Fungal Biomarkers Research Articles

Microecological insight to fungal structure and key fungal communities regulating nitrogen transformation based on spatial heterogeneity during cow manure composting by multi-angle and multi-aspect analyses

Composting is the mainstream technology for the treatment of agricultural solid waste, but limited efforts were made to investigate fungal composition and its contributions to nitrogen transformation in different depths of compost. In this study, spatial distributions of fungi were analyzed using high throughput sequencing by multi-angle analyses, and the key fungal communities determining nitrogen transformation were quantified and identified by multi-aspect analyses during cow manure composting. Multi-angle analyses showed that fungal structure, biomarkers and trophic mode composition varied in different layers, revealing that spatial heterogeneity is the distinctive attribute of composting system. Ascomycota and Basidiomycota were dominant phyla during composting, the two phyla peaked in top and bottom layer respectively. At mesophilic stage, Tremellales, and unclassified Ascomycota (order) were biomarkers in top and middle layer respectively, and so were Remersonia, Pyrenochaetopsis, and Wallemia in bottom layer by LEfSe analysis. Based on multi-aspect analyses, Unclassified Dothideomycetes mainly affected NH4+-N transformation both in top (1.2816***) and middle layers (1.1726*). Trichocladium asperum (0.9536***) and Zopfiella (−0.9484***) mainly affected TN transformation in top layer. Guehomyces pullulans (−0.9684**) and Preussia (−1.0508**) regulated NO3−-N transformation in middle layer. Thermomyces lanuginosus (0.7127***) and Typhula sp. UW973129 (0.7298***) were the key species promoting TN and C/N transformation in bottom layer, respectively. Interestingly, different fungal communities showed a complex network interaction driving nitrogen transformation, and the abundance of microbial community could be conducive to characterizing nitrogen transformation in the vertical space of composting.

Disease-specific gaps within fungal respiratory tract infections: clinical features, diagnosis, and management in critically ill patients

We aim to examine the most recent findings in the area of invasive pulmonary fungal infections to determine the appropriate/and or lack of prevention measures and treatment of upper fungal respiratory tract infections in the critically ill. This will be addressed by focusing on the pathogens and prognosis over different bedridden periods in ICU patients, the occurrence of invasive fungal respiratory superinfections in patients with severe coronavirus disease 2019 which has been recently noted following the SARS-CoV-2 pandemic. Relevant reports referenced within include randomized controlled trials, meta-analyses, observational studies, systematic reviews, and international guidelines, where applicable. Of note, it is clear there is a significant gap in our knowledge regarding whether bacterial and fungal infections in coronavirus disease 2019 are directly attributable to SARS-CoV-2 or a consequence of factors such as managing high numbers of critically unwell patients, and the prolonged duration of mechanical ventilation/ICU admission duration of stay. An optimal diagnostic algorithm incorporating fungal biomarkers and molecular tools for early and accurate diagnosis of Pneumocystis pneumonia, invasive aspergillosis, candidemia, and endemic mycoses continues to be limited clinically. There is a lack of standardized molecular approach to identify fungal pathogens directly in formalin-fixed paraffin-embedded tissues and suboptimal diagnostic approaches for mould blood cultures, tissue culture processing for Mucorales, and fungal respiratory cultures (i.e., the routine use of bronchoscopic examination in ICU patients with influenza-associated pulmonary aspergillosis) for fungal point-of-care testing to detect and identify new, emerging or underrecognized, rare, or uncommon fungal pathogens.

Molecular Profiling Reveals Characteristic and Decisive Signatures in Patients after Allogeneic Stem Cell Transplantation Suffering from Invasive Pulmonary Aspergillosis

Despite available diagnostic tests and recent advances, diagnosis of pulmonary invasive aspergillosis (IPA) remains challenging. We performed a longitudinal case-control pilot study to identify host-specific, novel, and immune-relevant molecular candidates indicating IPA in patients post allogeneic stem cell transplantation (alloSCT). Supported by differential gene expression analysis of six relevant in vitro studies, we conducted RNA sequencing of three alloSCT patients categorized as probable IPA cases and their matched controls without Aspergillus infection (66 samples in total). We additionally performed immunoassay analysis for all patient samples to gain a multi-omics perspective. Profiling analysis suggested LGALS2, MMP1, IL-8, and caspase-3 as potential host molecular candidates indicating IPA in investigated alloSCT patients. MMP1, IL-8, and caspase-3 were evaluated further in alloSCT patients for their potential to differentiate possible IPA cases and patients suffering from COVID-19-associated pulmonary aspergillosis (CAPA) and appropriate control patients. Possible IPA cases showed differences in IL-8 and caspase-3 serum levels compared with matched controls. Furthermore, we observed significant differences in IL-8 and caspase-3 levels among CAPA patients compared with control patients. With our conceptual work, we demonstrate the potential value of considering the human immune response during Aspergillus infection to identify immune-relevant molecular candidates indicating IPA in alloSCT patients. These human host candidates together with already established fungal biomarkers might improve the accuracy of IPA diagnostic tools.

Role of (1-3)-Β-D-Glucan Test in the Diagnosis of Invasive Fungal Infections among High-Risk Patients in a Tertiary Care Hospital.

Background Invasive fungal infections (IFI) are associated with high mortality. Serum fungal biomarkers offer an advantage over the traditional methods in early diagnosis and better clinical outcomes. The aim of the study was to evaluate the role of (1–3)-β-D-glucan (BDG) assay in the patients suspected of IFI. Materials and Methods This prospective study was conducted in the Department of Microbiology, Dayanand Medical College and Hospital, Ludhiana, over a period of 1 year. A total of 862 serum samples were received from patients suspected of IFI, for the BDG test (Fungitell, Associates of Cape Cod Inc., USA). The test was performed as per kit protocol. Appropriate samples were processed for KOH fungal smear and fungal culture. Blood culture was done by Bactec (Biomerieux). Statistical Analysis Results were analyzed using descriptive statistical methods. Sensitivity, specificity, accuracy, positive predictive value (PPV), and negative predictive value (NPV) were calculated at different cutoffs. In addition, the receiver operating characteristic (ROC) curve using SPSS 21.00 software was calculated and the diagnostic accuracy was shown by the area under the ROC curve (AUC). Results Among 862 patients, 546 (63.3%) were males. The predominant age group (25.6%) was between 61 and 70 years. The most common risk factor (54.8%) was prolonged intensive care unit stay. Out of the total samples, 455 (52.8%) samples were found positive for BDG. Fungal elements were seen in 48 (10.5%) KOH smears and fungal growth was obtained in 81 (17.8%) cultures. Comparison of BDG assay and culture at different cutoffs yielded AUC—0.823. Sensitivity (100%), specificity (51.3%), accuracy (55.6%), PPV (15.8%), and NPV (100%) were observed at the kit cutoff of 80 pg/mL. Optimum sensitivity and specificity of 79.2% and 70.3%, respectively, were observed at a cutoff of 142.4pg/mL. A significant correlation was observed between BDG positivity and piperacillin–tazobactam use and dialysis. Among BDG positive patients, 38(8.4%) succumbed to death. Conclusion Detection of BDG helps in the early diagnosis of IFI in critically ill patients. As the assay has a high NPV, a negative test can be used to stop the empirical antifungal drugs. The use of a higher cutoff can be useful to avoid false-positive results.

Seasonal airway microbiome and transcriptome interactions promote childhood asthma exacerbations

Seasonal variation in respiratory illnesses and exacerbations in pediatric populations with asthma is well described, though whether upper airway microbes play season-specific roles in these events is unknown. We hypothesized that nasal microbiota composition is seasonally dynamic and that discrete microbe-host interactions modify risk of asthma exacerbation in a season-specific manner. Repeated nasal samples from children with exacerbation-prone asthma collected during periods of respiratory health (baseline; n= 181 samples) or first captured respiratory illness (n= 97) across all seasons, underwent bacterial (16S ribosomal RNA gene) and fungal (internal transcribed spacer region 2) biomarker sequencing. Virus detection was performed by multiplex PCR. Paired nasal transcriptome data were examined for seasonal dynamics and integrative analyses. Upper airway bacterial and fungal microbiota and rhinovirus detection exhibited significant seasonal dynamics. In seasonally adjusted analysis, variation in both baseline and respiratory illness microbiota related to subsequent exacerbation. Specifically, in the fall, when respiratory illness and exacerbation events were most frequent, several Moraxella and Haemophilus members were enriched both in virus-positive respiratory illnesses and those that progressed to exacerbations. The abundance of 2 discrete bacterial networks, characteristically comprising either Streptococcus or Staphylococcus, exhibited opposing interactions with an exacerbation-associated SMAD3 nasal epithelial transcriptional module to significantly increase the odds of subsequent exacerbation (odds ratio= 14.7, 95% confidence interval= 1.50-144, P= .02; odds ratio= 39.17, 95% confidence interval= 2.44-626, P= .008, respectively). Upper airway microbiomes covary with season and with seasonal trends in respiratory illnesses and asthma exacerbations. Seasonally adjusted analyses reveal specific bacteria-host interactions that significantly increase risk of asthma exacerbation in these children.

Multi-kingdom microbiota analyses identifybacterial–fungal interactions and biomarkers of colorectal cancer acrosscohorts

Despite recent progress in our understanding of the association betweenthe gut microbiome and colorectal cancer (CRC), multi-kingdom gut microbiomedysbiosis in CRC across cohorts is unexplored. We investigated four-kingdommicrobiota alterations using CRC metagenomic datasets of 1,368 samples from 8distinct geographical cohorts. Integrated analysis identified 20 archaeal, 27bacterial, 20 fungal and 21 viral species for each single-kingdom diagnostic model.However, our data revealed superior diagnostic accuracy for models constructed withmulti-kingdom markers, in particular the addition of fungal species. Specifically,16 multi-kingdom markers including 11 bacterial, 4 fungal and 1 archaeal feature,achieved good performance in diagnosing patients with CRC (area under the receiveroperating characteristic curve (AUROC) = 0.83) and maintainedaccuracy across 3 independent cohorts. Coabundance analysis of the ecologicalnetwork revealed associations between bacterial and fungal species, such asTalaromyces islandicus and Clostridium saccharobutylicum. Using metagenome shotgunsequencing data, the predictive power of the microbial functional potential wasexplored and elevated D-amino acid metabolism and butanoate metabolism were observedin CRC. Interestingly, the diagnostic model based on functional EggNOG genesachieved high accuracy (AUROC = 0.86). Collectively, our findingsuncovered CRC-associated microbiota common across cohorts and demonstrate theapplicability of multi-kingdom and functional markers as CRC diagnostic tools and,potentially, as therapeutic targets for the treatment of CRC.

Multicenter Prospective Study of Biomarkers for Diagnosis of Invasive Candidiasis in Children and Adolescents.

Diagnosis of invasive candidiasis (IC) relies on insensitive cultures; the relative utility of fungal biomarkers in children is unclear. This multinational observational cohort study enrolled patients aged >120 days and <18 years with concern for IC from 1 January 2015 to 26 September 2019 at 25 centers. Blood collected at onset of symptoms was tested using T2Candida, Fungitell (1→3)-β-D-glucan, Platelia Candida Antigen (Ag) Plus, and Platelia Candida Antibody (Ab) Plus assays. Operating characteristics were determined for each biomarker, and assays meeting a defined threshold considered in combination. Sterile site cultures were the reference standard. Five hundred participants were enrolled at 22 centers in 3 countries, and IC was diagnosed in 13 (2.6%). Thirteen additional blood specimens were collected and successfully spiked with Candida species, to achieve a 5.0% event rate. Valid T2Candida, Fungitell, Platelia Candida Ag Plus, and Platelia Candida Ab Plus assay results were available for 438, 467, 473, and 473 specimens, respectively. Operating characteristics for T2Candida were most optimal for detecting IC due to any Candida species, with results as follows: sensitivity, 80.0% (95% confidence interval, 59.3%-93.2%), specificity 97.1% (95.0%-98.5%), positive predictive value, 62.5% (43.7%-78.9%), and negative predictive value, 98.8% (97.2%-99.6%). Only T2Candida and Platelia Candida Ag Plus assays met the threshold for combination testing. Positive result for either yielded the following results: sensitivity, 86.4% (95% confidence interval, 65.1%- 97.1%); specificity, 94.7% (92.0%-96.7%); positive predictive value, 47.5% (31.5%-63.9%); and negative predictive value, 99.2% (97.7%-99.8%). T2Candida alone or in combination with Platelia Candida Ag Plus may be beneficial for rapid detection of Candida species in children with concern for IC. NCT02220790.

Invasive fungal infections in acute and chronic liver impairment: A systematic review.

Patients with acute and chronic liver impairment are susceptible to invasive fungal infections such as candidemia and invasive pulmonary aspergillosis as a result of cirrhosis-associated immune dysfunction, humoral immunodeficiency, cell-mediated dysfunction and systemic inflammation. Besides classical risk factors for invasive fungal infection, acute-on-chronic liver failure, corticosteroid use, gastrointestinal bleeding, and prophylactic use of antibiotics are all additional conditions which are related to the potential development of fungal infections. Therefore, high-risk patients should be carefully followed by microbiological surveillance including cultures but also by imaging and fungal biomarkers for providing early diagnosis. Echinocandins are still the mainstay and first line antifungal therapy in cases of invasive candidiasis. Due to concerns of liver toxicity and in cases of renal impairment liposomal amphotericin B is a suitable alternative to voriconazole in patients with invasive pulmonary aspergillosis. Although, data of isavucoanzole and posaconazole use in those patients are also promising more specific studies in the subgroup of patients with liver impairment are needed. Especially, due to the late diagnosis and multiple organ dysfunction usually present in patients with liver impairment morbidity and mortality rates remain high. Based on the broad spectrum of diverse reports with varying content and quality and in some cases lack of evidence we performed a systematic review on this topic.

SARS-CoV-2 related ARDS and invasive fungal infections in intensive care patients.

SARS-CoV-2 infection can potentially necessitate intensive care management. An increasing number of case reports are found in the literature indicating patients admitted in an intensive care setting with COVID-19 pneumonitis being complicated with invasive fungal infections.In a retrospective assessment of a three-month period at the national hospital of Malta, examining patients who were suffering from SARS-CoV-2 acute respiratory distress syndrome, 6 out of 63 patients (9.5%) were found to have confirmation or high probability of invasive fungal infection. The consensus definition for invasive fungal disease developed by the European Organization for Research and Treatment of Cancer and the Mycoses Study Group Education and Research Consortium was utilised to aid in the identification of these patients.In total, 15 patients received treatment with an anti-fungal agent in this three-month period, the decision being led by both clinical suspicion and the use of fungal markers obtained from the serum and bronchoalveolar lavage. Although several risk factors are attributed for the development of invasive fungal disease, the main factors identified in our cohort of patients is the SARS-CoV-2 ARDS in itself, along with the use of high dose corticosteroids. The average period of time between admission in intensive care and diagnosis of invasive fungal infection was noted to be 10.5 days.This high incidence of invasive fungal disease in mechanically ventilated patients suffering from SARS-CoV-2 ARDS, relatively early in their course of disease, should guide the clinician to investigate further with fungal biomarkers and cultures in those patients who are clinically deteriorating despite optimal medical treatment, as well as possibly considering empirical anti-fungal treatment if suspicion remains high.

Consensus guidelines for the diagnosis and management of invasive aspergillosis, 2021.

Invasive aspergillosis (IA) in haematology/oncology patients presents as primary infection or breakthrough infection, which can become refractory to antifungal treatment and has a high associated mortality. Other emerging patient risk groups include patients in the intensive care setting with severe respiratory viral infections, including COVID-19. These guidelines present key diagnostic and treatment recommendations in light of advances in knowledge since the previous guidelines in 2014. Culture and histological-based methods remain central to the diagnosis of IA. There is increasing evidence for the utility of non-culture methods employing fungal biomarkers in pre-emptive screening for infection, as well as for IA diagnosis when used in combination. Although azole resistance appears to be uncommon in Australia, susceptibility testing of clinical Aspergillus fumigatus complex isolates is recommended. Voriconazole remains the preferred first-line antifungal agent for treating primary IA, including for extrapulmonary disease. Recommendations for paediatric treatment broadly follow those for adults. For breakthrough and refractory IA, a change in class of antifungal agent is strongly recommended, and agents under clinical trial may need to be considered. Newer immunological-based imaging modalities warrant further study, while surveillance for IA and antifungal resistance remain essential to informing the relevance of current treatment recommendations.

Plant Nitrogen Uptake From Insect Frass Is Affected by the Nitrification Rate as Revealed by Urease and Nitrification Inhibitors

Insect protein production is considered a sustainable alternative to livestock protein which furthermore utilizes waste streams. Its production can have positive but also potentially negative environmental effects, which require evaluation. Frass, the byproduct of insect production, is regarded an efficient organic fertilizer or soil amendment. However, several studies report negative frass effects on plant growth and nitrogen (N) cycling. Therefore, a pot trial was carried out which sought to understand N release from frass and subsequent growth and nutrient uptake of Italian ryegrass. Mealworm frass (MWF) or buffalo worm frass (BFW) was applied at two rates (1.5 and 3% w/w) to a soil-sand mix. To evaluate N release processes, frass was applied alone, with a nitrification inhibitor (NI), a urease inhibitor (UI), or both (NI+UI). Plant N, nutrient uptake and soil inorganic N were measured at the experiment's end. To gauge whether altered N fluxes induced changes in the microbial community, soil microbial biomass, bacterial/archaeal abundances and ergosterol content as a fungal biomarker, were determined. Both frass types and application rates stimulated microbial growth and N mineralization. The 3% rate inhibited seed germination, possibly due to salinity or ammonia toxicity. At the 1.5% rate, both frass types were effective fertilizers. MWF led to higher biomass and nutrient uptake, owing to its higher extractable nutrient concentrations. The 3% rate caused nitrite accumulation in the absence of NI. NI improved plant biomass, nutrient uptake, stimulated archaeal and bacterial abundances and prevented nitrite accumulation. UI reduced N mineralization, showing that a substantial fraction of frass organic N is ureic. UI enhanced fungal contribution to the microbial biomass, revealing the importance of bacteria in frass N mineralization processes when UI is not applied. NI and UI combined, induced greater N release from frass than UI or NI alone. Our study demonstrated the usefulness of NI and UI in studying N release from frass. NI can improve plant N uptake and minimize N losses following frass application, reducing its potentially negative effects. UI can retard N release from frass, allowing its application as a slow-release fertilizer, but should not be used concurrently with NI.

Fungal biomarker monitoring and CT scans for early detection of invasive fungal disease in neutropenic hematological patients

By using data from the CEDMIC trial (n=413), we conducted a post-hoc analysis of the diagnostic value of biomarker monitoring and chest computed tomography (CT) scans for the early detection of invasive fungal disease (IFD) in neutropenic hematological patients. IFDs were defined in accordance with the EORTC/MSG definition with some modifications. Biomarkers such as Aspergillus galactomannan (GM) and (1→3)-β-D-glucan (βDG) were measured weekly. The positive predictive value (PPV) of GM and βDG in cases of high-risk treatment were 0.70 and 0.69, while those in low-risk treatment were 0.08 and 0, respectively. All of the positive biomarkers that were measured before the development of fever in low-risk treatment were false positives. The proportion of patients who had abnormal chest CT findings was 19% in persistent fever at 4-6 days, 57% at 7 days or later and 36% in recurrent fever. Sixty-nine percent of the patients who had abnormal findings at 7 days or later did not have abnormalities at 4-6 days. Afebrile screening of biomarkers in low-risk treatment is not useful. Chest CT should be reevaluated in persistent fever lasting for 7 days or longer even in patients who did not have abnormalities within 6 days.

COVID-19-Associated Pulmonary Aspergillosis, Fungemia, and Pneumocystosis in the Intensive Care Unit: a Retrospective Multicenter Observational Cohort during the First French Pandemic Wave.

ABSTRACTThe aim of this study was to evaluate diagnostic means, host factors, delay of occurrence, and outcome of patients with COVID-19 pneumonia and fungal coinfections in the intensive care unit (ICU). From 1 February to 31 May 2020, we anonymously recorded COVID-19-associated pulmonary aspergillosis (CAPA), fungemia (CA-fungemia), and pneumocystosis (CA-PCP) from 36 centers, including results on fungal biomarkers in respiratory specimens and serum. We collected data from 154 episodes of CAPA, 81 of CA-fungemia, 17 of CA-PCP, and 5 of other mold infections from 244 patients (male/female [M/F] ratio = 3.5; mean age, 64.7 ± 10.8 years). CA-PCP occurred first after ICU admission (median, 1 day; interquartile range [IQR], 0 to 3 days), followed by CAPA (9 days; IQR, 5 to 13 days), and then CA-fungemia (16 days; IQR, 12 to 23 days) (P < 10−4). For CAPA, the presence of several mycological criteria was associated with death (P < 10−4). Serum galactomannan was rarely positive (<20%). The mortality rates were 76.7% (23/30) in patients with host factors for invasive fungal disease, 45.2% (14/31) in those with a preexisting pulmonary condition, and 36.6% (34/93) in the remaining patients (P = 0.001). Antimold treatment did not alter prognosis (P = 0.370). Candida albicans was responsible for 59.3% of CA-fungemias, with a global mortality of 45.7%. For CA-PCP, 58.8% of the episodes occurred in patients with known host factors of PCP, and the mortality rate was 29.5%. CAPA may be in part hospital acquired and could benefit from antifungal prescription at the first positive biomarker result. CA-fungemia appeared linked to ICU stay without COVID-19 specificity, while CA-PCP may not really be a concern in the ICU. Improved diagnostic strategy for fungal markers in ICU patients with COVID-19 should support these hypotheses.IMPORTANCE To diagnose fungal coinfections in patients with COVID-19 in the intensive care unit, it is necessary to implement the correct treatment and to prevent them if possible. For COVID-19-associated pulmonary aspergillosis (CAPA), respiratory specimens remain the best approach since serum biomarkers are rarely positive. Timing of occurrence suggests that CAPA could be hospital acquired. The associated mortality varies from 36.6% to 76.7% when no host factors or host factors of invasive fungal diseases are present, respectively. Fungemias occurred after 2 weeks in ICUs and are associated with a mortality rate of 45.7%. Candida albicans is the first yeast species recovered, with no specificity linked to COVID-19. Pneumocystosis was mainly found in patients with known immunodepression. The diagnosis occurred at the entry in ICUs and not afterwards, suggesting that if Pneumocystis jirovecii plays a role, it is upstream of the hospitalization in the ICU.

β-1,3-d-Glucan and Galactomannan as Biomarkers for the Detection of Invasive Geotrichum and Magnusiomyces Infections: a Retrospective Evaluation.

Magnusiomyces and Geotrichum species are ascomycetous yeasts that can cause potentially life-threatening invasive fungal infections commonly referred to as geotrichosis. In this study, we aimed to estimate the incidence and mortality of these infections in a German tertiary care center. Furthermore, we evaluated the suitability of the fungal biomarkers galactomannan (GM) and β-1,3-d-glucan (BDG), which are both recommended as surrogate markers for Magnusiomyces capitatus infection by the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) and the European Confederation of Medical Mycology (ECMM) joint clinical guidelines for the diagnosis and management of rare invasive yeast infections for detection of invasive geotrichosis. Cases meeting the inclusion criteria for invasive Magnusiomyces/Geotrichum infection were retrospectively identified. Serum samples and culture supernatants were analyzed with two commercially available fungal antigen tests (Platelia Aspergillus Ag EIA and Wako β-glucan test). For a control cohort, outpatient samples sent for lues testing were included. Thirty-eight cases of Magnusiomyces/Geotrichum infection were identified over an 11-year observation period. In the majority of cases, the fungus was isolated from intra-abdominal specimens of patients with a history of abdominal surgery/procedures (n = 32). All cases of fungemia occurred exclusively in haemato-oncologic patients (n = 14). Thirty-day survival was 42% in the fungemia and 43% in the intra-abdominal geotrichosis group. Serum samples were available for 23 patients (14 bloodstream and nine intra-abdominal infections). While BDG sensitivity was 65%, none of the sera was GM positive. This finding was supported by in vitro experiments analyzing fungal culture supernatants: M. capitatus secretes significant amounts of BDG but not GM. Specificity was 96% for BDG and 100% for GM. Magnusiomyces and Geotrichum infections are not limited to haemato-oncologic patients. Contrasting the current ESCMID/ECMM recommendation, our results indicate that GM is no suitable biomarker for the diagnosis of Magnusiomyces infection. Contrarily, BDG sensitivity is comparable to that of candidemia.

Soil bacteria respond to regional edapho-climatic conditions while soil fungi respond to management intensity in grasslands along a European transect

Soil microbial community structure is determined by environmental conditions and influenced by other factors, such as the intensity of the land use management. Studies addressing the effect of environmental factors and management on grassland soil microbial communities at the continental scale are missing, and the wide range of ecosystem services provided by these ecosystems are thus also wanting. To address this knowledge gap, this study presents data on grassland soil microbial communities along a pan-European agro-ecological gradient. The transect included five geographical locations (Sweden, Germany, Switzerland, Portugal mainland, Portugal Azores). At each location, soils were collected in two regions characterized by favourable and less favourable conditions for plant growth. In each of these ten regions, grasslands along a gradient of management intensity were selected, i.e. grassland under intensive, less intensive and extensive management. Phospholipid fatty acid analysis (PLFA) was used to characterize the microbial community structure (PLFA pattern) in relation to climatic and soil properties. Over the whole geographical range, the environmental properties determined the soil microbial community structure. In Sweden and Switzerland, the regional growth conditions had the strongest influence on the soil microbial communities, while in Germany, Portugal mainland and Azores the management intensity was more important. Splitting up this whole community response into individual groups reveals that, in general, saprotrophic fungal biomarkers were highest in extensively managed grasslands while bacterial biomarkers differed mainly between the regions. We conclude that at the transect level, climate and soil properties were the most important factors influencing soil bacterial community structure, while soil fungal groups were more responsive to grassland management intensity. Overall agricultural sustainability could benefit from informed soil health promoting management practices, and this study contributes to such knowledge, showing the importance of management for the soil microbial biomass and community structure.

Fungal Biomarkers Stability in Mars Regolith Analogues after Simulated Space and Mars-like Conditions.

The discovery of life on other planets and moons in our solar system is one of the most important challenges of this era. The second ExoMars mission will look for traces of extant or extinct life on Mars. The instruments on board the rover will be able to reach samples with eventual biomarkers until 2 m of depth under the planet’s surface. This exploration capacity offers the best chance to detect biomarkers which would be mainly preserved compared to samples on the surface which are directly exposed to harmful environmental conditions. Starting with the studies of the endolithic meristematic black fungus Cryomyces antarcticus, which has proved its high resistance under extreme conditions, we analyzed the stability and the resistance of fungal biomarkers after exposure to simulated space and Mars-like conditions, with Raman and Gas Chromatography–Mass Spectrometry, two of the scientific payload instruments on board the rover.

A fundamental landscape of fungal biogeographical patterns across the main Chinese wine-producing regions and the dominating shaping factors

The microbial terroir plays an indispensable role in the formation of regional wine characteristics. A fundamental landscape of the fungal biogeographical patterns across Chinese wine-producing regions was obtained by characterizing the fungal communities in spontaneous fermentation. After confirming the established national microbial terroir, the fungal heterogeneity was evaluated at different geographical levels. The result showed that the variation between the wineries was more evident than at a regional level. Moreover, the microbial comparability from various regions with similar climates or wineries within the same regions was revealed. Further discriminant analysis determined the specific fungal biomarkers in different regions, while the associated reverse identification model displayed reliable accuracy (>70%). Correlation analysis illustrated the primary role of the geoclimatic factors (>41%) in shaping the fungal geographical patterns, and the relationship between the microbiome and spontaneous fermentation performance. In addition to expanding the knowledge regarding wine microbes, these findings provided a new benchmark for harnessing the microbial terroir to enhance regional wine expression.

Fungal biomarkers are detectable in Martian rock-analogues after space exposure: implications for the search of life on Mars

AbstractMars is a primary target of astrobiological interest: its past environmental conditions may have been favourable to the emergence of a prebiotic chemistry and, potentially, biological activity. In situ exploration is currently underway at the Mars surface, and the subsurface (2 m depth) will be explored in the future ESA ExoMars mission. In this context, BIOlogy and Mars EXperiment was performed to evaluate the stability and detectability of organic biomarkers under space and Mars-like conditions. Our data suggested that some target molecules, namely melanin, azelaic acid and nucleic acids, can be detected even after 16 months exposure to Low Earth Orbit conditions by multidisciplinary approaches. We used the same techniques as onboard the ExoMars rover, as Raman and infrared spectroscopies and gas chromatograph-mass spectrometer, and polymerase chain reaction even if this is not planned for the imminent mission to Mars. These results should be taken into account for future Mars exploration.

Diagnosis of Pneumonia Due to Invasive Molds.

Pneumonia is the most common presentation of invasive mold infections (IMIs), and is pathogenetically characterized as angioinvasion by hyphae, resulting in tissue infarction and necrosis. Aspergillus species are the typical etiologic cause of mold pneumonia, with A. fumigatus in most cases, followed by the Mucorales species. Typical populations at risk include hematologic cancer patients on chemotherapy, bone marrow and solid organ transplant patients, and patients on immunosuppressive medications. Invasive lung disease due to molds is challenging to definitively diagnose based on clinical features and imaging findings alone, as these methods are nonspecific. Etiologic laboratory testing is limited to insensitive culture techniques, non-specific and not readily available PCR, and tissue biopsies, which are often difficult to obtain and impact on the clinical fragility of patients. Microbiologic/mycologic analysis has limited sensitivity and may not be sufficiently timely to be actionable. Due to the inadequacy of current diagnostics, clinicians should consider a combination of diagnostic modalities to prevent morbidity in patients with mold pneumonia. Diagnosis of IMIs requires improvement, and the availability of noninvasive methods such as fungal biomarkers, microbial cell-free DNA sequencing, and metabolomics-breath testing could represent a new era of timely diagnosis and early treatment of mold pneumonia.

Prospective Evaluation of Galactomannan and (1→3) β-d-Glucan Assays as Diagnostic Tools for Invasive Fungal Disease in Children, Adolescents, and Young Adults With Acute Myeloid Leukemia Receiving Fungal Prophylaxis.

Patients receiving chemotherapy for acute myeloid leukemia (AML) are at high risk for invasive fungal disease (IFD). Diagnosis of IFD is challenging, leading to interest in fungal biomarkers. The objective was to define the utility of surveillance testing with Platelia Aspergillus galactomannan (GM) enzyme immunoassay (EIA) and Fungitell β-d-glucan (BDG) assay in children with AML receiving antifungal prophylaxis. Twice-weekly surveillance blood testing with GM EIA and BDG assay was performed during periods of neutropenia in the context of a randomized trial of children, adolescents, and young adults with AML allocated to fluconazole or caspofungin prophylaxis. Proven or probable IFD was adjudicated using blinded central reviewers. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated for Platelia and Fungitell assays alone and in combination for the outcomes of proven and probable invasive aspergillosis (IA) or invasive candidiasis (IC). Among 471 patients enrolled, 425 participants (209 fluconazole and 216 caspofungin) contributed ≥1 blood specimen. In total, 6103 specimens were evaluated, with a median of 15 specimens per patient (range 1-43). The NPV was >99% for GM EIA and BDG assay alone and in combination. However, there were no true positive results, resulting in sensitivity and PPV for each assay of 0%. The GM EIA and the BDG assay alone or in combination were not successful at detecting IA or IC during periods of neutropenia in children, adolescents, and young adults with AML receiving antifungal prophylaxis. Utilization of these assays for surveillance in this clinical setting should be discouraged.