Revelations for global change and conservation: determining European fungal species’ patterns via a large-scale fruit body ‘meta-database’

For several hundred years, millions of fungal sporocarps have been collected and deposited in worldwide collections (fungaria) to support fungal taxonomy. Owing to large-scale digitization programs, metadata associated with the records are now becoming publicly available, including information on taxonomy, sampling location, collection date and habitat/substrate information. This metadata, as well as data extracted from the physical fungarium specimens themselves, such as DNA sequences and biochemical characteristics, provide a rich source of information not only for taxonomy but also for other lines of biological inquiry. Here, we highlight and discuss how this information can be used to investigate emerging topics in fungal global change biology and beyond. Fungarium data are a prime source of knowledge on fungal distributions and richness patterns, and for assessing red-listed and invasive species. Information on collection dates has been used to investigate shifts in fungal distributions as well as phenology of sporocarp emergence in response to climate change. In addition to providing material for taxonomy and systematics, DNA sequences derived from the physical specimens provide information about fungal demography, dispersal patterns, and are emerging as a source of genomic data. As DNA analysis technologies develop further, the importance of fungarium specimens as easily accessible sources of information will likely continue to grow. This article is part of the theme issue ‘Biological collections for understanding biodiversity in the Anthropocene’.

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Climate change as a unifying theme in Antarctic research

Antarctic Science ◽

10.1017/s0954102001000499 ◽

2001 ◽

Vol 13 (4) ◽

pp. 353-353

Author(s):

Clive Howard-Williams

Keyword(s):

Climate Change ◽

Global Change ◽

Large Scale ◽

Polar Regions ◽

Ice Dynamics ◽

Stream Flows ◽

Sea Ice Dynamics ◽

Ipcc Report ◽

Pond Ecosystem ◽

The Difference

How many times have you seen statements similar to the following: “Antarctica is a global barometer”, “Antarctica is a warning beacon for global change”, or “Antarctica is a warning beacon for global change”, or “Antarctica is the most sensitive continent to climate change”? The frequency of such statements in this, and other polar journals, is significant. We know that the polar regions are highly sensitive to natural and human induced changes that originate elsewhere on our planet, and the literature is extensive and growing. At the large scale there is increasing evidence of both direct and indirect linkages between climate patterns (e.g. ENSO) in the Pacific and Atlantic oceans and Antarctic climate. At a smaller scale are the follow-on linkages to glacier dynamics, including surface melt, glacier stream flows, lake levels, beaches, sea-ice dynamics and ice tongues. All of these have major repercussions on Antarctic ecosystems. The phase change from water (liquid) to ice (solid) occurs over avery small temperature range (depending on salinity, pressure etc). Thus, for a pond ecosystem, a change in temperature of less than one degree Celsius means the difference between a functioning aquatic ecosystem, and a frozen ecosystem. The recent IPCC report (Climate Change 2001 [3 vols], Cambridge University Press) leaves little doubt of the significant changes to world climate now taking place. As Antarctic scientists we surely must therefore consider that the principal issue to be addressed in Antarctica at present is that of “Responses to a changing climate”.

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The Human Dimensions of Global Change

Geography in America at the Dawn of the 21st Century ◽

10.1093/oso/9780198233923.003.0029 ◽

2004 ◽

Author(s):

Diana Liverman ◽

Brent Yarnal

Keyword(s):

Global Change ◽

Environmental Change ◽

Large Scale ◽

Information Science ◽

Global Environmental Change ◽

Human Dimensions ◽

Water Diversion ◽

Human Environment ◽

Natural Systems ◽

Global Environmental

The human–environment condition has emerged as one of the central issues of the new millennium, especially as it has become apparent that human activity is transforming nature at a global scale in both systemic and cumulative ways. Originating with concerns about potential climate warming, the global environmental change agenda rapidly enlarged to include changes in structure and function of the earth’s natural systems, notably those systems critical for life, and the policy implications of these changes, especially focused on the coupled human–environment system. Recognition of the unprecedented pace, magnitude, and spatial scale of global change, and of the pivotal role of humankind in creating and responding to it, has led to the emergence of a worldwide, interdisciplinary effort to understand the human dimensions of global change. The term “global change” now encompasses a range of research issues including those relating to economic, political, and cultural globalization, but in this chapter we limit our focus to global environmental change and to the field that has become formally known as the human dimensions of global (or global environmental) change. We also focus mainly on the work of geographers rather than attempting to review the whole human dimensions research community. Intellectually, geography is well positioned to contribute to global environmental change research (Liverman 1999). The large-scale human transformation of the planet through activities such as agriculture, deforestation, water diversion, fossil fuel use, and urbanization, and the impacts of these on living conditions through changes in, for example, climate and biodiversity, has highlighted the importance of scholarship that analyzes the human–environmental relationship and can inform policy. Geography is one of the few disciplines that has historically claimed human–environment relationships as a definitional component of itself (Glacken 1967; Marsh 1864) and has fostered a belief in and reward system for engaging integrative approaches to problem solving (Golledge 2002; Turner 2002). Moreover, global environmental change is intimately spatial and draws upon geography-led remote sensing and geographic information science (Liverman et al. 1998). Geographers anticipated the emergence of current global change concerns (Thomas et al. 1956; Burton et al. 1978) and were seminal in the development of the multidisciplinary programs of study into the human dimensions of global change.

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Diversified Microbial Community Developed in Different Fruit Juice of Wine Fermentation

Applied Mechanics and Materials ◽

10.4028/www.scientific.net/amm.866.57 ◽

2017 ◽

Vol 866 ◽

pp. 57-60 ◽

Cited By ~ 1

Author(s):

Duongruitai Nicomrat ◽

Siriphatrc Chamutpong

Keyword(s):

Large Scale ◽

Raw Materials ◽

Agar Plate ◽

Fungal Species ◽

Wine Fermentation ◽

Wine Production ◽

Alcohol Production ◽

Nutrient Sources ◽

Fermented Broth ◽

Grape Varieties

In the process of grape wine fermentation, it has been long known that different flavor, aroma and taste characteristics are usually from various microbes associated grape strains and grape varieties. In the study, we were interested in understanding diversity of microbial niches of fermented glutinous rice ball developed in variety of fruit wine fermentation. Since different raw materials, fruits together with different microbial consortium associated with fruit surface itself affected various dominant culturable bacterial and fungal species. In the study, freshly prepared juices of fruits; mangoes and apples after processing without the pasteurization at 65°C for 30 min revealed dissimilar pH profiles and reducing sugar contents as well as alcohol production. Under microbiological examination as well as serial dilution agar plate technique, diverse dominant bacterial and fungal isolates were detected in the wine sample of the fruits pasteurized. The nutrients originated in apple sample caused more populations of microbes, including dominant bacilli, detected in the fermented broth since they were found in apples than in mangoes (104-1013 and 104-106 cells/ mL, respectively). From the results, it was shown that different nutrient sources played more important roles in stimulation of variations in microbial assort and possibly more complex in fermented juice qualification. The understanding in microflora consortium involving in wine fermentation for each fruit type should be helpful in monitoring and reflecting the concurrent microbial activity present in the large scale of wine production, reducing the risks of existing spoilage species.

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The Frontier Research System for Global Change—The International Arctic Research Center (Frontier-IARC): its Origin and Tentative Science Plan

Marine Technology Society Journal ◽

10.4031/mtsj.33.1.10 ◽

1999 ◽

Vol 33 (1) ◽

pp. 81-84

Author(s):

Jinro Ukila ◽

Moloyoshi Ikeda

Keyword(s):

Climate Change ◽

Global Change ◽

Global Climate Change ◽

Large Scale ◽

Global Climate ◽

Research Effort ◽

Arctic Region ◽

Research Center ◽

The Arctic ◽

Research System

The Frontier Research System for Global Change—the International Arctic Research Center (Frontier-IARC) is a research program funded by the Frontier Research System for Global Change. The program is jointly run under a cooperative agreement between the Frontier Research System for Global Change and the University of Alaska Fairbanks. The aim of the program is to understand the role of the Arctic region in global climate change. The program concentrates its research effort initially on the areas of air-sea-ice interactions, bio-geochemical processes and the ecosystem. To understand the arctic climate system in the context of global climate change, we focus on mechanisms controlling arctic-subarctic interactions, and identify three key components: the freshwater balance, the energy balance, and the large-scale atmospheric processes. Knowledge of details of these components and their interactions will be gained through long-term monitoring, process studies, and modeling; our focus will be on the latter two categories.

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Altitudinal upwards shifts in fungal fruiting in the Alps

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2019.2348 ◽

2020 ◽

Vol 287 (1919) ◽

pp. 20192348 ◽

Cited By ~ 4

Author(s):

Jeffrey Diez ◽

Håvard Kauserud ◽

Carrie Andrew ◽

Einar Heegaard ◽

Irmgard Krisai-Greilhuber ◽

...

Keyword(s):

Environmental Changes ◽

Fruit Body ◽

Wood Decay ◽

Fungal Species ◽

Ecosystem Functions ◽

European Alps ◽

Decay Fungi ◽

Wood Decay Fungi ◽

Physiological Limit ◽

The Alps

Many plant and animal species are changing their latitudinal and/or altitudinal distributions in response to climate change, but whether fungi show similar changes is largely unknown. Here, we use historical fungal fruit body records from the European Alps to assess altitudinal changes in fungal fruiting between 1960 and 2010. We observe that many fungal species are fruiting at significantly higher elevations in 2010 compared to 1960, and especially so among soil-dwelling fungi. Wood-decay fungi, being dependent on the presence of one or a few host trees, show a slower response. Species growing at higher elevations changed their altitudinal fruiting patterns significantly more than lowland species. Environmental changes in high altitudes may lead to proportionally stronger responses, since high-altitude species live closer to their physiological limit. These aboveground changes in fruiting patterns probably mirror corresponding shifts in belowground fungal communities, suggesting parallel shifts in important ecosystem functions.

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A genome-scale phylogeny of Fungi; insights into early evolution, radiations, and the relationship between taxonomy and phylogeny

10.1101/2020.08.23.262857 ◽

2020 ◽

Cited By ~ 3

Author(s):

Yuanning Li ◽

Jacob L. Steenwyk ◽

Ying Chang ◽

Yan Wang ◽

Timothy Y. James ◽

...

Keyword(s):

Large Scale ◽

Sequence Divergence ◽

Fungal Species ◽

Data Matrix ◽

Evolutionary Divergence ◽

A Genome ◽

Taxonomic Groups ◽

Taxonomic Studies ◽

Genome Scale ◽

Data Matrices

AbstractPhylogenomic studies based on genome-scale amounts of data have greatly improved understanding of the tree of life. Despite their diversity, ecological significance, and biomedical and industrial importance, large-scale phylogenomic studies of Fungi are lacking. Furthermore, several evolutionary relationships among major fungal lineages remain controversial, especially those at the base of the fungal phylogeny. To begin filling these gaps and assess progress toward a genome-scale phylogeny of the entire fungal kingdom, we compiled a phylogenomic data matrix of 290 genes from the genomes of 1,644 fungal species that includes representatives from most major fungal lineages; we also compiled 11 additional data matrices by subsampling genes or taxa based on filtering criteria previously shown to improve phylogenomic inference. Analyses of these 12 data matrices using concatenation- and coalescent-based approaches yielded a robust phylogeny of the kingdom in which ∼85% of internal branches were congruent across data matrices and approaches used. We found support for several relationships that have been historically contentious (e.g., for the placement of Wallemiomycotina (Basidiomycota), as sister to Agaricomycotina), as well as evidence for polytomies likely stemming from episodes of ancient diversification (e.g., at the base of Basidiomycota). By examining the relative evolutionary divergence of taxonomic groups of equivalent rank, we found that fungal taxonomy is broadly aligned with genome sequence divergence, but also identified lineages, such as the subphylum Saccharomycotina, where current taxonomic circumscription does not fully account for their high levels of evolutionary divergence. Our results provide a robust phylogenomic framework to explore the tempo and mode of fungal evolution and directions for future fungal phylogenetic and taxonomic studies.

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Cyberinfrastructure for an integrated botanical information network to investigate the ecological impacts of global climate change on plant biodiversity

10.7287/peerj.preprints.2615 ◽

2016 ◽

Cited By ~ 3

Author(s):

Brian J Enquist ◽

Rick Condit ◽

Robert K Peet ◽

Mark Schildhauer ◽

Barbara M. Thiers

Keyword(s):

Global Change ◽

Large Scale ◽

Plant Ecology ◽

Plant Evolution ◽

Ecological Impacts ◽

Grand Challenge ◽

Ecological Knowledge ◽

Plant Biodiversity ◽

Data Resource ◽

Global Change Biology

To answer many of the major questions in comparative botany, ecology, and global change biology it is necessary to extrapolate across enormous geographic, temporal and taxonomic scales. Yet much ecological knowledge is still based on observations conducted within a local area or even a few hundred square meters. Understanding ecological patterns and how plants respond to global warming and human alteration of landscapes and ecosystems necessitates a holistic approach. Such an approach must be conducted at a scale that is commensurate with the breadth of the questions being asked. Further, it requires identification, retrieval, and integration of diverse data from a global confederation of collaborating scientists across a broad range of disciplines. We propose to network core databases and data networks to create a novel resource for quantitative plant biodiversity science. The grand challenge is to assemble and share the world’s rapidly accumulating botanical information from plots and collections to create a distributed, web-accessible, readily analyzable data resource. With such a resource, we will answer major questions of direct relevance to plant ecology, plant evolution, plant geography, conservation, global change biology, and protection of biodiversity and ecosystem services. In particular, how does climate influence the distribution and abundance of plant species, how does the phylogenetic diversity of plants vary across broad environmental and climatic gradients, and how are plants assembled into ecological communities? While these and associated questions are at the core of many research endeavors in comparative botany and ecology, our past collective inability to integrate data on a large scale has significantly limited our ability to address these questions head on. This proposed Grand Challenge team will create a data resource of unprecedented size and scope together with the tools for its use, thereby empowering botanists and the general public to better address fundamental issues in plant ecology and global change biology. Although we will focus on plants of the New World, the infrastructure and protocols developed will be scalable to all geographic regions and all types of organisms. Future steps will enable cross-cutting linkages to emerging networks on plant genomics, physiology, and phylogeny, allowing us to address fundamental genetic and evolutionary questions at unprecedented spatial and temporal scales.

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Predicting species and community responses to global change in Australian mountain ecosystems using structured expert judgement

10.1101/2020.09.23.309377 ◽

2020 ◽

Author(s):

James S. Camac ◽

Kate D.L. Umbers ◽

John W. Morgan ◽

Sonya R. Geange ◽

Anca Hanea ◽

...

Keyword(s):

Global Change ◽

Empirical Data ◽

Large Scale ◽

Expert Knowledge ◽

Rapid Change ◽

Life Cycles ◽

Expert Elicitation ◽

Alpine Plants ◽

Ecological Data ◽

Australian Alps

AbstractConservation managers are under increasing pressure to make decisions about the allocation of finite resources to protect biodiversity under a changing climate. However, the impacts of climate and global change drivers on species are outpacing our capacity to collect the empirical data necessary to inform these decisions. This is particularly the case in the Australian Alps which has already undergone recent changes in climate and experienced more frequent large-scale bushfires. In lieu of empirical data, we used a structured expert elicitation method (the IDEA protocol) to estimate the abundance and distribution of nine vegetation groups and 89 Australian alpine and subalpine species by the year 2050. Experts predicted that most alpine vegetation communities would decline in extent by 2050; only woodlands and heathlands were predicted to increase in extent. Predicted species-level responses for alpine plants and animals were highly variable and uncertain. In general, alpine plants spanned the range of possible responses, with some expected to increase, decrease or not change in cover. By contrast, almost all animal species were predicted to decline or not change in abundance or elevation range; more species with water-centric life-cycles were expected to decline in abundance than other species. In the face of rapid change and a paucity of data, the method and outcomes outlined here provide a pragmatic and coherent basis upon which to start informing conservation policy and management, although this approach does not diminish the importance of collecting long-term ecological data.Article Impact StatementExpert knowledge is used to quantify the adaptive capacity and thus, the risk posed by global change, to Australian mountain flora and fauna.

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Biomass and Cordycepin Production by the Medicinal Mushroom Cordyceps militaris—A Review of Various Aspects and Recent Trends towards the Exploitation of a Valuable Fungus

Journal of Fungi ◽

10.3390/jof7110986 ◽

2021 ◽

Vol 7 (11) ◽

pp. 986

Author(s):

Dimitrios Kontogiannatos ◽

Georgios Koutrotsios ◽

Savvina Xekalaki ◽

Georgios I. Zervakis

Keyword(s):

Large Scale ◽

Fruit Body ◽

Cordyceps Militaris ◽

Economic Losses ◽

Ophiocordyceps Sinensis ◽

Wide Range ◽

Significant Research ◽

Caterpillar Fungus ◽

Recent Trends ◽

Large Scale Cultivation

Cordyceps militaris is an entomopathogenic ascomycete with similar pharmacological importance to that of the wild caterpillar fungus Ophiocordyceps sinensis. C. militaris has attracted significant research and commercial interest due to its content in bioactive compounds beneficial to human health and the relative ease of cultivation under laboratory conditions. However, room for improvement exists in the commercial-scale cultivation of C. militaris and concerns issues principally related to appropriate strain selection, genetic degeneration of cultures, and substrate optimization. In particular, culture degeneration—usually expressed by abnormal fruit body formation and reduced sporulation—results in important economic losses and is holding back investors and potential growers (mainly in Western countries) from further developing this highly promising sector. In the present review, the main factors that influence the generation of biomass and metabolites (with emphasis on cordycepin biosynthesis) by C. militaris are presented and evaluated in conjunction with the use of a wide range of supplements or additives towards the enhancement of fungal productivity in large-scale cultivation processes. Moreover, physiological and genetic factors that increase or reduce the manifestation of strain degeneration in C. militaris are outlined. Finally, methodologies for developing protocols to be used in C. militaris functional biology studies are discussed.

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