Small RNAs from plants, bacteria and fungi within the order Hypocreales are ubiquitous in human plasma

Background

The human microbiome plays a significant role in maintaining normal physiology. Changes in its composition have been associated with bowel disease, metabolic disorders and atherosclerosis. Sequences of microbial origin have been observed within small RNA sequencing data obtained from blood samples. The aim of this study was to characterise the microbiome from which these sequences are derived.

Abundant non-human small RNA sequences were identified in plasma and plasma exosomal samples. Assembly of these short sequences into longer contigs was the pivotal novel step in ascertaining their origin by BLAST searches. Most reads mapped to rRNA sequences. The taxonomic profiles of the microbes detected were very consistent between individuals but distinct from microbiomes reported at other sites. The majority of bacterial reads were from the phylum Proteobacteria, whilst for 5 of 6 individuals over 90% of the more abundant fungal reads were from the phylum Ascomycota; of these over 90% were from the order Hypocreales. Many contigs were from plants, presumably of dietary origin.  In addition, extremely abundant small RNAs derived from human Y RNAs were detected.

A characteristic profile of a subset of the human microbiome can be obtained by sequencing small RNAs present in the blood. The source and functions of these molecules remain to be determined, but the specific profiles are likely to reflect health status. The potential to provide biomarkers of diet and for the diagnosis and prognosis of human disease is immense.

Just a matter of time: Fungi and roots significantly and rapidly aggregate soil over four decades along the Tagliamento River, NE Italy

Fluvial islands are emergent landforms which form at the interface between the permanently inundated areas of the river channel and the more stable areas of the floodplain as a result of interactions between physical river processes, wood and riparian vegetation. These highly dynamical systems are ideal to study soil structure development in the short to medium term, a process in which soil biota and plants play a substantial role. We investigated soil structure development on islands along a 40 year chronosequence within a 3 km island-braided reach of the Tagliamento River, Northeastern Italy. We used several parameters to capture different aspects of the soil structure, and measured biotic (e.g., fungal and plant root parameters) and abiotic (e.g. organic carbon) factors expected to determine the structure. We estimated models relating soil structure to its determinants, and, in order to confer statistical robustness to our results, we explicitly took into account spatial autocorrelation, which is present due to the space for time substitution inherent in the study of chronosequences and may have confounded results of previous studies. We found that, despite the eroding forces from the hydrological and geomorphological dynamics to which the system is subject, all soil structure variables significantly, and in some case greatly increased with site age. We interpret this as a macroscopic proxy for the major direct and indirect binding effects exerted by root variables and extraradical hyphae of arbuscular mycorrhizal fungi (AMF). Key soil structure parameters such as percentage of water stable aggregates (WSA) can double from the time the island landform is initiated (mean WSA = 30%) to the full 40 years (mean WSA = 64%) covered by our chronosequence. The study demonstrates the fundamental role of soil biota and plant roots in aggregating soils even in a system in which intense short to medium term physical disturbances are common.

Invading and expanding: range dynamics and ecological consequences of the greater white-toothed shrew (Crocidura russula) invasion in Ireland

Establishing how invasive species impact upon pre-existing species is a fundamental question in ecology and conservation biology. The greater white-toothed shrew (Crocidura russula) is an invasive species in Ireland that was first recorded in 2007 and which, according to initial data, may be limiting the abundance/distribution of the pygmy shrew (Sorex minutus), previously Ireland’s only shrew species. Because of these concerns, we undertook an intensive live-trapping survey (and used other data from live-trapping, sightings and bird of prey pellets/nest inspections collected between 2006 and 2013) to model the distribution and expansion of C. russula in Ireland and its impacts on Ireland’s small mammal community. The main distribution range of C. russula was found to be approximately 7,600 km2 in 2013, with established outlier populations suggesting that the species is dispersing with human assistance within the island. The species is expanding rapidly for a small mammal, with a radial expansion rate of 5.5 km/yr overall (2008–2013), and independent estimates from live-trapping in 2012–2013 showing rates of 2.4–14.1 km/yr, 0.5–7.1 km/yr and 0–5.6 km/yr depending on the landscape features present. S. minutus is negatively associated with C. russula. S. minutus is completely absent at sites where C. russula is established and is only present at sites at the edge of and beyond the invasion range of C. russula. The speed of this invasion and the homogenous nature of the Irish landscape may mean that S. minutus has not had sufficient time to adapt to the sudden appearance of C. russula. This may mean the continued decline/disappearance of S. minutus as C. russula spreads throughout the island.

Water and Temperature Relations of Growth of the Entomogenous Fungi Beauveria bassiana, Metarhizium anisopliae, and Paecilomyces farinosus

The effects of temperature (5-50°C), water availability (0.998-0.88 water activity, aw), and aw × temperature interactions (15-45°C) on growth of three entomogenous fungi, Beauveria bassiana, Metarhizium anisopliae, and Paecilomyces farinosus, were evaluated on a Sabouraud dextrose-based medium modified with the ionic solute KCl, the non-ionic solute glycerol, and an inert solute, polyethylene glycol (PEG) 600. The temperature ranges for growth of B. bassiana, M. anisopliae, and P. farinosus were 5-30, 5-40, and 5-30°C, and optimum growth temperatures were 25, 30, and 20°C, respectively. All three species grew over a similar aw range (0.90-0.998) at optimum temperatures for growth. However, there were significant interspecies variations in growth rates on media modified with each of the three aw-modifying solutes. Growth aw optima ranged between 0.99 and 0.97 on KCl-, glycerol-, and PEG 600-modified media for M. anisopliae and P. farinosus. B. bassiana grew optimally at 0.998 aw, regardless of aw. Comprehensive two-dimensional profiles of aw × temperature relations for growth of these three species were constructed for the first time. The results are discussed in relation to the environmental limits that determine efficacy of entomogenous fungi as biocontrol agents in nature. © 1999 Academic Press.

Effects of KCl concentration on accumulation of acyclic sugar alcohols and trehalose in conidia of three entomopathogenic fungi

Beauveria bassiana, Metarhizium anisopliae and Paecilomyces farinosus were grown on Sabouraud Dextrose Agar (SDA) modified with KCl to give a range of water activity (a(w)) from 0.938 to 0.998. Growth of all three species was optimal at 0.983 a(w) and growth occurred over the a(w) range tested. Acyclic sugar alcohol (polyol) and trehalose content of conidia was determined by HPLC and found to vary with species and a(w). Conidia of B. bassiana and P. farinosus were found to contain totals of 1.5% and 2.3% polyols respectively at 0.998 a(w), and double these amounts at <0.950 a(w). Conidia of M. anisopliae contained from 5.7% to 6.8% polyols at each a(w) tested. In conidia of all three species the predominant polyol was mannitol. The lower molecular weight polyols, arabitol and erythritol, were found to accumulate at reduced a(w). Small amounts of glycerol were present in conidia of each species; <15% total polyols. Conidia of B. bassiana and M. anisopliae contained about 0.5% trehalose from 0.970 to 0.998 a(w), but only trace amounts below 0.950 a(w). Conidia of P. farinosus contained 2.1% trehalose at 0.998 a(w) and this decreased to <0.1% below 0.950 a(w). Potential to manipulate the endogenous reserves of conidia of these biological control agents to enhance viability and desiccation tolerance is discussed.

Effect of carbohydrate type and concentration on polyhydroxy alcohol and trehalose content of conidia of three entomopathogenic fungi

The entomopathogenic fungi Beauveria bassiana, Metarhizium anisopliae and Paecilomyces farinosus were cultured on solid agar media containing different carbohydrate components (glycerol, glucose, trehalose or starch) at concentrations of ≤ 142.7 g added carbon 1-1 for 30 d at 25°C. The water activity (a(w)) of the media ranged from 0.925 to 0.998. Growth of M. anisopliae and P. farinosus was stimulated between 0.975 and 0.995 a(w) on glucose media and that of P. farinosus at 0. 975 a(w) on glycerol media. At < 0.970 a(w), growth of each fungal species was significantly reduced (P < 0.05). Polyhydroxy alcohols (polyols) and trehalose were extracted from conidia produced on different media and quantified using HPLC. Total polyol content of conidia produced on glucose media varied between 5.2 and 52.2 mg g-1 for B. bassiana, 77.3 and 90.3 mg g-1 for M. anisopliae, and 26.7 and 76.1 mg g-1 for P. farinosus. The amounts of specific polyols in conidia varied significantly from media of different glucose concentrations. Mannitol was the predominant polyol in conidia of all three species, with conidia of M. anisopliae, for example, containing as much as 75.2 mg mannitol g-1 when cultured on glucose media. The amount of the lower molecular mass polyols glycerol and erythritol was greater in conidia produced on glucose media with > 50.0 g added carbon 1-1 than that in conidia produced at lower glucose concentrations. Conidia contained between 10.8 and 20.8 mg glycerol plus erythritol g-1 on glucose media with 142.7 g added carbon 1-1, depending on species. Conversely, conidia of B. bassiana and P. farinosus contained maximum amounts of trehalose ( ≤ 23.5 mg g-1) when produced on glucose media with < 50.0 g added carbon l-1, and trehalose content was considerably less at higher glucose concentrations. There were accumulations of glycerol and erythritol in conidia of all three species when grown on glycerol media with > 25.0 g added carbon 1-1; conidia of B. bassiana contained up to 154.0 mg glycerol plus erythritol g-1. hen B. bassiana and P. farinosus were grown on trehalose media, conidia contained up to 222.1 mg trehalose g-1. By contrast, conidia of M. anisopliae contained < 17.0 mg trehalose g-1 under all conditions tested. The water availability of solutions of different polyols is discussed in relation to their potential to act in osmotic adjustment during germination. The ability to manipulate polyol and trehalose content of fungal propagules may be critical in enhancing the storage life and efficacy of biological control agents.

Stress tolerance and virulence of insect-pathogenic fungi are determined by environmental conditions during conidial formation

The virulence to insects and tolerance to heat and UV-B radiation of conidia of entomopathogenic fungi are greatly influenced by physical, chemical, and nutritional conditions during mycelial growth. This is evidenced, for example, by the stress phenotypes of Metarhizium robertsii produced on various substrates. Conidia from minimal medium (Czapek's medium without sucrose), complex medium, and insect (Lepidoptera and Coleoptera) cadavers had high, moderate, and poor tolerance to UV-B radiation, respectively. Furthermore, conidia from minimal medium germinated faster and had increased heat tolerance and were more virulent to insects than those from complex medium. Low water-activity or alkaline culture conditions also resulted in production of conidia with high tolerance to heat or UV-B radiation. Conidia produced on complex media exhibited lower stress tolerance, whereas those from complex media supplemented with NaCl or KCl (to reduce water activity) were more tolerant to heat and UV-B than those from the unmodified complex medium. Osmotic and nutritive stresses resulted in production of conidia with a robust stress phenotype, but also were associated with low conidial yield. Physical conditions such as growth under illumination, hypoxic conditions, and heat shock before conidial production also induced both higher UV-B and heat tolerance; but conidial production was not decreased. In conclusion, physical and chemical parameters, as well as nutrition source, can induce great variability in conidial tolerance to stress for entomopathogenic fungi. Implications are discussed in relation to the ecology of entomopathogenic fungi in the field, and to their use for biological control. This review will cover recent technologies on improving stress tolerance of entomopathogenic fungi for biological control of insects.

Microbial Communities Associated with Healthy and White Syndrome-Affected Echinopora lamellosa in Aquaria and Experimental Treatment with the Antibiotic Ampicillin

Prokaryotic and ciliate communities of healthy and aquarium White Syndrome (WS)-affected coral fragments were screened using denaturing gradient gel electrophoresis (DGGE). A significant difference (R = 0.907, p < 0.001) in 16S rRNA prokaryotic diversity was found between healthy (H), sloughed tissue (ST), WS-affected (WSU) and antibiotic treated (WST) samples. Although 3 Vibrio spp were found inWS-affected samples, two of these species were eliminated following ampicillin treatment, yet lesions continued to advance, suggesting they play a minor or secondary role in the pathogenesis. The third Vibrio sp increased slightly in relative abundance in diseased samples and was abundant in non-diseased samples. Interestingly, a Tenacibaculum sp showed the greatest increase in relative abundance between healthy and WS-affected samples, demonstrating consistently high abundance across all WS-affected and treated samples, suggesting Tenacibaculum sp could be a more likely candidate for pathogenesis in this instance. In contrast to previous studies bacterial abundance did not vary significantly (ANOVA, F2, 6 = 1.000, p = 0.422) between H, ST, WSU or WST. Antimicrobial activity (assessed on Vibrio harveyi cultures) was limited in both H and WSU samples (8.1% ±8.2 and 8.0% ±2.5, respectively) and did not differ significantly (Kruskal-Wallis, χ2 (2) = 3.842, p = 0.146). A Philaster sp, a Cohnilembus sp and a Pseudokeronopsis sp. were present in all WS-affected samples, but not in healthy samples. The exact role of ciliates in WS is yet to be determined, but it is proposed that they are at least responsible for the neat lesion boundary observed in the disease.

Exposure to aflatoxin B1 in utero is associated with DNA methylation in white blood cells of infants in The Gambia

BACKGROUND: Exposure to environmental toxins during embryonic development may lead to epigenetic changes that influence disease risk in later life. Aflatoxin is a contaminant of staple foods in sub-Saharan Africa, is a known human liver carcinogen and has been associated with stunting in infants.

METHODS: We have measured aflatoxin exposure in 115 pregnant women in The Gambia and examined the DNA methylation status of white blood cells from their infants at 2-8 months old (mean 3.6 ± 0.9). Aflatoxin exposure in women was assessed using an ELISA method to measure aflatoxin albumin (AF-alb) adducts in plasma taken at 1-16 weeks of pregnancy. Genome-wide DNA methylation of infant white blood cells was measured using the Illumina Infinium HumanMethylation450beadchip.

RESULTS: AF-alb levels ranged from 3.9 to 458.4 pg/mg albumin. We found that aflatoxin exposure in the mothers was associated to DNA methylation in their infants for 71 CpG sites (false discovery rate < 0.05), with an average effect size of 1.7% change in methylation. Aflatoxin-associated differential methylation was observed in growth factor genes such as FGF12 and IGF1, and immune-related genes such as CCL28, TLR2 and TGFBI. Moreover, one aflatoxin-associated methylation region (corresponding to the miR-4520b locus) was identified.

CONCLUSIONS: This study shows that maternal exposure to aflatoxin during the early stages of pregnancy is associated with differential DNA methylation patterns of infants, including in genes related to growth and immune function. This reinforces the need for interventions to reduce aflatoxin exposure, especially during critical periods of fetal and infant development.

Deflagrations in hybrid CONe white dwarfs: a route to explain the faint Type Iax supernova 2008ha

Stellar evolution models predict the existence of hybrid white dwarfs (WDs) with a carbon-oxygen core surrounded by an oxygen-neon mantle. Being born with masses similar to 1.1 M-aS (TM), hybrid WDs in a binary system may easily approach the Chandrasekhar mass (M-Ch) by accretion and give rise to a thermonuclear explosion. Here, we investigate an off-centre deflagration in a near-M-Ch hybrid WD under the assumption that nuclear burning only occurs in carbon-rich material. Performing hydrodynamics simulations of the explosion and detailed nucleosynthesis post-processing calculations, we find that only 0.014 M-aS (TM) of material is ejected while the remainder of the mass stays bound. The ejecta consist predominantly of iron-group elements, O, C, Si and S. We also calculate synthetic observables for our model and find reasonable agreement with the faint Type Iax SN 2008ha. This shows for the first time that deflagrations in near-M-Ch WDs can in principle explain the observed diversity of Type Iax supernovae. Leaving behind a near-M-Ch bound remnant opens the possibility for recurrent explosions or a subsequent accretion-induced collapse in faint Type Iax SNe, if further accretion episodes occur. From binary population synthesis calculations, we find the rate of hybrid WDs approaching M-Ch to be of the order of 1 per cent of the Galactic SN Ia rate.

High-affinity phosphate/arsenate transport in white lupin (Lupinus albus) is relatively insensitive to phosphate status

The development of proteoid roots under phosphorus deficiency by white lupin (Lupinus albus) may result in increased arsenate uptake, as arsenate is a phosphate analogue. This, together with its high biomass production, rapid growth and ability to survive in soils with low phosphate and nitrogen contents, low pH and high metal contents make them an interesting species to investigate with respect to revegetation, and possibly also for long-term phytoremediation, of arsenic contaminated soils. Kinetic parameters for arsenate uptake for P-deficient and P-sufficient plants, as well as for proteoid and nonproteoid roots were obtained. Down-regulation of arsenate uptake by phosphate, as well as phosphate/arsenate competition for P-deficient and P-sufficient plants was studied. Arsenate uptake was reduced by phosphate, but small differences were found between P-deficient and P-sufficient plants. Arsenate uptake by proteoid roots was higher than for nonproteoid roots of P-deficient plants, with higher V_max and similar K_m values. Down-regulation of the high affinity phosphate/arsenate uptake system by phosphate does take place but seems to be slower than in other plants. This study suggests that the low sensitivity of the phosphate/arsenate uptake system to regulation by phosphate may be related to the adaptations of white lupin to low P available environments. Such adaptation are absent in plants unable to develop proteoid roots.

Interactions between ectomycorrhizal fungi and soil saprotrophs:Implications for decomposition of organic matter in soils and degradation of organic pollutants in the rhizosphere

Ectomycorrhizal fungi and saprotrophic microorganisms coexist and interact in the mycorrhizosphere. We review what is known regarding these interactions and how they may influence processes such as ectomycorrhiza formation, mycelial growth, and the dynamics of carbon movement to and within the rhizosphere. Particular emphasis is placed on the potential importance of interactions in decomposition of soil organic matter and degradation of persistant organic pollutants in soil. While our knowledge is currently fairly limited, it seems likely that interactions have profound effects on mycorrhizosphere processes. More extensive research is warranted to provide novel insights into mycorrhizosphere ecology and to explore the potential for manipulating the ectomycorrhizosphere environment for biotechnological purposes.