Beyond biogeographic patterns: Processes shaping the microbial landscape in soils and sediments along the Yangtze River.

Deciphering biogeographic patterns of microorganisms is important for evaluating the maintenance of microbial diversity with respect to the ecosystem functions they drives. However, ecological processes shaping distribution patterns of microorganisms across large spatial-scale watersheds remain largely unknown. Using Illumina sequencing and multiple statistical methods, we characterized distribution patterns and maintenance diversity of microorganisms (i.e., archaea, bacteria, and fungi) in soils and sediments along the Yangtze River. Distinct microbial distribution patterns were found between soils and sediments, and microbial community similarity significantly decreased with increasing geographical distance. Physicochemical properties showed a larger effect on microbial community composition than geospatial and climatic factors. Archaea and fungi displayed stronger species replacements and weaker environmental constraints in soils than that in sediments, but opposite for bacteria. Archaea, bacteria, and fungi in soils showed broader environmental breadths and stronger phylogenetic signals compared to those in sediments, suggesting stronger environmental adaptation. Stochasticity dominated community assemblies of archaea and fungi in soils and sediments, whereas determinism dominated bacterial community assembly. Our results have therefore highlighted distinct microbial distribution patterns and diversity maintenance mechanisms between soils and sediments, and emphasized important roles of species replacement, environmental adaptability, and ecological assembly processes on microbial landscape. Our findings are helpful in predicting loss of microbial diversity in the Yangtze River Basin, and might assist the establishment of environmental policies for protecting fragile watersheds.

The Third International Symposium on Fungal Stress - ISFUS.

Stress is a normal part of life for fungi, which can survive in environments considered inhospitable or hostile for other organisms. Due to the ability of fungi to respond to, survive in, and transform the environment, even under severe stresses, many researchers are exploring the mechanisms that enable fungi to adapt to stress. The International Symposium on Fungal Stress (ISFUS) brings together leading scientists from around the world who research fungal stress. This article discusses presentations given at the third ISFUS, held in São José dos Campos, São Paulo, Brazil in 2019, thereby summarizing the state-of-the-art knowledge on fungal stress, a field that includes microbiology, agriculture, ecology, biotechnology, medicine, and astrobiology.

Fungal formation of selenium and tellurium nanoparticles.

The fungi Aureobasidium pullulans, Mortierella humilis, Trichoderma harzianum and Phoma glomerata were used to investigate the formation of selenium- and tellurium-containing nanoparticles during growth on selenium- and tellurium-containing media. Most organisms were able to grow on both selenium- and tellurium-containing media at concentrations of 1 mM resulting in extensive precipitation of elemental selenium and tellurium on fungal surfaces as observed by the red and black colour changes. Red or black deposits were confirmed as elemental selenium and tellurium, respectively. Selenium oxide and tellurium oxide were also found after growth of Trichoderma harzianum with 1 mM selenite and tellurite as well as the formation of elemental selenium and tellurium. The hyphal matrix provided nucleation sites for metalloid deposition with extracellular protein and extracellular polymeric substances localizing the resultant Se or Te nanoparticles. These findings are relevant to remedial treatments for selenium and tellurium and to novel approaches for selenium and tellurium biorecovery.

The second International Symposium on Fungal Stress: ISFUS.

The topic of 'fungal stress' is central to many important disciplines, including medical mycology, chronobiology, plant and insect pathology, industrial microbiology, material sciences, and astrobiology. The International Symposium on Fungal Stress (ISFUS) brought together researchers, who study fungal stress in a variety of fields. The second ISFUS was held in May 8-11 2017 in Goiania, Goiás, Brazil and hosted by the Instituto de Patologia Tropical e Saúde Pública at the Universidade Federal de Goiás. It was supported by grants from CAPES and FAPEG. Twenty-seven speakers from 15 countries presented their research related to fungal stress biology. The Symposium was divided into seven topics: 1. Fungal biology in extreme environments; 2. Stress mechanisms and responses in fungi: molecular biology, biochemistry, biophysics, and cellular biology; 3. Fungal photobiology in the context of stress; 4. Role of stress in fungal pathogenesis; 5. Fungal stress and bioremediation; 6. Fungal stress in agriculture and forestry; and 7. Fungal stress in industrial applications. This article provides an overview of the science presented and discussed at ISFUS-2017.

Biogeochemical spatio-temporal transformation of copper in Aspergillus niger colonies grown on malachite with different inorganic nitrogen sources.

This work elucidates spatio-temporal aspects of the biogeochemical transformation of copper mobilized from malachite (Cu2 (CO3 )(OH)2 ) and bioaccumulated within Aspergillus niger colonies when grown on different inorganic nitrogen sources. It was shown that the use of either ammonium or nitrate determined how copper was distributed within the colony and its microenvironment and the copper oxidation state and succession of copper coordinating ligands within the biomass. Nitrate-grown colonies yielded ∼1.7× more biomass, bioaccumulated ∼7× less copper, excreted ∼1.9× more oxalate and produced ∼1.75× less water-soluble copper in the medium in contrast to ammonium-grown colonies. Microfocus X-ray absorption spectroscopy revealed that as the mycelium matured, bioaccumulated copper was transformed from less stable and more toxic Cu(I) into less toxic Cu(II) which was coordinated predominantly by phosphate/malate ligands. With time, a shift to oxalate coordination of bioaccumulated copper occurred in the central older region of ammonium-grown colonies.

The roles of endolithic fungi in bioerosion and disease in marine ecosystems. II. Potential facultatively parasitic anamorphic ascomycetes can cause disease in corals and molluscs.

Anamorphic ascomycetes have been implicated as causative agents of diseases in tissues and skeletons of hard corals, in tissues of soft corals (sea fans) and in tissues and shells of molluscs. Opportunist marine fungal pathogens, such as Aspergillus sydowii, are important components of marine mycoplankton and are ubiquitous in the open oceans, intertidal zones and marine sediments. These fungi can cause infection in or at least can be associated with animals which live in these ecosystems. A. sydowii can produce toxins which inhibit photosynthesis in and the growth of coral zooxanthellae. The prevalence of many documented infections has increased in frequency and severity in recent decades with the changing impacts of physical and chemical factors, such as temperature, acidity and eutrophication. Changes in these factors are thought to cause significant loss of biodiversity in marine ecosystems on a global scale in general, and especially in coral reefs and shallow bays.

The roles of endolithic fungi in bioerosion and disease in marine ecosystems. I. General concepts.

Endolithic true fungi and fungus-like microorganisms penetrate calcareous substrates formed by living organisms, cause significant bioerosion and are involved in diseases of many host animals in marine ecosystems. A theoretical interactive model for the ecology of reef-building corals is proposed in this review. This model includes five principle partners that exist in a dynamic equilibrium: polyps of a colonial coelenterate, endosymbiotic zooxanthellae, endolithic algae (that penetrate coral skeletons), endolithic fungi (that attack the endolithic algae, the zooxanthellae and the polyps) and prokaryotic and eukaryotic microorganisms (which live in the coral mucus). Endolithic fungi and fungus-like boring microorganisms are important components of the marine calcium carbonate cycle because they actively contribute to the biodegradation of shells of animals composed of calcium carbonate and calcareous geological substrates.

Lost in Translation: Pitfalls in Deciphering Plant Alternative Splicing Transcripts.

Transcript annotation in plant databases is incomplete and often inaccurate, leading to misinterpretation. As more and more RNA-seq data are generated, plant scientists need to be aware of potential pitfalls and understand the nature and impact of specific alternative splicing transcripts on protein production. A primary area of concern and the topic of this article is the (mis)annotation of open reading frames and premature termination codons. The basic message is that to adequately address expression and functions of transcript isoforms, it is necessary to be able to predict their fate in terms of whether protein isoforms are generated or specific transcripts are unproductive or degraded.

Regulation of vectorial supply of vesicles to the hyphal tip determines thigmotropism in Neurospora crassa.

Thigmotropism is the ability of an organism to respond to a topographical stimulus by altering its axis of growth. The thigmotropic response of the model fungus Neurospora crassa was quantified using microfabricated glass slides with ridges of defined height. We show that the polarity machinery at the hyphal tip plays a role in the thigmotropic response of N. crassa. Deletion of N. crassa genes encoding the formin, BNI-1, and the Rho-GTPase, CDC-42, an activator of BNI-1 in yeast, CDC-24, its guanine nucleotide exchange factor (GEF), and BEM-1, a scaffold protein in the same pathway, were all shown to significantly decrease the thigmotropic response. In contrast, deletion of genes encoding the cell end-marker protein, TEA-1, and KIP-1, the kinesin responsible for the localisation of TEA-1, significantly increased the thigmotropic response. These results suggest a mechanism of thigmotropism involving vesicle delivery to the hyphal tip via the actin cytoskeleton and microtubules. Neurospora crassa thigmotropic response differed subtly from that of Candida albicans where the stretch-activated calcium channel, Mid1, has been linked with thigmotropic behaviour. The MID-1 deficient mutant of N. crassa (Δmid-1) and the effects of calcium depletion were examined here but no change in the thigmotropic response was observed. However, SPRAY, a putative calcium channel protein, was shown to be required for N. crassa thigmotropism. We propose that the thigmotropic response is a result of changes in the polarity machinery at the hyphal tip which are thought to be downstream effects of calcium signalling pathways triggered by mechanical stress at the tip.

Biotransformation of manganese oxides by fungi: solubilization and production of manganese oxalate biominerals.

The ability of the soil fungi Aspergillus niger and Serpula himantioides to tolerate and solubilize manganese oxides, including a fungal-produced manganese oxide and birnessite, was investigated. Aspergillus niger and S. himantioides were capable of solubilizing all the insoluble oxides when incorporated into solid medium: MnO(2) and Mn(2) O(3) , mycogenic manganese oxide (MnO(x) ) and birnessite [(Na(0.3) Ca(0.1) K(0.1) )(Mn(4+) ,Mn(3+) )(2) O(4) ·1.5H(2) O]. Manganese oxides were of low toxicity and A. niger and S. himantioides were able to grow on 0.5% (w/v) of all the test compounds, with accompanying acidification of the media. Precipitation of insoluble manganese and calcium oxalate occurred under colonies growing on agar amended with all the test manganese oxides after growth of A. niger and S. himantioides at 25°C. The formation of manganese oxalate trihydrate was detected after growth of S. himantioides with birnessite which subsequently was transformed to manganese oxalate dihydrate. Our results represent a novel addition to our knowledge of the biogeochemical cycle of manganese, and the roles of fungi in effecting transformations of insoluble metal-containing compounds in the environment.

Membrane-electrode assembly enhances performance of a microbial fuel cell type biological oxygen demand sensor.

A membrane-electrode assembly (MEA) was applied to a microbial fuel cell (MFC) type biological oxygen demand (BOD) sensor and the performance of the sensor was assessed. To establish the optimal conditions for MEA fabrication, platinum-catalysed carbon cloth cathodic electrodes were assembled with cation exchange membranes under various temperatures and pressures. By analysing coulombs from the MFCs, it could be determined that the optimal hot-pressing conditions were 120 degrees C and 150 kg cm(-2) for 30 s. When the MEA fabricated under optimal conditions and an air cathode were utilized for the construction of the MFC type BOD sensor, coulombs increased to 4.65 C from 0.52 C and power increased to 69,080 mW m(-3) from 880 mW m(-3) (at a BOD concentration of 200 mg L(-1)), respectively, compared with the conventional MFC lacking a MEA. The increased power improved the performance of the MFC type BOD sensor: sensitivity increased from 1.2 x 10(-3) to 1.8 x 10(-2) C per mg L(-1) of BOD, with good linearity (r2 = 0.97) and over 97% repeatability. We conclude that the MEA can be successfully applied to MFCs to make them highly sensitive BOD sensors.

A novel biomonitoring system using microbial fuel cells.

A novel biomonitoring system using microbial fuel cells for detecting the inflow of toxic substances into water systems has been developed for the purpose of on-site and on-line monitoring. The characteristics of electric current generation by electrochemically-active bacteria were conveniently monitored using a microbial fuel cell format and a computer-controlled potentiometer. When toxic substances (an organophosphorus compound, Pb, Hg, and PCBs) were added to the microbial fuel cell, rapid decreases in the current were observed. The inhibition ratios caused by inflow of these toxic substances (1 mg l(-1)) were 61%, 46%, 28% and 38%, respectively, when compared to the control, and generally increased in proportion to the addition time and concentration of toxic substances. When real wastewater was applied from a local wastewater treatment plant, more significant current decreases and higher inhibition ratios were observed following the introduction of toxic substances than in the laboratory tests. For example, the inhibition ratio was 76% on addition of a 1 mg l(-1) Cd and 1 mg l(-1) Pb mixture. Application of the microbial fuel cell for pollutant biomonitoring is discussed.

Challenges in microbial fuel cell development and operation.

A microbial fuel cell (MFC) is a device that converts chemical energy into electricity through the catalytic activities of microorganisms. Although there is great potential of MFCs as an alternative energy source, novel wastewater treatment process, and biosensor for oxygen and pollutants, extensive optimization is required to exploit the maximum microbial potential. In this article, the main limiting factors of MFC operation are identified and suggestions are made to improve performance.

Geomycology: biogeochemical transformations of rocks, minerals, metals and radionuclides by fungi, bioweathering and bioremediation.

The study of the role that fungi have played and are playing in fundamental geological processes can be termed 'geomycology' and this article seeks to emphasize the fundamental importance of fungi in several key areas. These include organic and inorganic transformations and element cycling, rock and mineral transformations, bioweathering, mycogenic mineral formation, fungal-clay interactions, metal-fungal interactions, and the significance of such processes in the environment and their relevance to areas of environmental biotechnology such as bioremediation. Fungi are intimately involved in biogeochemical transformations at local and global scales, and although such transformations occur in both aquatic and terrestrial habitats, it is the latter environment where fungi probably have the greatest influence. Within terrestrial aerobic ecosystems, fungi may exert an especially profound influence on biogeochemical processes, particularly when considering soil, rock and mineral surfaces, and the plant root-soil interface. The geochemical transformations that take place can influence plant productivity and the mobility of toxic elements and substances, and are therefore of considerable socio-economic relevance, including human health. Of special significance are the mutualistic symbioses, lichens and mycorrhizas. Some of the fungal transformations discussed have beneficial applications in environmental biotechnology, e.g. in metal leaching, recovery and detoxification, and xenobiotic and organic pollutant degradation. They may also result in adverse effects when these processes are associated with the degradation of foodstuffs, natural products, and building materials, including wood, stone and concrete. It is clear that a multidisciplinary approach is essential to understand fully all the phenomena encompassed within geomycology, and it is hoped that this review will serve to catalyse further research, as well as stimulate interest in an area of mycology of global significance.

Induction of contour sensing in Aspergillus niger by stress and its relevance to fungal growth mechanics and hyphal tip structure.

Thigmotropism (contour sensing) has been assigned an important role in both plant and human fungal pathogens. However, outside these systems, our knowledge of the function of thigmotropism in fungal growth control is relatively poor. Furthermore, the effects of environmental stress on thigmotropic responses have received scant attention. To try to elucidate some of the mechanisms behind hyphal contour sensing in response to nutrient-poor environments, we have used micro-engineered substrates and several imaging techniques to investigate the thigmotropic reactions of the ubiquitous fungus Aspergillus niger. This organism not appear to demonstrate thigmotropic growth under normal conditions. Our results show that A. niger undergoes significant morphological changes during growth on solid substrates and demonstrate that the intensity of contour sensing varies depending on the area of the hyphal tip which initiates contact with the substrate. We propose that growth under nutrient-limited conditions triggers several factors that combine to increase thigmotropic sensitivity while conversely creating a 60 degrees arc at the hyphal tip which is blind to topographical variations. This has important consequences for our general understanding of the hyphal mode of growth in fungi as well as more specific aspects of hyphal tip development under stress.

X-ray absorption spectroscopy (XAS) of toxic metal mineral transformations by fungi.

Fungi can be highly efficient biogeochemical agents and accumulators of soluble and particulate forms of metals. This work aims to understand some of the physico-chemical mechanisms involved in toxic metal transformations focusing on the speciation of metals accumulated by fungi and mycorrhizal associations. The amorphous state or poor crystallinity of metal complexes within biomass and relatively low metal concentrations make the determination of metal speciation in biological systems a challenging problem but this can be overcome by using synchrotron-based element-specific X-ray absorption spectroscopy (XAS) techniques. In this research, we have exposed fungi and ectomycorrhizas to a variety of copper-, zinc- and lead-containing minerals. X-ray absorption spectroscopy studies revealed that oxygen ligands (phosphate, carboxylate) played a major role in toxic metal coordination within the fungal and ectomycorrhizal biomass during the accumulation of mobilized toxic metals. Coordination of toxic metals within biomass depended on the fungal species, initial mineral composition, the nitrogen source, and the physiological state/age of the fungal mycelium.

The development of fungal networks in complex environments.

Fungi are of fundamental importance in terrestrial ecosystems playing important roles in decomposition, nutrient cycling, plant symbiosis and pathogenesis, and have significant potential in several areas of environmental biotechnology such as biocontrol and bioremediation. In all of these contexts, the fungi are growing in environments exhibiting spatio-temporal nutritional and structural heterogeneities. In this work, a discrete mathematical model is derived that allows detailed understanding of how events at the hyphal level are influenced by the nature of various environmental heterogeneities. Mycelial growth and function is simulated in a range of environments including homogeneous conditions, nutritionally-heterogeneous conditions and structurally-heterogeneous environments, the latter emulating porous media such as soils. Our results provide further understanding of the crucial processes involved in fungal growth, nutrient translocation and concomitant functional consequences, e.g. acidification, and have implications for the biotechnological application of fungi.