laboratory models of androgenetic alopecia: A systematic review

Background

Androgenetic alopecia (AGA) is the most common form of non‐scarring alopecia in humans. Several studies have used different laboratory models to study the pathogenesis and interventions for AGA. These study models have proved beneficial and have led to the approval of two drugs. However, the need to build on existing knowledge remains by examining the relevance of study models to the disease.

Objective

We sought to appraise laboratory or pre‐clinical models of AGA.

Method

We searched through databases (PubMed, ScienceDirect, Web of Science, World CAT, Scopus and Google Scholar) for articles on AGA‐related studies from 1942 to March 2019 with a focus on study models.

Results

The search rendered 101 studies after screening and deduplication. Several studies (70) used in vitro models, mostly consisting of two‐dimensional monolayer cells for experiments involving the characterization of androgen and 5‐alpha reductase (5AR) and inhibition thereof, the effects of dihydrotestosterone (DHT) and biomarker(s) of AGA. Twenty‐seven studies used in vivo models of mice and monkeys to investigate DHT synthesis, the expression and inhibition of 5AR and hair growth. Only four studies used AGA‐related or healthy excisional/punch biopsy explants as ex vivo models to study the action of 5AR inhibitors and AGA‐associated genes. No study used three‐dimensional [3‐D] organoids or organotypic human skin culture models.

Conclusion

We recommend clinically relevant laboratory models like human or patient‐derived 3‐D organoids or organotypic skin in AGA‐related studies. These models are closer to human scalp tissue and minimize the use of laboratory animals and could ultimately facilitate novel therapeutics.

Spatio-temporal analysis of the risk of depression at district-level and association with greenness based on the Heinz Nixdorf Recall Study

In urban health studies where spatial and temporal changes are of importance, spatio-temporal variations are usually neglected. For the Heinz Nixdorf Recall Study, we investigate spatio-temporal variation in analyses of effects of urban greenness on depression by including spatio-temporal random effect terms in a Poisson model on district level. Our results show negative associations between greenness and depression. The findings suggest strong temporal autocorrelation and weak spatial effects. Even if the weak spatial effects are suggestive of neglecting them, as in our case, spatio-temporal random effects should be taken into account to provide reliable inference in urban health studies.

Topographic bone thickness maps to evaluate the intuitive placement of titanium miniplates for nasal prostheses

The aim of this study was to evaluate the intuitive placement of titanium miniplates. The hypothesis was that virtual planning can improve miniplate placement. Twenty patients were included in the study. These patients were fitted with 21 titanium miniplates (16 y-plates, three t-plates, and two u-plates) to retain nasal prostheses between 2005 and 2017. Colour-coded topographic bone thickness maps (TBTMs) were created in fused pre- and postoperative computed tomography. Implants were virtually transposed at the position of highest bone thickness. The bone thickness index (BTI) was calculated as the sum of points assigned at each screw (1 point per millimetre up to 4 mm, and 5 points for greater values) divided by the number of screws. One plate broke after 2.8 years, thus plate survival after 5 years was 91% using the Kaplan-Meier method. The BTI for all 21 plates increased from 3.4 to 4.1 points using virtual transposition (P<0.001). No significant changes were observed in t- and u-plates, but the median BTI increased from 3.1 to 4.1 points (P<0.0005) in 16 y-plates. The change was substantial (≥0.5 points) in 9/16 y-plates. Therefore, the hypothesis that virtual planning improves implant placement was accepted.

A T-DNA mutant screen that combines high-throughput phenotyping with the efficient identification of mutated genes by targeted genome sequencing

BACKGROUND

Nitrogen dioxide (NO₂) triggers hypersensitive response (HR)-like cell death in Arabidopsis thaliana. A high-throughput mutant screen was established to identify genes involved in this type of programmed cell death.

RESULTS

Altogether 14,282 lines of SALK T-DNA insertion mutants were screened. Growing 1000 pooled mutant lines per tray and simultaneous NO₂ fumigation of 4 trays in parallel facilitated high-throughput screening. Candidate mutants were selected based on visible symptoms. Sensitive mutants showed lesions already after fumigation for 1 h with 10 ppm (ppm) NO₂ whereas tolerant mutants were hardly damaged even after treatment with 30 ppm NO₂. Identification of T-DNA insertion sites by adapter ligation-mediated PCR turned out to be successful but rather time consuming. Therefore, next generation sequencing after T-DNA-specific target enrichment was tested as an alternative screening method. The targeted genome sequencing was highly efficient due to (1.) combination of the pooled DNA from 124 candidate mutants in only two libraries, (2.) successful target enrichment using T-DNA border-specific 70mer probes, and (3.) stringent filtering of the sequencing reads. Seventy mutated genes were identified by at least 3 sequencing reads. Ten corresponding mutants were re-screened of which 8 mutants exhibited NO₂-sensitivity or -tolerance confirming that the screen yielded reliable results. Identified candidate genes had published functions in HR, pathogen resistance, and stomata regulation.

CONCLUSIONS

The presented NO₂ dead-or-alive screen combined with next-generation sequencing after T-DNA-specific target enrichment was highly efficient. Two researchers finished the screen within 3 months. Moreover, the target enrichment approach was cost-saving because of the limited number of DNA libraries and sequencing runs required. The experimental design can be easily adapted to other screening approaches e.g. involving high-throughput treatments with abiotic stressors or phytohormones.

The prognostic significance of the lymph node ratio in oral cancer differs for anatomical subsites

The aim of this study was to validate the prognostic significance of the lymph node ratio (LNR) in patients suffering from oral squamous cell carcinoma in regard to different anatomical subsites. A cohort of 430 patients was investigated to determine the rates of primary metastasis and local and regional disease recurrence. Correlation analysis of the LNR with relevant clinical and pathological parameters was performed. Receiver operating characteristic (ROC) curve analysis was conducted to evaluate the prognostic impact for different subsites. Significantly differing rates of primary metastasis and loco-regional disease recurrence were found for cancer of different anatomical subsites of the head and neck. Furthermore, ROC curve analysis suggested that LNR has prognostic relevance in subsets of cancer (tongue, P< 0.001; alveolar process, P= 0.04; maxilla, P= 0.03; buccal mucosa, P= 0.02). The LNR of cancer located in the soft palate (P= 0.6) and floor of the mouth (P= 0.11) showed little or no association with the clinical outcome. There is the need for a more sensitive consideration of the LNR as a factor in the assessment of risk and the treatment decision, as the anatomical subsite plays a crucial role in its impact on the clinical outcome.

Long-term donor site morbidity in head and neck cancer patients and its impact on quality of life: a cross-sectional study

Modern head and neck reconstructive surgery offers a multitude of different reconstructive options. In such cases, donor site morbidity is an important factor in the affected patient's decision-making. The aim of this study was to perform an objective comparison of donor site morbidity for the five most frequent microvascular donor sites in head and neck reconstructive surgery (radial forearm, anterolateral thigh, fibula, iliac crest, and scapula) using a uniform testing system. In this cross-sectional study, 117 donor sites were analyzed (106 for malignant disease and 11 for non-malignant disease): 73 radial forearm, 14 scapula, 12 anterolateral thigh, 10 fibula, and eight iliac crest. Testing consisted of range of motion, muscle strength, and sensation. The non-affected side served as the control. Quality of life was assessed using the Washington Quality of Life Questionnaire version 4 in its German translation. Range of motion was restricted in 15 cases (12.8%). Muscle strength was decreased in 58 cases (49.6%). Sensation was reduced in 70 cases (60%). Concerning quality of life, 31.2% of patients were limited in their daily activities. The scapula flap showed the highest incidence of overall donor site morbidity. However, correlation between objective and subjective donor site impairment was weak and the majority of patients experienced only minor limitations.

MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data

Background

With the advent of the age of big data in bioinformatics, large volumes of data and high-performance computing power enable researchers to perform re-analyses of publicly available datasets at an unprecedented scale. Ever more studies imply the microbiome in both normal human physiology and a wide range of diseases. RNA sequencing technology (RNA-seq) is commonly used to infer global eukaryotic gene expression patterns under defined conditions, including human disease-related contexts; however, its generic nature also enables the detection of microbial and viral transcripts.

Findings

We developed a bioinformatic pipeline to screen existing human RNA-seq datasets for the presence of microbial and viral reads by re-inspecting the non-human-mapping read fraction. We validated this approach by recapitulating outcomes from six independent, controlled infection experiments of cell line models and compared them with an alternative metatranscriptomic mapping strategy. We then applied the pipeline to close to 150 terabytes of publicly available raw RNA-seq data from  more than 17,000 samples from more than 400 studies relevant to human disease using state-of-the-art high-performance computing systems. The resulting data from this large-scale re-analysis are made available in the presented MetaMap resource.

Conclusions

Our results demonstrate that common human RNA-seq data, including those archived in public repositories, might contain valuable information to correlate microbial and viral detection patterns with diverse diseases. The presented MetaMap database thus provides a rich resource for hypothesis generation toward the role of the microbiome in human disease. Additionally, codes to process new datasets and perform statistical analyses are made available.

Development of a Stable Lung Microbiome in Healthy Neonatal Mice

The lower respiratory tract has been previously considered sterile in a healthy state, but advances in culture-independent techniques for microbial identification and characterization have revealed that the lung harbors a diverse microbiome. Although research on the lung microbiome is increasing and important questions were already addressed, longitudinal studies aiming to describe developmental stages of the microbial communities from the early neonatal period to adulthood are lacking. Thus, little is known about the early-life development of the lung microbiome and the impact of external factors during these stages. In this study, we applied a barcoding approach based on high-throughput sequencing of 16S ribosomal RNA gene amplicon libraries to determine age-dependent differences in the bacterial fraction of the murine lung microbiome and to assess potential influences of differing "environmental microbiomes" (simulated by the application of used litter material to the cages). We could clearly show that the diversity of the bacterial community harbored in the murine lung increases with age. Interestingly, bacteria belonging to the genera Delftia and Rhodococcus formed an age-independent core microbiome. The addition of the used litter material influenced the lung microbiota of young mice but did not significantly alter the community composition of adult animals. Our findings elucidate the dynamic nature of the early-life lung microbiota and its stabilization with age. Further, this study indicates that even slight environmental changes modulate the bacterial community composition of the lung microbiome in early life, whereas the lung microbes of adults demonstrate higher resilience towards environmental variations.

The emerging role of mRNA methylation in normal and pathological behavior

Covalent RNA modifications were recently rediscovered as abundant RNA chemical tags. Similarly to DNA epigenetic modifications, they have been proposed as essential regulators of gene expression. Here we focus on 3 of the most abundant adenosine methylations: N6-methyladenosine (m⁶ A), N6,2'-O-dimethyladenosine (m⁶ Am) and N1-methyladenosine (m¹ A). We review the potential role of these modifications on mature mRNA in regulating gene expression within the adult brain, nervous system function and normal and pathological behavior. Dynamic mRNA modifications, summarized as the epitranscriptome, regulate transcript maturation, translation and decay, and thus crucially determine gene expression beyond primary transcription regulation. However, the extent of this regulation in the healthy and maladapted adult brain is poorly understood. Analyzing this novel layer of gene expression control in addition to epigenetics and posttranslational regulation of proteins will be highly relevant for understanding the molecular underpinnings of behavior and psychiatric disorders.

Influence of lung CT changes in chronic obstructive pulmonary disease (COPD) on the human lung microbiome

BACKGROUND

Changes in microbial community composition in the lung of patients suffering from moderate to severe COPD have been well documented. However, knowledge about specific microbiome structures in the human lung associated with CT defined abnormalities is limited.

METHODS

Bacterial community composition derived from brush samples from lungs of 16 patients suffering from different CT defined subtypes of COPD and 9 healthy subjects was analyzed using a cultivation independent barcoding approach applying 454-pyrosequencing of 16S rRNA gene fragment amplicons.

RESULTS

We could show that bacterial community composition in patients with changes in CT (either airway or emphysema type changes, designated as severe subtypes) was different from community composition in lungs of patients without visible changes in CT as well as from healthy subjects (designated as mild COPD subtype and control group) (PC1, Padj = 0.002). Higher abundance of Prevotella in samples from patients with mild COPD subtype and from controls and of Streptococcus in the severe subtype cases mainly contributed to the separation of bacterial communities of subjects. No significant effects of treatment with inhaled glucocorticoids on bacterial community composition were detected within COPD cases with and without abnormalities in CT in PCoA. Co-occurrence analysis suggests the presence of networks of co-occurring bacteria. Four communities of positively correlated bacteria were revealed. The microbial communities can clearly be distinguished by their associations with the CT defined disease phenotype.

CONCLUSION

Our findings indicate that CT detectable structural changes in the lung of COPD patients, which we termed severe subtypes, are associated with alterations in bacterial communities, which may induce further changes in the interaction between microbes and host cells. This might result in a changed interplay with the host immune system.

Environmental and mucosal microbiota and their role in childhood asthma

BACKGROUND

High microbial diversity in the environment has been associated with lower asthma risk, particularly in children exposed to farming. It remains unclear whether this effect operates through an altered microbiome of the mucosal surfaces of the airways.

METHODS

DNA from mattress dust and nasal samples of 86 school age children was analyzed by 454 pyrosequencing of the 16S rRNA gene fragments. Based on operational taxonomic units (OTUs), bacterial diversity and composition were related to farm exposure and asthma status.

RESULTS

Farm exposure was positively associated with bacterial diversity in mattress dust samples as determined by richness (P = 8.1 × 10^-6 ) and Shannon index (P = 1.3 × 10^-5 ). Despite considerable agreement of richness between mattress and nasal samples, the association of richness with farming in nasal samples was restricted to a high gradient of farm exposure, that is, exposure to cows and straw vs no exposure at all. In mattress dust, the genera Clostridium, Facklamia, an unclassified genus within the family of Ruminococcaceae, and six OTUs were positively associated with farming. Asthma was inversely associated with richness [aOR = 0.48 (0.22-1.02)] and Shannon index [aOR = 0.41 (0.21-0.83)] in mattress dust and to a lower extent in nasal samples [richness aOR 0.63 = (0.38-1.06), Shannon index aOR = 0.66 (0.39-1.12)].

CONCLUSION

The stronger inverse association of asthma with bacterial diversity in mattress dust as compared to nasal samples suggests microbial involvement beyond mere colonization of the upper airways. Whether inhalation of metabolites of environmental bacteria contributes to this phenomenon should be the focus of future research.

Effects of multiple but low pesticide loads on aquatic fungal communities colonizing leaf litter

In the first tier risk assessment (RA) of pesticides, risk for aquatic communities is estimated by using results from standard laboratory tests with algae, daphnids and fish for single pesticides such as herbicides, fungicides, and insecticides. However, fungi as key organisms for nutrient cycling in ecosystems as well as multiple pesticide applications are not considered in the RA. In this study, the effects of multiple low pesticide pulses using regulatory acceptable concentrations (RACs) on the dynamics of non-target aquatic fungi were investigated in a study using pond mesocosm. For that, fungi colonizing black alder (Alnus glutinosa) leaves were exposed to multiple, low pulses of 11 different pesticides over a period of 60days using a real farmer's pesticide application protocol for apple cropping. Four pond mesocosms served as treatments and 4 as controls. The composition of fungal communities colonizing the litter material was analyzed using a molecular fingerprinting approach based on the terminal Restriction Fragment Length Polymorphism (t-RFLP) of the fungal Internal Transcribed Spacer (ITS) region of the ribonucleic acid (RNA) gene(s). Our data indicated a clear fluctuation of fungal communities based on the degree of leaf litter degradation. However significant effects of the applied spraying sequence were not observed. Consequently also degradation rates of the litter material were not affected by the treatments. Our results indicate that the nutrient rich environment of the leaf litter material gave fungal communities the possibility to express genes that induce tolerance against the applied pesticides. Thus our data may not be transferred to other fresh water habitats with lower nutrient availability.

Gut Immunity and Type 1 Diabetes: a Mélange of Microbes, Diet, and Host Interactions?

Type 1 diabetes (T1D) is a complex autoimmune disease, and first stages of the disease typically develop early in life. Genetic as well as environmental factors are thought to contribute to the risk of developing autoimmunity against pancreatic beta cells. Several environmental factors, such as breastfeeding or early introduction of solid food, have been associated with increased risk for developing T1D. During the first years of life, the gut microbial community is shaped by the environment, in particular by dietary factors. Moreover, the gut microbiome has been described for its role in shaping the immune system early in life and early data suggest associations between T1D risk and alterations in gut microbial communities. In this article, we discuss environmental factors influencing the colonization process of the gut microbial community. Furthermore, we review possible interactions between the microbiome and the host that might contribute to the risk of developing T1D.

Towards a functional hypothesis relating anti-islet cell autoimmunity to the dietary impact on microbial communities and butyrate production

BACKGROUND

The development of anti-islet cell autoimmunity precedes clinical type 1 diabetes and occurs very early in life. During this early period, dietary factors strongly impact on the composition of the gut microbiome. At the same time, the gut microbiome plays a central role in the development of the infant immune system. A functional model of the association between diet, microbial communities, and the development of anti-islet cell autoimmunity can provide important new insights regarding the role of the gut microbiome in the pathogenesis of type 1 diabetes.

RESULTS

A novel approach was developed to enable the analysis of the microbiome on an aggregation level between a single microbial taxon and classical ecological measures analyzing the whole microbial population. Microbial co-occurrence networks were estimated at age 6 months to identify candidates for functional microbial communities prior to islet autoantibody development. Stratification of children based on these communities revealed functional associations between diet, gut microbiome, and islet autoantibody development. Two communities were strongly associated with breast-feeding and solid food introduction, respectively. The third community revealed a subgroup of children that was dominated by Bacteroides abundances compared to two subgroups with low Bacteroides and increased Akkermansia abundances. The Bacteroides-dominated subgroup was characterized by early introduction of non-milk diet, increased risk for early autoantibody development, and by lower abundances of genes for the production of butyrate via co-fermentation of acetate. By combining our results with information from the literature, we provide a refined functional hypothesis for a protective role of butyrate in the pathogenesis of type 1 diabetes.

CONCLUSIONS

Based on functional traits of microbial communities estimated from co-occurrence networks, we provide evidence that alterations in the composition of mucin degrading bacteria associate with early development of anti-islet cell autoimmunity. We hypothesize that lower levels of Bacteroides in favor of increased levels of Akkermansia lead to a competitive advantage of acetogens compared to sulfate reducing bacteria, resulting in increased butyrate production via co-fermentation of acetate. This hypothesis suggests that butyrate has a protective effect on the development of anti-islet cell autoantibodies.

Intracranial volume (ICV) in isolated sagittal craniosynostosis measured by 3D photocephalometry: A new perspective on a controversial issue

BACKGROUND

There are still controversies regarding the intracranial volumes in patients with isolated sagittal craniosynostosis compared to a healthy population. This study aimed to compare the intracranial volume of children with sagittal synostosis and scaphocephaly to an age- and gender-matched control cohort using three-dimensional (3D) photogrammetry.

METHODS

62 boys and nine girls with sagittal craniosynostosis were included in this study. The intracranial volume was measured at the first clinical presentation. However, 3D photogrammetry was performed at children not younger than 3 months. The 3D photogrammetric data of 547 healthy boys and 287 healthy girls between the ages of 3-10 month was analyzed to establish an age- and gender-matched control group.

RESULTS

Male patients with sagittal synostosis showed a significantly reduced intracranial volume compared to the reference group. For female patients, the intracranial volume was slightly lower compared to the norm group, but not significantly.

CONCLUSIONS

Male children with sagittal synostosis showed significantly decreased intracranial volume between the age of 3 and 10 months compared to an age- and gender-matched control group. Female patients in the same age group presented a lower intracranial volume compared to the norm group. Measuring intracranial volume using 3D photogrammetry is a comparable and valuable alternative to CT scans that leads to a significant reduction of radiation exposure to the growing brain.

Phosphorus depletion in forest soils shapes bacterial communities towards phosphorus recycling systems

Phosphorus (P) is an important macronutrient for all biota on earth but similarly a finite resource. Microorganisms play on both sides of the fence as they effectively mineralize organic and solubilize precipitated forms of soil phosphorus but conversely also take up and immobilize P. Therefore, we analysed the role of microbes in two beech forest soils with high and low P content by direct sequencing of metagenomic deoxyribonucleic acid. For inorganic P solubilization, a significantly higher microbial potential was detected in the P-rich soil. This trait especially referred to Candidatus Solibacter usiatus, likewise one of the dominating species in the data sets. A higher microbial potential for efficient phosphate uptake systems (pstSCAB) was detected in the P-depleted soil. Genes involved in P starvation response regulation (phoB, phoR) were prevalent in both soils. This underlines the importance of effective phosphate (Pho) regulon control for microorganisms to use alternative P sources during phosphate limitation. Predicted genes were primarily harboured by Rhizobiales, Actinomycetales and Acidobacteriales.

Prokaryotes in Subsoil-Evidence for a Strong Spatial Separation of Different Phyla by Analysing Co-occurrence Networks

Microbial communities in soil provide a wide range of ecosystem services. On the small scale, nutrient rich hotspots in soil developed from the activities of animals or plants are important drivers for the composition of microbial communities and their functional patterns. However, in subsoil, the spatial heterogeneity of microbes with differing lifestyles has been rarely considered so far. In this study, the phylogenetic composition of the bacterial and archaeal microbiome based on 16S rRNA gene pyrosequencing was investigated in the soil compartments bulk soil, drilosphere, and rhizosphere in top- and in the subsoil of an agricultural field. With co-occurrence network analysis, the spatial separation of typically oligotrophic and copiotrophic microbes was assessed. Four bacterial clusters were identified and attributed to bulk topsoil, bulk subsoil, drilosphere, and rhizosphere. The bacterial phyla Proteobacteria and Bacteroidetes, representing mostly copiotrophic bacteria, were affiliated mainly to the rhizosphere and drilosphere—both in topsoil and subsoil. Acidobacteria, Actinobacteria, Gemmatimonadetes, Planctomycetes, and Verrucomicrobia, bacterial phyla which harbor many oligotrophic bacteria, were the most abundant groups in bulk subsoil. The bacterial core microbiome in this soil was estimated to cover 7.6% of the bacterial sequencing reads including both oligotrophic and copiotrophic bacteria. In contrast the archaeal core microbiome includes 56% of the overall archaeal diversity. Thus, the spatial variability of nutrient quality and quantity strongly shapes the bacterial community composition and their interaction in subsoil, whereas archaea build a stable backbone of the soil prokaryotes due to their low variability in the different soil compartments.

Seasonal and spatial patterns of microbial diversity along a trophic gradient in the interconnected lakes of the Osterseen Lake District, Bavaria

The Osterseen Lake District in Bavaria consists of 19 small interconnected lakes that exhibit a pronounced trophic gradient from eutrophic to oligotrophic. It therefore presents a unique model system to address ecological questions regarding niche adaptation and Baas Becking's long standing hypothesis of "everything is everywhere, but the environment selects." Here, we present the first assessment of the microbial diversity in these lakes. We sampled the lakes in August and December and used 454 pyrosequencing of 16S rRNA amplicons to analyze the microbial diversity. The diversity patterns between lakes and seasons were compared and the bacterial community composition was correlated with key chemical and physical parameters. Distinct patterns of bacterial diversity only emerged at the level of individual OTUs (operational taxonomic units), but not at the level of the major bacterial phyla. This emphasizes the high functional and physiological diversity among bacterial species within a phylum and calls for analysis of biodiversity at the level of OTUs in order to understand fine-scale biogeography. We were able to identify a number of cosmopolitan OTUs as well as specialist OTUs that were restricted to certain lakes or seasons, suggesting adaptation to specific ecological niches.

Characterizing Aquifer Heterogeneity Using Bacterial and Bacteriophage Tracers

Gravel aquifers act as important potable water sources in central western Europe, yet they are subject to numerous contamination pressures. Compositional and textural heterogeneity makes protection zone delineation around groundwater supplies in these units challenging; artificial tracer testing aids characterization. This paper reappraises previous tracer test results in light of new geological and microbiological data. Comparative passive gradient testing, using a fluorescent solute (Uranine), virus (H40/1 bacteriophage), and comparably sized bacterial tracers and , was used to investigate a calcareous gravel aquifer's ability to remove microbiological contaminants at a test site near Munich, Germany. Test results revealed relative recoveries could exceed those of H40/1 at monitoring wells, 10 m and 20 m from an injection well, by almost four times; recoveries varied by a factor of up to three between wells. Application of filtration theory suggested greater attenuation of H40/1 relative to similarly charged occurred due to differences in microorganism size, while estimated collision efficiencies appeared comparable. By contrast, more positively charged experienced greater attenuation at one monitoring point, while lower attenuation rates at the second location indicated the influence of geochemical heterogeneity. Test findings proved consistent with observations from nearby fresh outcrops that suggested thin open framework gravel beds dominated mass transport in the aquifer, while discrete intervals containing stained clasts reflect localized geochemical heterogeneity. Study results highlight the utility of reconciling outcrop observations with artificial tracer test responses, using microbiological tracers with well-defined properties, to characterize aquifer heterogeneity.

pH as a Driver for Ammonia-Oxidizing Archaea in Forest Soils

In this study, we investigated the impact of soil pH on the diversity and abundance of archaeal ammonia oxidizers in 27 different forest soils across Germany. DNA was extracted from topsoil samples, the amoA gene, encoding ammonia monooxygenase, was amplified; and the amplicons were sequenced using a 454-based pyrosequencing approach. As expected, the ratio of archaeal (AOA) to bacterial (AOB) ammonia oxidizers' amoA genes increased sharply with decreasing soil pH. The diversity of AOA differed significantly between sites with ultra-acidic soil pH (<3.5) and sites with higher pH values. The major OTUs from soil samples with low pH could be detected at each site with a soil pH <3.5 but not at sites with pH >4.5, regardless of geographic position and vegetation. These OTUs could be related to the Nitrosotalea group 1.1 and the Nitrososphaera subcluster 7.2, respectively, and showed significant similarities to OTUs described from other acidic environments. Conversely, none of the major OTUs typical of sites with a soil pH >4.6 could be found in the ultra- and extreme acidic soils. Based on a comparison with the amoA gene sequence data from a previous study performed on agricultural soils, we could clearly show that the development of AOA communities in soils with ultra-acidic pH (<3.5) is mainly triggered by soil pH and is not influenced significantly by the type of land use, the soil type, or the geographic position of the site, which was observed for sites with acido-neutral soil pH.