Dating the Cryptococcus gattii Dispersal to the North American Pacific Northwest.

The emergence of Cryptococcus gattii, previously regarded as a predominantly tropical pathogen, in the temperate climate of the North American Pacific Northwest (PNW) in 1999 prompted several questions. The most prevalent among these was the timing of the introduction of this pathogen to this novel environment. Here, we infer tip-dated timing estimates for the three clonal C. gattii populations observed in the PNW, VGIIa, VGIIb, and VGIIc, based on whole-genome sequencing of 134 C. gattii isolates and using Bayesian evolutionary analysis by sampling trees (BEAST). We estimated the nucleotide substitution rate for each lineage (1.59 × 10-8, 1.59 × 10-8, and 2.70 × 10-8, respectively) to be an order of magnitude higher than common neutral fungal mutation rates (2.0 × 10-9), indicating a microevolutionary rate (e.g., successive clonal generations in a laboratory) in comparison to a species' slower, macroevolutionary rate (e.g., when using fossil records). The clonal nature of the PNW C. gattii emergence over a narrow number of years would therefore possibly explain our higher mutation rates. Our results suggest that the mean time to most recent common ancestor for all three sublineages occurred within the last 60 to 100 years. While the cause of C. gattii dispersal to the PNW is still unclear, our research estimates that the arrival is neither ancient nor very recent (i.e., <25 years ago), making a strong case for an anthropogenic introduction. IMPORTANCE The recent emergence of the pathogenic fungus Cryptococcus gattii in the Pacific Northwest (PNW) resulted in numerous investigations into the epidemiological and enzootic impacts, as well as multiple genomic explorations of the three primary molecular subtypes of the fungus that were discovered. These studies lead to the general conclusion that the subtypes identified likely emerged out of Brazil. Here, we conducted genomic dating analyses to determine the ages of the various lineages seen in the PNW and propose hypothetical causes for the dispersal events. Bayesian evolutionary analysis strongly suggests that these independent fungal populations in the PNW are all 60 to 100 years old, providing a timing that is subsequent to the opening of the Panama Canal, which allowed for more direct shipping between Brazil and the western North American coastline, a possible driving event for these fungal translocation events

Discovery of a New Natural Product and a Deactivation of a Quorum Sensing System by Culturing a “Producer” Bacterium With a Heat-Killed “Inducer” Culture

Herein we describe a modified bacterial culture methodology as a tool to discover new natural products via supplementing actinomycete fermentation media with autoclaved cultures of “inducer” microbes. Using seven actinomycetes and four inducer microbes, we detected 28 metabolites that were induced in UHPLC-HRESIMS-based analysis of bacterial fermentations. Metabolomic analysis indicated that each inducer elicited a unique response from the actinomycetes and that some chemical responses were specific to each inducer-producer combination. Among these 28 metabolites, hydrazidomycin D, a new hydrazide-containing natural product was isolated from the pair Streptomyces sp. RKBH-B178 and Mycobacterium smegmatis. This result validated the effectiveness of the strategy in discovering new natural products. From the same set of induced metabolites, an in-depth investigation of a fermentation of Streptomyces sp. RKBH-B178 and autoclaved Pseudomonas aeruginosa led to the discovery of a glucuronidated analog of the pseudomonas quinolone signal (PQS). We demonstrated that RKBH-B178 is able to biotransform the P. aeruginosa quorum sensing molecules, 2-heptyl-4-quinolone (HHQ), and PQS to form PQS-GlcA. Further, PQS-GlcA was shown to have poor binding affinity to PqsR, the innate receptor of HHQ and PQS

Transcriptomic and Exometabolomic Profiling Reveals Antagonistic and Defensive Modes of Clonostachys rosea Action Against Fusarium graminearum

The mycoparasite Clonostachys rosea ACM941 is under development as a biocontrol organism against Fusarium graminearum, the causative agent of Fusarium head blight in cereals. To identify molecular factors associated with this interaction, the transcriptomic and exometabolomic profiles of C. rosea and F. graminearum GZ3639 were compared during coculture. Prior to physical contact, the antagonistic activity of C. rosea correlated with a response heavily dominated by upregulation of polyketide synthase gene clusters, consistent with the detected accumulation of corresponding secondary metabolite products. Similarly, prior to contact, trichothecene gene clusters were upregulated in F. graminearum, while those responsible for fusarielin and fusarin biosynthesis were downregulated, correlating with an accumulation of trichothecene products in the interaction zone over time. A concomitant increase in 15-acetyl deoxynivalenol-3-glucoside in the interaction zone was also detected, with C. rosea established as the source of this detoxified mycotoxin. After hyphal contact, C. rosea was found to predominantly transcribe genes encoding cell wall–degradation enzymes, major facilitator superfamily sugar transporters, anion:cation symporters, as well as alternative carbon source utilization pathways, together indicative of a transition to necrotropism at this stage. F. graminearum notably activated the transcription of phosphate starvation pathway signature genes at this time. Overall, a number of signature molecular mechanisms likely contributing to antagonistic activity by C. rosea against F. graminearum, as well as its mycotoxin tolerance, are identified in this report, yielding several new testable hypotheses toward understanding the basis of C. rosea as a biocontrol agent for continued agronomic development and application

Evidence for multiple rhythmic skills

Rhythms, or patterns in time, play a vital role in both speech and music. Proficiency in a number of rhythm skills has been linked to language ability, suggesting that certain rhythmic processes in music and language rely on overlapping resources. However, a lack of understanding about how rhythm skills relate to each other has impeded progress in understanding how language relies on rhythm processing. In particular, it is unknown whether all rhythm skills are linked together, forming a single broad rhythmic competence, or whether there are multiple dissociable rhythm skills. We hypothesized that beat tapping and rhythm memory/sequencing form two separate clusters of rhythm skills. This hypothesis was tested with a battery of two beat tapping and two rhythm memory tests. Here we show that tapping to a metronome and the ability to adjust to a changing tempo while tapping to a metronome are related skills. The ability to remember rhythms and to drum along to repeating rhythmic sequences are also related. However, we found no relationship between beat tapping skills and rhythm memory skills. Thus, beat tapping and rhythm memory are dissociable rhythmic aptitudes. This discovery may inform future research disambiguating how distinct rhythm competencies track with specific language functions

The role of war in deep transitions: exploring mechanisms, imprints and rules in sociotechnical systems

This paper explores in what ways the two world wars influenced the development of sociotechnical systems underpinning the culmination of the first deep transition. The role of war is an underexplored aspect in both the Techno-Economic Paradigms (TEP) approach and the Multi-level perspective (MLP) which form the two key conceptual building blocks of the Deep Transitions (DT) framework. Thus, we develop a conceptual approach tailored to this particular topic which integrates accounts of total war and mechanisms of war from historical studies and imprinting from organisational studies with the DT framework’s attention towards rules and meta-rules. We explore in what ways the three sociotechnical systems of energy, food, and transport were affected by the emergence of new demand pressures and logistical challenges during conditions of total war; how war impacted the directionality of sociotechnical systems; the extent to which new national and international policy capacities emerged during wartime in the energy, food, and transport systems; and the extent to which these systems were influenced by cooperation and shared sacrifice under wartime conditions. We then explore what lasting changes were influenced by the two wars in the energy, food, and transport systems across the transatlantic zone. This paper seeks to open up a hitherto neglected area in analysis on sociotechnical transitions and we discuss the importance of further research that is attentive towards entanglements of warfare and the military particularly in the field of sustainability transitions

Fungal Planet description sheets: 1478-1549

Novel species of fungi described in this study include those from various countries as follows: Australia, Aschersonia mackerrasiae on whitefly, Cladosporium corticola on bark of Melaleuca quinquenervia, Penicillium nudgee from soil under Melaleuca quinquenervia, Pseudocercospora blackwoodiae on leaf spot of Persoonia falcata, and Pseudocercospora dalyelliae on leaf spot of Senna alata. Bolivia, Aspicilia lutzoniana on fully submersed siliceous schist in high-mountain streams, and Niesslia parviseta on the lower part and apothecial discs of Erioderma barbellatum onatwig. Brazil, Cyathus bonsai on decaying wood, Geastrum albofibrosum from moist soil with leaf litter, Laetiporus pratigiensis on a trunk of a living unknown hardwood tree species, and Scytalidium synnematicum on dead twigs of unidentified plant. Bulgaria, Amanita abscondita on sandy soil in a plantation of Quercus suber. Canada, Penicillium acericola on dead bark of Acer saccharum, and Penicillium corticola on dead bark of Acer saccharum. China, Colletotrichum qingyuanense on fruit lesion of Capsicum annuum. Denmark, Helminthosphaeria leptospora on corticioid Neohypochnicium cremicolor. Ecuador (Galapagos), Phaeosphaeria scalesiae on Scalesia sp. Finland, Inocybe jacobssonii on calcareouss oils in dry forests and park habitats. France, Cortinarius rufomyrrheus on sandy soil under Pinus pinaster, and Periconia neominutissima on leaves of Poaceae. India, Coprinopsis fragilis on decaying bark of logs, Filoboletus keralensis on unidentified woody substrate, Penicillium sankaranii from soil, Physisporinus tamilnaduensis on the trunk of Azadirachta indica, and Poronia nagaraholensis on elephant dung. Iran, Neosetophoma fic on infected leaves of Ficus elastica. Israel, Cnidariophoma eilatica (incl. Cnidariophoma gen. nov.) from Stylophora pistillata. Italy, Lyophyllum obscurum on acidic soil. Namibia, Aureobasidium faidherbiae on dead leaf of Faidherbia albida, and Aureobasidium welwitschiae on dead leaves of Welwitschia mirabilis. Netherlands, Gaeumannomycella caricigena on dead culms of Carex elongata, Houtenomyces caricicola (incl. Houtenomyces gen. nov.) on culms of Carex disticha, Neodacampia ulmea (incl. Neodacampia gen. nov.) on branch of Ulmus laevis, Niesslia phragmiticola on dead standing culms of Phragmites australis, Pseudopyricularia caricicola on culms of Carex disticha, and Rhodoveronaea nieuwwulvenica on dead bamboo sticks. Norway, Arrhenia similis half-buried and moss-covered pieces of rotting wood in grass-grownpath. Pakistan, Mallocybe ahmadii on soil. Poland, Beskidomyces laricis (incl. Beskidomyces gen. nov.) from resin of Larix decidua ssp. polonica, Lapidomyces epipinicola from sooty mould community on Pinus nigra, and Leptographium granulatum from a gallery of Dendroctonus micans on Picea abies. Portugal, Geoglossum azoricum on mossy areas of laurel forest areas planted with Cryptomeria japonica, and Lunasporangiospora lusitanica from a biofilm covering a bio deteriorated limestone wall. Qatar, Alternaria halotolerans from hypersaline sea water, and Alternaria qatarensis from water sample collected from hypersaline lagoon. South Africa, Alfaria thamnochorti on culm of Thamnochortus fraternus, Knufia aloeicola on Aloe gariepensis, Muriseptatomyces restionacearum (incl.Muriseptatomyces gen. nov.) on culms of Restionaceae, Neocladosporium arctotis on nest of cases of bagworm moths(Lepidoptera, Psychidae) on Arctotis auriculata, Neodevriesia scadoxi on leaves of Scadoxus puniceus, Paraloratospora schoenoplecti on stems of Schoenoplectus lacustris, Tulasnella epidendrea from the roots of Epidendrum × obrienianum, and Xenoidriella cinnamomi (incl. Xenoidriella gen. nov.) on leaf of Cinnamomum camphora. South Korea, Lemonniera fraxinea on decaying leaves of Fraxinus sp. frompond. Spain, Atheniella lauri on the bark of fallen trees of Laurus nobilis, Halocryptovalsa endophytica from surface-sterilised, asymptomatic roots of Salicornia patula, Inocybe amygdaliolens on soil in mixed forest, Inocybe pityusarum on calcareous soil in mixed forest, Inocybe roseobulbipes on acidic soils, Neonectria borealis from roots of Vitis berlandieri × Vitis rupestris, Sympoventuria eucalyptorum on leaves of Eucalyptus sp., and Tuber conchae fromsoil. Sweden, Inocybe bidumensis on calcareous soil. Thailand, Cordyceps sandindaengensis on Lepidoptera pupa, buried in soil, Ophiocordyceps kuchinaraiensis on Coleoptera larva, buried in soil, and Samsoniella winandae on Lepidoptera pupa, buriedinsoil. Taiwan region (China), Neophaeosphaeria livistonae on dead leaf of Livistona rotundifolia. Türkiye, Melanogaster anatolicus on clay loamy soils. UK, Basingstokeomyces allii (incl. Basingstokeomyces gen. nov.) on leaves of Allium schoenoprasum. Ukraine, Xenosphaeropsis corni on recently dead stem of Cornus alba. USA, Nothotrichosporon aquaticum (incl. Nothotrichosporon gen. nov.) from water, and Periconia philadelphiana from swab of coil surface. Morphological and culture characteristics for these new taxa are supported by DNA barcodes.The work of P.W. Crous and colleagues benefitted from funding by the European Union’s Horizon 2020 research and innovation program (RISE) under the Marie Skłodowska-Curie grant agreement No. 101008129, project acronym ‘Mycobiomics’, and the Dutch NWO Roadmap grant agreement No. 2020/ENW/00901156, project ‘Netherlands Infrastructure for Ecosystem and Biodiversity Analysis – Authoritative and Rapid Identification System for Essential biodiversity information’(acronym NIEBAARISE). G. Gulden, B. Rian and I. Saar thank K. Bendiksen at the fungarium and G. Marthinsen at NorBol, both Natural History Museum, University of Oslo for valuable help with the collections, and the sequencing of our finds of A. similis from 2022. Sincere thanks to A. Voitk for assistance with the colour plate and review of the manuscript. I. Saar was supported by the Estonian Research Council (grant PRG1170). P. Rodriguez-Flakus and co-authors are greatly indebted to their colleagues and all staff of the Herbario Nacional de Bolivia, Instituto de Ecología, Universidad Mayor de SanAndrés, La Paz, for their generous long-term cooperation. Their research was financially supported by the National Science Centre (NCN) in Poland (grants numbers 2018/02/X/NZ8/02362 and 2021/43/B/NZ8/02902). Y.P. Tan and colleagues thank M.K. Schutze (Department of Agriculture and Fisheries, Queensland, Australia) for determining the identity of the insect hosts for Aschersonia mackerrasiae. The Australian Biological Resources Study funded the project that led to the discovery of Aschersonia mackerrasiae. K.G.G. Ganga acknowledges support from the University Grants Commission (UGC), India, in the form of a UGC research fellowship (Ref No. 20/12/2015(ii) EU-V), and the authorities of the University of Calicut for providing facilities to conduct this study. S. Mahadevakumar acknowledges the Director, KSCSTE - Kerala Forest Research Institute and Head of Office, Botanical Survey of India,Andaman and Nicobar Regional Centre, Port Blair for the necessary support and M. Madappa, Department of Studies in Botany, University of Mysore for technical assistance. A.R. Podile thanks the Department of Science and Technology, Govt. of India for the JC Bose Fellowship (Grant No. JCB/2017/000053) & MoE and IOE-Directorate-UOH for project (Grant No.UOH-IOE-RC3-21-065). Financial support was provided to R. de L. Oliveira and K.D. Barbosa by the Coordenação deAperfeiçoamento de Pessoal de Nível Superior - Brazil (CAPES) – Finance code 001, and to I.G. Baseia and M.P. Martín by the National Council for Scientific and Technological Development (CNPq) under CNPq-Universal 2016 (409960/2016-0) and CNPq-visiting researcher (407474/2013-7). E. Larsson acknowledges the Swedish Taxonomy Initiative, SLU Artdatabanken, Uppsala, Sweden. H.Y. Mun and J. Goh were supported by a grant from the Nakdonggang National Institute of Biological Resources (NNIBR), funded by the Ministry of Environment (MOE) of the Republic of Korea (NNIBR202301106). J. Trovão and colleagues were financed by FEDER - Fundo Europeu de Desenvolvimento Regional funds through the COMPETE 2020 - Operational Programme for Competitiveness and Internationalisation (POCI), and by Portuguese funds through FCT- Fundação para a Ciência e a Tecnologia in the framework of the project POCI-01-0145-FEDER-PTDC/EPH-PAT/3345/ 2014. Their research was carried out at the R & D Unit Centre for Functional Ecology – Science for People and the Planet (CFE), with reference UIDB/04004/2020, financed by FCT/MCTES through national funds (PIDDAC). João Trovão was supported by POCH - Programa Operacional Capital Humano (co-funding by the European Social Fund and national funding by MCTES), through a ‘FCT- Fundação para a Ciência e Tecnologia’ PhD research grant (SFRH/ BD/132523/2017). O. Kaygusuz and colleagues thank the Research Fund of the Isparta University ofApplied Sciences for their financial support under the project number 2021-ILK1-0155. They also thank N. Sánchez Biezma of the Department of Drawing and Scientific Photography at the Alcalá University for his help in the digital preparation of the photographs. The research of M. Spetik and co-authors was supported by project No. IGAZF/2021-SI1003. V. Darmostuk and colleagues acknowledge our colleagues and all staff of the Herbario Nacional de Bolivia, Instituto de Ecología, Universidad Mayor de San Andrés, La Paz, for their generous long-term cooperation. They would also like to thank the SERNAP (http://sernap.gob.bo), and all protected areas staff, for providing permits for scientific studies, as well as their assistance and logistical support during the field works. This research was financially supported by the National Science Centre (NCN) in Poland (grant number DEC-2013/11/D/NZ8/ 03274). M. Kaliyaperumal and co-authors thank the Centre of Advanced Studies in Botany, University of Madras for the laboratory facilities. M. Kaliyaperumal thanks the Extramural Research-SERB, DST (EMR/2016/003078), Government of India, for financial assistance. M. Kaliyaperumal and K. Kezo thanks RUSA 2.0 (Theme-1, Group-1/2021/49) for providing a grant. M. Shivannegowda and colleagues thank C.R. Santhosh, Department of Studies in Microbiology, University of Mysore, Manasagangotri, Mysuru for technical support. They also thank K.R. Sridhar, Mangalore University, Karnataka, India and S.S.N. Maharachchikumbura, University of Electronic Science and Technology of China, Chengdu for their support and helping with technical inputs. The study of G.G. Barreto and co-authors was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brazil (CAPES - Finance Code 001), and the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq - Proc. 131503/2019-7; Proc. 312984/2018-9); the authors also thank to Programa de Pós-Graduação em Botânica – PPGBOT. L.F.P. Gusmão thanks to Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) for a research grant. T. Nkomo and colleagues thank the National Research Foundation of SouthAfrica for funding this study, with additional funding from the Forestry and Agricultural Biotechnology Institute and the University of Pretoria. G. Delgado is grateful to W. Colbert and S. Ward (Eurofins Built Environment) for continual encouragement and provision of laboratory facilities. J.G. Maciá-Vicente acknowledges support from the Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz (LOEWE) of the state of Hesse within the framework of the Cluster for Integrative Fungal Research (IPF) of Goethe University Frankfurt. F. Esteve-Raventós and colleagues acknowledge P. Juste and J.C. Campos for the loan of some collections for study and N. Subervielle and L. Hugot (Conservatoire Botanique National de Corse, Office de l’Environnement de la Corse, Corti) for their assistance. They also acknowledge the Balearic Mycology Group (FCB) for their permanent help in the search for collections in the Balearic Islands, and Y. Turégano for obtaining some of the sequences presented here, and L. Parra for his suggestions and help on nomenclatural issues. S. Mongkolsamrit and colleagues were financially supported by the Platform Technology Management Section, National Centre for Genetic Engineering and Biotechnology (BIOTEC), Project Grant No. P19-50231. S. De la Peña-Lastra and colleagues thank the Atlantic Islands National Maritime-Terrestrial Park authorities and guards. A. Mateos and co-authors would like to thank Secretaria Regional doAmbiente eAlterações Climáticas Açores for the permission granted for the sampling (Licença nº 16/2021/ DRAAC). To the ECOTOX group for co-funding the trip. J. Mack & D.P. Overy were funded byAgriculture &Agri-Food Canada (Project ID#002272: Fungal and Bacterial Biosystematics-bridging taxonomy and “omics” technology in agricultural research and regulation) and are grateful for molecular sequencing support from the Molecular Technologies Laboratory (MTL) at the Ottawa Research & Development Centre of Agriculture & Agri-Food Canada. The study of P. Czachura was funded by the National Science Centre, Poland, under the project 2019/35/N/NZ9/04173. The study of M. Piątek and coauthors was funded by the National Science Centre, Poland, under the project 2017/27/B/NZ9/02902. O. Yarden and L. Granit were funded by the Israel Science Foundation (grant number 888/19). H. Taşkın and colleagues received support from the BulgarianAcademy of Sciences and the Scientific and Technological Research Council of Türkiye (Bilateral grant agreement between BAS and TÜBİTAK, project number 118Z640). The authors would also like to thank S. Şahin (İzmir, Türkiye) for conveying one of the localities of A. abscondita. Andrew Miller would like to thank the Roy J. Carver Biotechnology Center at the University of Illinois for Sanger sequencing. E.R. Osieck thanks Staatsbosbeheer for permission to collect fungi in Nieuw Wulven, in the Netherlands. P. van ‘t Hof and co-authors thank the Galapagos Genetic Barcode project supported by UK Research and Innovation, Global Challenges Research Fund, Newton Fund, University of Exeter, Galapagos Science Center, Universidad San Francisco de Quito, Galapagos Conservation Trust, and Biosecurity Agency of Galapagos (ABG).Peer reviewe