Molecular identification of fungi microfossils in a Neoproterozoic shale rock

A taxon-rich and genome-scale phylogeny of Opisthokonta

Ancient divergences within Opisthokonta-a major lineage that includes organisms in the kingdoms Animalia, Fungi, and their unicellular relatives-remain contentious. To assess progress toward a genome-scale Opisthokonta phylogeny, we conducted the most taxon rich phylogenomic analysis using sets of genes inferred with different orthology inference methods and established the geological timeline of Opisthokonta diversification. We also conducted sensitivity analysis by subsampling genes or taxa from the full data matrix based on filtering criteria previously shown to improve phylogenomic inference. We found that approximately 85% of internal branches were congruent across data matrices and the approaches used. Notably, the use of different orthology inference methods was a substantial contributor to the observed incongruence: analyses using the same set of orthologs showed high congruence of 97% to 98%, whereas different sets of orthologs resulted in somewhat lower congruence (87% to 91%). Examination of unicellular Holozoa relationships suggests that the instability observed across varying gene sets may stem from weak phylogenetic signals. Our results provide a comprehensive Opisthokonta phylogenomic framework that will be useful for illuminating ancient evolutionary episodes concerning the origin and diversification of the 2 major eukaryotic kingdoms and emphasize the importance of investigating effects of orthology inference on phylogenetic analyses to resolve ancient divergences.

Electroenzymatic cascade reaction on a biohybrid boosts the chiral epoxidation reaction

The chiral epoxidation of styrene and its derivatives is an important transformation that has attracted considerable scientific interest in the chemical industry. Herein, we integrate enzymatic catalysis and electrocatalysis to propose a new route for the chiral epoxidation of styrene and its derivatives. Chloroperoxidase (CPO) functionalized with 1-ethyl-3-methylimidazolium bromide (ILEMB) was loaded onto cobalt nitrogen-doped carbon nanotubes (CoN@CNT) to form a biohybrid (CPO-ILEMB/CoN@CNT). H2O2 species were generated in situ through a two-electron oxygen reduction reaction (2e-ORR) at CoN@CNT to initiate the following enzymatic epoxidation of styrene by CPO. CoN@CNT had high electroactivity for the ORR to produce H2O2 at a more positive potential, prohibiting the conversion of FeIII to FeII in the heme of CPO to maintain enzymatic activity. Meanwhile, CoN@CNT could serve as an ideal carrier for the immobilization of CPO-ILEMB. Hence, the coimmobilization of CPO-ILEMB and CoN@CNT could facilitate the diffusion of intermediate H2O2, which achieved 17 times higher efficiency than the equivalent amounts of free CPO-ILEMB in bulk solution for styrene epoxidation. Notably, an enhancement (∼45%) of chiral selectivity for the epoxidation of styrene was achieved.

Comparative metabolomic study of fungal foliar endophytes and their long-lived host Astrocaryum sciophilum: a model for exploring the chemodiversity of host-microbe interactions

Introduction

In contrast to the dynamics observed in plant/pathogen interactions, endophytic fungi have the capacity to establish enduring associations within their hosts, leading to the development of a mutually beneficial relationship that relies on specialized chemical interactions. Research indicates that the presence of endophytic fungi has the ability to significantly modify the chemical makeup of the host organism. Our hypothesis proposes the existence of a reciprocal exchange of chemical signals between plants and fungi, facilitated by specialized chemical processes that could potentially manifest within the tissues of the host. This research aimed to precisely quantify the portion of the cumulative fungal endophytic community's metabolome detectable within host leaves, and tentatively evaluate its relevance to the host-endophyte interplay. The understory palm Astrocaryum sciophilum (Miq.) Pulle was used as a interesting host plant because of its notable resilience and prolonged life cycle, in a tropical ecosystem.

Method

Using advanced metabolome characterization, including UHPLC-HRMS/MS and molecular networking, the study explored enriched metabolomes of both host leaves and 15 endophytic fungi. The intention was to capture a metabolomic "snapshot" of both host and endophytic community, to achieve a thorough and detailed analysis.

Results and discussion

This approach yielded an extended MS-based molecular network, integrating diverse metadata for identifying host- and endophyte-derived metabolites. The exploration of such data (>24000 features in positive ionization mode) enabled effective metabolome comparison, yielding insights into cultivable endophyte chemodiversity and occurrence of common metabolites between the holobiont and its fungal communities. Surprisingly, a minor subset of features overlapped between host leaf and fungal samples despite significant plant metabolome enrichment. This indicated that fungal metabolic signatures produced in vitro remain sparingly detectable in the leaf. Several classes of primary metabolites were possibly shared. Specific fungal metabolites and/or compounds of their chemical classes were only occasionally discernible in the leaf, highlighting endophytes partial contribution to the overall holobiont metabolome. To our knowledge, the metabolomic study of a plant host and its microbiome has rarely been performed in such a comprehensive manner. The general analytical strategy proposed in this paper seems well-adapted for any study in the field of microbial- or microbiome-related MS and can be applied to most host-microbe interactions.

Spectroscopic investigations of fungal biomarkers after exposure to heavy ion irradiation

The main objective of the ongoing and future space exploration missions is the search for traces of extant or extinct life (biomarkers) on Mars. One of the main limiting factors on the survival of Earth-like life is the presence of harmful space radiation, that could damage or modify also biomolecules, therefore understanding the effects of radiation on terrestrial biomolecules stability and detectability is of utmost importance. Which terrestrial molecules could be preserved in a Martian radiation scenario? Here, we investigated the potential endurance of fungal biomolecules, by exposing de-hydrated colonies of the Antarctic cryptoendolithic black fungus Cryomyces antarcticus mixed with Antarctic sandstone and with two Martian regolith analogues to increasing doses (0, 250 and 1000 Gy) of accelerated ions, namely iron (Fe), argon (Ar) and helium (He) ions. We analyzed the feasibility to detect fungal compounds with Raman and Infrared spectroscopies after exposure to these space-relevant radiations.

Fossil history of fungus host-specificity: Association of conidia of fossil Asterosporium asterospermum with macro- and microremains of Fagus

Fossil staurosporous conidia almost identical to modern conidia of Asterosporium asterospermum were found from three Central European localities ranging from the Late Oligocene (Germany) to Middle/Late Miocene (Poland). Extant A. asterospermum is strictly host-specific and found only on branches or bark of various Fagus species from Europe, Asia and North America. Conspicuous association of conidia of A. asterospermum with numerous macro- and microremains of Fagus were reported from all the localities where fossil conidia of Asterosporium were found confirming the host-specificity of fossil A. asterospermum to ancient beeches. The host-specific relationship of A. asterospermum and beech was presumably established early in the history of the Fagus genus.

Fungal-induced fossil biomineralization

Exceptional preservation of fossils has often been attributed to the actions of bacteria that aid in the preservation of soft tissues that normally decay rapidly. However, it is well known that fungi play a major role in organic matter decomposition, biogeochemical cycling of elements, and metal-mineral transformations in modern ecosystems. Although the fungal fossil record can be traced back over a billion years, there are only a few recorded examples of fungal roles in fossilization. In this research, we have carried out a detailed geobiological investigation on early Pleistocene hyena coprolites (fossilized dung) in an attempt to ascertain possible fungal involvement in their formation. Using an advanced microscopic and mineralogical approach, we found that numerous hydroxyapatite nanofibers (25-34 nm on average), interwoven to form spheroidal structures, constituted the matrix of the coprolites in addition to food remains. These structures were found to be extremely similar in texture and mineral composition to biominerals produced during laboratory culture of a common saprophytic and geoactive fungus, Aspergillus niger, in the presence of a solid source of calcium (Ca) and phosphorus (P). This observation, and our other data obtained, strongly suggests that fungal metabolism can provide a mechanism that can result in fossil biomineralization, and we hypothesize, therefore, that this may have contributed to the formation of well-preserved fossils (Lagerstätten) in the geological record. The characteristic polycrystalline nanofibers may also have served as a potential biosignature for fungal life in early Earth and extraterrestrial environments.

Seeking the Psilocybiome: Psychedelics meet the microbiota-gut-brain axis

Moving towards a systems psychiatry paradigm embraces the inherent complex interactions across all levels from micro to macro and necessitates an integrated approach to treatment. Cortical 5-HT2A receptors are key primary targets for the effects of serotonergic psychedelics. However, the therapeutic mechanisms underlying psychedelic therapy are complex and traverse molecular, cellular, and network levels, under the influence of biofeedback signals from the periphery and the environment. At the interface between the individual and the environment, the gut microbiome, via the gut-brain axis, plays an important role in the unconscious parallel processing systems regulating host neurophysiology. While psychedelic and microbial signalling systems operate over different timescales, the microbiota-gut-brain (MGB) axis, as a convergence hub between multiple biofeedback systems may play a role in the preparatory phase, the acute administration phase, and the integration phase of psychedelic therapy. In keeping with an interconnected systems-based approach, this review will discuss the gut microbiome and mycobiome and pathways of the MGB axis, and then explore the potential interaction between psychedelic therapy and the MGB axis and how this might influence mechanism of action and treatment response. Finally, we will discuss the possible implications for a precision medicine-based psychedelic therapy paradigm.

The Addition of Reishi and Lion’s Mane Mushroom Powder to Pasta Influences the Content of Bioactive Compounds and the Antioxidant, Potential Anti-Inflammatory, and Anticancer Properties of Pasta

The influence of a 2.5% and 5% addition of dried Reishi and Lion’s Mane mushrooms on the content of bioactive compounds and some pro-health properties of pasta was studied. In samples subjected to gastrointestinal digestion, the content of phenolic compounds and the antioxidant, potential anti-inflammatory, and antiproliferative properties were significantly higher. The qualitative–quantitative analysis of phenolic compounds performed using the LC-MS/MS technique indicated that the Reishi-enriched pasta was characterized by a higher content of syringic (R2.5 sample), while pasta supplemented with Lion’ Mane had a higher content of vanillin in relation to the control pasta. In the case of ethanolic extracts, samples supplemented with the Reishi mushrooms (R5 sample) were characterized by higher ABTS antiradical properties and a reducing power while the sample supplemented with Lion’s Mane (L5 sample) had a higher ability to inhibit lipoxygenase in relation to the control sample. In conclusion, the results suggest that Reishi and Lion’s Mane mushroom powder can be used for the fortification of semolina pasta, conferring slightly healthier characteristics of the product.

Molecular fingerprints resolve affinities of Rhynie chert organic fossils

The affinities of extinct organisms are often difficult to resolve using morphological data alone. Chemical analysis of carbonaceous specimens can complement traditional approaches, but the search for taxon-specific signals in ancient, thermally altered organic matter is challenging and controversial, partly because suitable positive controls are lacking. Here, we show that non-destructive Fourier Transform Infrared Spectroscopy (FTIR) resolves in-situ molecular fingerprints in the famous 407 Ma Rhynie chert fossil assemblage of Aberdeenshire, Scotland, an important early terrestrial Lagerstätte. Remarkably, unsupervised clustering methods (principal components analysis and K-mean) separate the fossil spectra naturally into eukaryotes and prokaryotes (cyanobacteria). Additional multivariate statistics and machine-learning approaches also differentiate prokaryotes from eukaryotes, and discriminate eukaryotic tissue types, despite the overwhelming influence of silica. We find that these methods can clarify the affinities of morphologically ambiguous taxa; in the Rhynie chert for example, we show that the problematic "nematophytes" have a plant-like composition. Overall, we demonstrate that the famously exquisite preservation of cells, tissues and organisms in the Rhynie chert accompanies similarly impressive preservation of molecular information. These results provide a compelling positive control that validates the use of infrared spectroscopy to investigate the affinity of organic fossils in chert.

Biogeochemical and historical drivers of microbial community composition and structure in sediments from Mercer Subglacial Lake, West Antarctica

Ice streams that flow into Ross Ice Shelf are underlain by water-saturated sediments, a dynamic hydrological system, and subglacial lakes that intermittently discharge water downstream across grounding zones of West Antarctic Ice Sheet (WAIS). A 2.06 m composite sediment profile was recently recovered from Mercer Subglacial Lake, a 15 m deep water cavity beneath a 1087 m thick portion of the Mercer Ice Stream. We examined microbial abundances, used 16S rRNA gene amplicon sequencing to assess community structures, and characterized extracellular polymeric substances (EPS) associated with distinct lithologic units in the sediments. Bacterial and archaeal communities in the surficial sediments are more abundant and diverse, with significantly different compositions from those found deeper in the sediment column. The most abundant taxa are related to chemolithoautotrophs capable of oxidizing reduced nitrogen, sulfur, and iron compounds with oxygen, nitrate, or iron. Concentrations of dissolved methane and total organic carbon together with water content in the sediments are the strongest predictors of taxon and community composition. δ¹³C values for EPS (-25 to -30‰) are consistent with the primary source of carbon for biosynthesis originating from legacy marine organic matter. Comparison of communities to those in lake sediments under an adjacent ice stream (Whillans Subglacial Lake) and near its grounding zone provide seminal evidence for a subglacial metacommunity that is biogeochemically and evolutionarily linked through ice sheet dynamics and the transport of microbes, water, and sediments beneath WAIS.

Prototaxites reinterpreted as mega-rhizomorphs, facilitating nutrient transport in early terrestrial ecosystems

The enigmatic fossil Prototaxites found in successions ranging from the Middle Ordovician to the Upper Devonian was originally described as having conifer affinity. The current debate, however, suggests that they probably represent gigantic algal-fungal symbioses. Our re-investigation of permineralized Prototaxites specimens from two localities, the Heider quarry in Germany and the Bordeaux quarry in Canada, reveals striking anatomical similarities with modern fungal rhizomorphs Armillaria mellea. We analysed extant fungal rhizomorphs and fossil Prototaxites through light microscopy of their anatomy, Fourier transform infrared spectroscopy, X-ray microscopy, and Raman spectroscopy. Based on these comparisons, we interpret the Prototaxites as fungi. The detailed preservation of cell walls and possible organelles seen in transverse sections of Prototaxites reveal that fossilization initiated while the organism was alive, inhibiting the collapse of delicate cellular structures. Prototaxites has been interpreted to grow vertically by many previous workers. Here we propose an alternative view that Prototaxites represents a complex hyphal aggregation (rhizomorph) that may have grown horizontally similar to modern complex aggregated mycelial growth forms, such as cords and rhizomorphs. Their main function was possibly to redistribute water and nutrition from nutrient-rich to nutrient-poor areas facilitating the expansion for early land plant communities.

The first fossil record of the anamorphic genus Zygosporium Mont. from the Oligocene of Csolnok (N Hungary)

Remains of a fungus with unique morphological characters were found on the leaf cuticle of a fossil leaf preserved in Oligocene deposits from Csolnok, Hungary. Vesicular conidiophores with characteristic, darkly pigmented, incurved vesicles were compared with those of the modern representatives of the anamorphic genus Zygosporium. Based on the fossil find, a new fossil-species, Zygosporium oligocenicum G. Worobiec sp. nov., having vesicular conidiophores that arise directly from the mycelium, was described. The fossil Zygosporium oligocenicum presumably preferred warm climate and, similarly to most modern members of the genus, was a saprophyte on fallen, decaying leaves.

Bioconversion of Some Agro-Residues into Organic Acids by Cellulolytic Rock-Phosphate-Solubilizing Aspergillus japonicus

Biological-based conversion of agricultural residues into bioactive compounds may be considered to be the basis for various vital industries. However, finding a suitable microorganism is a challenge in the bioconversion process. Therefore, this study was conducted to find local fungal isolates able to convert a combination of plant biomass residues into organic acids (OAs). Based on their cellulase and phytase activities and rock phosphate (RP) solubilization potential, an efficient 15 fungal isolates (named F1 to F15) were selected and identified by both morphological and molecular methods using the 18S rRNA sequencing technique. The best fungal isolate (F15) was identified as Aspergillus japonicus. After 4 weeks of incubation below solid-state fermentation (SSF) with a mix of sugarcane bagasse and faba bean straw (3:7), with 7.5% (v/w) fungal inoculum to the growth medium, the biodegradation process by the fungus reached its peak, i.e., maximum cellulolytic activity and RP solubilization ability. Under such fermentation conditions, seven organic acids were detected using HPLC, in the following order: ascorbic acid > oxalic acid > formic acid > malic acid > succinic acid > lactic acid > citric acid. Based on the results, Aspergillus japonicus (F15) could produce OAs and cellulose enzymes, and could be considered a new single-step bio-converter of sugarcane bagasse and faba bean straw residues into OAs. Furthermore, this fungus could be a new source of fungal cellulose, and could present a practical approach to reducing environmental contamination. Additional work is encouraged for more optimization of fermentation conditions.

Nutritional value of commercial broiler feed supplemented with olive mill waste fermented with probiotic Rhizopus oryzae strains

AIMS

The changes in chemical composition and metabolizable energy of both olive mill waste (OMW) upon fermentation by three potential probiotic Rhizopus oryzae strains and commercial feed (CF) upon its supplementation by fermented olive mill waste (FOMW) were investigated. The objective was to test if there will be an enhancement in the nutritional value of olive mill waste after fermentation and/or commercial broiler feed upon supplementation by potentially probiotic filamentous fungi.

METHODS AND RESULTS

A three Rhizopus oryzae strains (92/1, 236/2, and 284) isolated from agricultural soil that were proven to have good probiotic properties (non-toxic, antimicrobial activity, antioxidant capacity, and gastrointestinal tolerance) were used to ferment OMW, then the chemical composition was analyzed after 7 and 14 days of fermentation. The FOMW with the R. oryzae 284 strain, which gave the best results, was added to a commercial broiler feed at 20%, 30%, and 40% supplementation ratios. Then proximal analyses were done to compare non-supplemented with supplemented CF. Chemical analyses included dry weight, crude protein, crude fats, crude fibers, crude ash, sugars, and starch, then metabolizable energy was calculated from the given values.

CONCLUSIONS

Compared to non-fermented OMW, the best results were obtained by the R. oryzae 284 strain allowing an increase in crude protein content by 23.4% after 7 days of fermentation, a decrease in crude fiber content by 9.8% after 14 days of fermentation, and an increase in metabolizable energy by 3.6% after 7 days of fermentation. Compared to non-supplemented CF, the metabolizable energy changes of 20, 30, and 40% supplementation increased by 8.38, 2.83%, and decreased by 4.27% respectively.

SIGNIFICANCE AND IMPACT OF STUDY

FOMW can be incorporated into broiler feed rations until 30% without causing any decrease in metabolizable energy. It can be a cheaper alternative with promising productivity and chicken health improvements.

Molecular Trade-Offs between Lattice Oxygen and Oxygen Vacancy Drive Organic Pollutant Degradation in Fungal Biomineralized Exoskeletons

Fungal-mineral interactions can effectively alleviate cellular stress from organic pollutants, the production of which are expected to rapidly increase owing to the Earth moving into an unprecedented geological epoch, the Anthropocene. The underlying mechanisms that may enable fungi to combat organic pollution during fungal-mineral interactions remain unclear. Inspired by the natural fungal sporulation process, we demonstrate for the first time that fungal biomineralization triggers the formation of an ultrathin (hundreds of nanometers thick) exoskeleton, enriched in nanosized iron (oxyhydr)oxides and biomolecules, on the hyphae. Mapped biochemical composition of this coating at a subcellular scale via high spatial resolution (down to 50 nm) synchrotron radiation-based techniques confirmed aromatic C, C-N bonds, amide carbonyl, and iron (oxyhydr)oxides as the major components of the coatings. This nanobiohybrid system appeared to impart a strong (×2) biofunctionality for fungal degradation of bisphenol A through altering molecular-level trade-offs between lattice oxygen and oxygen vacancy. Together, fungal coatings could act as "artificial spores", which enable fungi to combat physical and chemical stresses in natural environments, providing crucial insights into fungal biomineralization and coevolution of the Earth's lithosphere and biosphere.

Eukaryogenesis and oxygen in Earth history

The endosymbiotic origin of mitochondria during eukaryogenesis has long been viewed as an adaptive response to the oxygenation of Earth's surface environment, presuming a fundamentally aerobic lifestyle for the free-living bacterial ancestors of mitochondria. This oxygen-centric view has been robustly challenged by recent advances in the Earth and life sciences. While the permanent oxygenation of the atmosphere above trace concentrations is now thought to have occurred 2.2 billion years ago, large parts of the deep ocean remained anoxic until less than 0.5 billion years ago. Neither fossils nor molecular clocks correlate the origin of mitochondria, or eukaryogenesis more broadly, to either of these planetary redox transitions. Instead, mitochondria-bearing eukaryotes are consistently dated to between these two oxygenation events, during an interval of pervasive deep-sea anoxia and variable surface-water oxygenation. The discovery and cultivation of the Asgard archaea has reinforced metabolic evidence that eukaryogenesis was initially mediated by syntrophic H₂ exchange between an archaeal host and an α-proteobacterial symbiont living under anoxia. Together, these results temporally, spatially and metabolically decouple the earliest stages of eukaryogenesis from the oxygen content of the surface ocean and atmosphere. Rather than reflecting the ancestral metabolic state, obligate aerobiosis in eukaryotes is most probably derived, having only become globally widespread over the past 1 billion years as atmospheric oxygen approached modern levels.

Preservation of Terrestrial Microorganisms and Organics Within Alteration Products of Chondritic Meteorites from the Nullarbor Plain, Australia

Meteorites that fall to Earth quickly become contaminated with terrestrial microorganisms. These meteorites are out of chemical equilibrium in the environments where they fall, and equilibration promotes formation of low-temperature alteration minerals that can entomb contaminant microorganisms and thus preserve them as microfossils. Given the well-understood chemistry of meteorites and their recent discovery on Mars by rovers, a similarly weathered meteorite on Mars could preserve organic and fossil evidence of a putative past biosphere at the martian surface. Here, we used several techniques to assess the potential of alteration minerals to preserve microfossils and biogenic organics in terrestrially weathered ordinary chondrites from the Nullarbor Plain, Australia. We used acid etching of ordinary chondrites to reveal entombed fungal hyphae, modern biofilms, and diatoms within alteration minerals. We employed synchrotron X-ray fluorescence microscopy of alteration mineral veins to map the distribution of redox-sensitive elements of relevance to chemolithotrophic organisms, such as Mn-cycling bacteria. We assessed the biogenicity of fungal hyphae within alteration veins using a combination of Fourier-transform infrared spectroscopy and pyrolysis gas chromatography-mass spectrometry, which showed that alteration minerals sequester and preserve organic molecules at various levels of decomposition. Our combined analyses results show that fossil microorganisms and the organic molecules they produce are preserved within calcite-gypsum admixtures in meteorites. Furthermore, the distributions of redox-sensitive elements (e.g., Mn) within alteration minerals are localized, which qualitatively suggests that climatically or microbially facilitated element mobilization occurred during the meteorite's residency on Earth. If returned as part of a sample suite from the martian surface, ordinary chondrites could preserve similar, recognizable evidence of putative past life and/or environmental change.

Identification of Chitin in Pliocene Fungi Using Py-GC × GC-TOFMS: Potential Implications for the Study of the Evolution of the Fungal Clade in Deep Time

Molecular dating estimates the origin of the fungal clade to the Pre-Cambrian. Yet, the oldest unambiguous fungal fossils date to the Ordovician and show remarkable diversity and organizational development. Recent studies have suggested that the dates for the emergence of fungi in the fossil record may be pushed back to the Proterozoic. However, the nonspecificity of the methods used in those studies necessitates the employment of a wider variety of analytical techniques that can independently verify the presence of chitin, a crucial prerequisite in the assignment of fungal affinity, particularly of putative fossils from the Pre-Cambrian. In this paper, we propose Py-GC × GC-TOFMS as an example of one such technique. We analyze fungal fossils from the Pliocene. We find that a suite of N-bearing compounds are present in the pyrolysis products of these fossils, from which we suggest that 3-acetamidopyrones and their methylated homologues can serve as specific pyrolytic markers for chitin. We discuss both how this technique can potentially be used to differentiate between biopolymers, including those similar to chitin such as peptidoglycan, and the potential implications of identifying such markers in fossils from deep time. We conclude that Py-GC × GC-TOFMS is a promising technique that can potentially be used alongside, or independent of, staining methods to detect the presence of chitin in fossils.

Fungal-Mineral Interactions Modulating Intrinsic Peroxidase-like Activity of Iron Nanoparticles: Implications for the Biogeochemical Cycles of Nutrient Elements and Attenuation of Contaminants

Fungal-mediated extracellular reactive oxygen species (ROS) are essential for biogeochemical cycles of carbon, nitrogen, and contaminants in terrestrial environments. These ROS levels may be modulated by iron nanoparticles that possess intrinsic peroxidase (POD)-like activity (nanozymes). However, it remains largely undescribed how fungi modulate the POD-like activity of the iron nanoparticles with various crystallinities and crystal facets. Using well-controlled fungal-mineral cultivation experiments, here, we showed that fungi possessed a robust defect engineering strategy to modulate the POD-like activity of the attached iron minerals by decreasing the catalytic activity of poorly ordered ferrihydrite but enhancing that of well-crystallized hematite. The dynamics of POD-like activity were found to reside in molecular trade-offs between lattice oxygen and oxygen vacancies in the iron nanoparticles, which may be located in a cytoprotective fungal exoskeleton. Together, our findings unveil coupled POD-like activity and oxygen redox dynamics during fungal-mineral interactions, which increase the understanding of the catalytic mechanisms of POD-like nanozymes and microbial-mediated biogeochemical cycles of nutrient elements as well as the attenuation of contaminants in terrestrial environments.

Fungi as mediators linking organisms and ecosystems

Fungi form a major and diverse component of most ecosystems on Earth. They are both micro and macroorganisms with high and varying functional diversity as well as great variation in dispersal modes. With our growing knowledge of microbial biogeography, it has become increasingly clear that fungal assembly patterns and processes differ from other microorganisms such as bacteria, but also from macroorganisms such as plants. The success of fungi as organisms and their influence on the environment lies in their ability to span multiple dimensions of time, space, and biological interactions, that is not rivalled by other organism groups. There is also growing evidence that fungi mediate links between different organisms and ecosystems, with the potential to affect the macroecology and evolution of those organisms. This suggests that fungal interactions are an ecological driving force, interconnecting different levels of biological and ecological organisation of their hosts, competitors, and antagonists with the environment and ecosystem functioning. Here we review these emerging lines of evidence by focusing on the dynamics of fungal interactions with other organism groups across various ecosystems. We conclude that the mediating role of fungi through their complex and dynamic ecological interactions underlie their importance and ubiquity across Earth's ecosystems.

Structural and chemical heterogeneity of Proterozoic organic microfossils of the ca. 1 Ga old Angmaat Formation, Baffin Island, Canada

Organic microfossils in Meso- and Neoproterozoic rocks are of key importance to track the emergence and evolution of eukaryotic life. An increasing number of studies combine Raman spectroscopy with synchrotron-based methods to characterize these microfossils. A recurring observation is that Raman spectra of organic microfossils show negligible variation on a sample scale and that variation between different samples can be explained by differences in thermal maturation or in the biologic origin of organic precursor material. There is a paucity of work, however, that explores the extent to which the petrographic framework and diagenetic processes might influence the chemical structure of organic materials. We present a detailed Raman spectroscopy-based study of a complex organic microfossil assemblage in the ca. 1 Ga old Angmaat Formation, Baffin Island, Canada. This formation contains abundant early diagenetic chert that preserves silicified microbial mats with numerous, readily identifiable organic microfossils. Individual chert beds show petrographic differences with discrete episodes of cementation and recrystallization. Raman spectroscopy reveals measurable variation of organic maturity between samples and between neighboring organic microfossils of the same taxonomy and taphonomic state. Scanning transmission X-ray microscopy performed on taphonomically similar coccoidal microfossils from the same thin section shows distinct chemical compositions, with varying ratios of aromatic compounds to ketones and phenols. Such observations imply that geochemical variation of organic matter is not necessarily coupled to thermal alteration or organic precursor material. Variation of the Raman signal across single samples is most likely linked to the diagenetic state of analyzed materials and implies an association between organic preservation and access to diagenetic fluids. Variation in the maturity of individual microfossils may be a natural outcome of local diagenetic processes and potentially exceeds differences derived from precursor organic material. These observations stress the importance of detailed in situ characterization by Raman spectroscopy to identify target specimens for further chemical analysis.

Cryptic terrestrial fungus-like fossils of the early Ediacaran Period

The colonization of land by fungi had a significant impact on the terrestrial ecosystem and biogeochemical cycles on Earth surface systems. Although fungi may have diverged ~1500-900 million years ago (Ma) or even as early as 2400 Ma, it is uncertain when fungi first colonized the land. Here we report pyritized fungus-like microfossils preserved in the basal Ediacaran Doushantuo Formation (~635 Ma) in South China. These micro-organisms colonized and were preserved in cryptic karstic cavities formed via meteoric water dissolution related to deglacial isostatic rebound after the terminal Cryogenian snowball Earth event. They are interpreted as eukaryotes and probable fungi, thus providing direct fossil evidence for the colonization of land by fungi and offering a key constraint on fungal terrestrialization.

Culinary and Medicinal Mushrooms: Insight into Growing Technologies

Humans have used mushrooms from the beginning of their history. However, during the last few decades, the market demand for these fruiting bodies has increased significantly owing to the spread in the capabilities of culinary and pharmacological exploitation. Natural mushroom resources have become insufficient to meet the support needs. Therefore, traditional methods of extensive cultivation as well as modern technologies have been exploited to develop effective growing recommendations for dozens of economically important mushroom species. Mushrooms can decompose a wide range of organic materials, including organic waste. They play a fundamental role in nutrient cycling and exchange in the environment. The challenge is a proper substrate composition, including bio-fortified essential elements, and the application of growing conditions to enable a continuous supply of fruiting bodies of market quality and stabilized chemical composition. Many mushroom species are used for food preparation. Moreover, they are treated as functional foods, because they have health benefits beyond their nutritional value, and are used as natural medicines in many countries. Owing to the rapid development of mushroom farming, we reviewed the growing technologies used worldwide for mushroom species developed for food, processing, and pharmacological industries.

Genomic and fossil windows into the secret lives of the most ancient fungi

Fungi have crucial roles in modern ecosystems as decomposers and pathogens, and they engage in various mutualistic associations with other organisms, especially plants. They have a lengthy geological history, and there is an emerging understanding of their impact on the evolution of Earth systems on a large scale. In this Review, we focus on the roles of fungi in the establishment and early evolution of land and freshwater ecosystems. Today, questions of evolution over deep time are informed by discoveries of new fossils and evolutionary analysis of new genomes. Inferences can be drawn from evolutionary analysis by comparing the genes and genomes of fungi with the biochemistry and development of their plant and algal hosts. We then contrast this emerging picture against evidence from the fossil record to develop a new, integrated perspective on the origin and early evolution of fungi.

Intrinsic enzyme-like activity of magnetite particles is enhanced by cultivation with Trichoderma guizhouense

Fungal-mineral interactions can produce large amounts of biogenic nano-size (~ 1-100 nm) minerals, yet their influence on fungal physiology and growth remains largely unexplored. Using Trichoderma guizhouense NJAU4742 and magnetite (Mt) as a model fungus and mineral system, we have shown for the first time that biogenic Mt nanoparticles formed during fungal-mineral cultivation exhibit intrinsic peroxidase-like activity. Specifically, the average peroxidase-like activity of Mt nanoparticles after 72 h cultivation was ~ 2.4 times higher than that of the original Mt. Evidence from high resolution X-ray photoelectron spectroscopy analyses indicated that the unique properties of magnetite nanoparticles largely stemmed from their high proportion of surface non-lattice oxygen, through occupying surface oxygen-vacant sites, rather than Fe redox chemistry, which challenges conventional Fenton reaction theories that assume iron to be the sole redox-active centre. Nanoscale secondary ion mass spectrometry with a resolution down to 50 nm demonstrated that a thin (< 1 μm) oxygen-film was present on the surface of fungal hyphae. Furthermore, synchrotron radiation-based micro-FTIR spectra revealed that surface oxygen groups corresponded mainly to organic OH, mineral OH and carbonyl groups. Together, these findings highlight an important, but unrecognized, catalytic activity of mineral nanoparticles produced by fungal-mineral interactions and contribute substantially to our understanding of mineral nanoparticles in natural ecosystems.

Graphite-shell-chains selectively and efficiently produced from biomass rich in cellulose and chitin

Graphite-shell-chains have a worm-like nanocarbon configuration with a graphitic structure and mesopores, and they are easily produced from wood by using iron-group metal-catalysed carbonization at 900 °C. The simple production process with natural resources convinced us that this process may occur somewhere on Earth; the product of this process was indeed discovered as biogenic graphite by geochemists. However, the biogenic graphite was 3.7 billion years old, thus occurring long before wood appeared in the world. Here, we investigated appropriate carbon precursors other than wood in various materials and showed that carbon is selectively and efficiently obtained from biomass rich in cellulose and chitin. To enable selective and efficient production from this biomass, it seems the precursors provide a perfect amorphous carbon matrix where metal catalysts can reside at an active size to constantly create a graphite shell during carbonization. The results suggest that graphite-shell-chains could have existed in ancient times. Application developments of this biomass-derived nanocarbon will be useful for sustainable development goals.

Application of FIB-SEM Techniques for the Advanced Characterization of Earth and Planetary Materials

Advanced microanalytical techniques such as high-resolution transmission electron microscopy (HRTEM), atom probe tomography (APT), and synchrotron-based scanning transmission X-ray microscopy (STXM) enable one to characterize the structure and chemical and isotopic compositions of natural materials down towards the atomic scale. Dual focused ion beam-scanning electron microscopy (FIB-SEM) is a powerful tool for site-specific sample preparation and subsequent analysis by TEM, APT, and STXM to the highest energy and spatial resolutions. FIB-SEM also works as a stand-alone technique for three-dimensional (3D) tomography. In this review, we will outline the principles and challenges when using FIB-SEM for the advanced characterization of natural materials in the Earth and Planetary Sciences. More specifically, we aim to highlight the state-of-the-art applications of FIB-SEM using examples including (a) traditional FIB ultrathin sample preparation of small particles in the study of space weathering of lunar soil grains, (b) migration of Pb isotopes in zircons by FIB-based APT, (c) coordinated synchrotron-based STXM characterization of extraterrestrial organic material in carbonaceous chondrite, and finally (d) FIB-based 3D tomography of oil shale pores by slice and view methods. Dual beam FIB-SEM is a powerful analytical platform, the scope of which, for technological development and adaptation, is vast and exciting in the field of Earth and Planetary Sciences. For example, dual beam FIB-SEM will be a vital technique for the characterization of fine-grained asteroid and lunar samples returned to the Earth in the near future.