scholarly journals Tree Diversity Reduces Fungal Endophyte Richness and Diversity in a Large-Scale Temperate Forest Experiment

Diversity ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 234 ◽  
Author(s):  
Eric A. Griffin ◽  
Joshua G. Harrison ◽  
Melissa K. McCormick ◽  
Karin T. Burghardt ◽  
John D. Parker
Keyword(s):  
Phylogenetic Diversity ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Spatial Scales ◽  
Fungal Endophytes ◽  
Fungal Endophyte ◽  
Tree Diversity ◽  
Trophic Levels ◽  
Community Diversity ◽  
And Function

Although decades of research have typically demonstrated a positive correlation between biodiversity of primary producers and associated trophic levels, the ecological drivers of this association are poorly understood. Recent evidence suggests that the plant microbiome, or the fungi and bacteria found on and inside plant hosts, may be cryptic yet important drivers of important processes, including primary production and trophic interactions. Here, using high-throughput sequencing, we characterized foliar fungal community diversity, composition, and function from 15 broadleaved tree species (N = 545) in a recently established, large-scale temperate tree diversity experiment using over 17,000 seedlings. Specifically, we tested whether increases in tree richness and phylogenetic diversity would increase fungal endophyte diversity (the “Diversity Begets Diversity” hypothesis), as well as alter community composition (the “Tree Diversity–Endophyte Community” hypothesis) and function (the “Tree Diversity–Endophyte Function” hypothesis) at different spatial scales. We demonstrated that increasing tree richness and phylogenetic diversity decreased fungal species and functional guild richness and diversity, including pathogens, saprotrophs, and parasites, within the first three years of a forest diversity experiment. These patterns were consistent at the neighborhood and tree plot scale. Our results suggest that fungal endophytes, unlike other trophic levels (e.g., herbivores as well as epiphytic bacteria), respond negatively to increasing plant diversity.

scholarly journals Climate and plant community diversity in space and time

2020 ◽  
Vol 117 (9) ◽  
pp. 4464-4470 ◽  
Author(s):  
Susan Harrison ◽  
Marko J. Spasojevic ◽  
Daijiang Li
Keyword(s):  
Plant Community ◽  
Plant Diversity ◽  
Phylogenetic Diversity ◽  
Spatial Scales ◽  
Community Diversity ◽  
Niche Conservatism ◽  
Space And Time ◽  
Drying Trend ◽  
Functional And Phylogenetic Diversity ◽  
Over Time

Climate strongly shapes plant diversity over large spatial scales, with relatively warm and wet (benign, productive) regions supporting greater numbers of species. Unresolved aspects of this relationship include what causes it, whether it permeates to community diversity at smaller spatial scales, whether it is accompanied by patterns in functional and phylogenetic diversity as some hypotheses predict, and whether it is paralleled by climate-driven changes in diversity over time. Here, studies of Californian plants are reviewed and new analyses are conducted to synthesize climate–diversity relationships in space and time. Across spatial scales and organizational levels, plant diversity is maximized in more productive (wetter) climates, and these consistent spatial relationships are mirrored in losses of taxonomic, functional, and phylogenetic diversity over time during a recent climatic drying trend. These results support the tolerance and climatic niche conservatism hypotheses for climate–diversity relationships, and suggest there is some predictability to future changes in diversity in water-limited climates.

scholarly journals High-throughput metabarcoding characterises fungal endophyte diversity in the phyllosphere of a barley crop

2021 ◽  
Author(s):  
Carla Bridget Milazzo ◽  
Katherine Grace Zulak ◽  
Mariano Jordi Muria-Gonzalez ◽  
Darcy Jones ◽  
Matthew Power ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Large Subunit ◽  
Fungal Endophytes ◽  
Environmental Dna ◽  
Fungal Endophyte ◽  
Bioinformatics Pipeline ◽  
Pests And Diseases ◽  
Key Factor ◽  
Agroecosystem Management

Over the last decade, the microbiome has received increasing attention as a key factor in macroorganism fitness. Sustainable pest management requires an understanding of the complex microbial endophyte communities existing symbiotically within plants and the way synthetic pesticides interact with them. Fungal endophytes are known to benefit plant growth and fitness and may deter pests and diseases. Recent advances in high-throughput sequencing (HTS) have enabled integrative microbiome studies especially in agricultural contexts. Here we profile the fungal endophyte community in the phyllosphere of two barley (Hordeum vulgare) cultivars exposed to two systemic foliar fungicides using metabarcoding, a HTS tool that constructs community profiles from environmental DNA (eDNA). We studied the fungal nuclear ribosomal large subunit (LSU) D2 and ITS2 DNA markers through a bioinformatics pipeline introduced here. We found 88 and 128 unique amplicon sequence variants (ASVs) using the D2 and ITS2 metabarcoding assays, respectively. With principal coordinate analysis (PCoA) and PERMANOVA, ASV diversity did not change in response to barley cultivar or fungicide treatment, however the community structure of unsprayed plants did change between two collection times eight days apart. The workflow described here can be applied to other microbiome studies in agriculture and we hope it encourages further research into crop microbiomes to improve agroecosystem management.

scholarly journals Linking Terrestrial and Aquatic Biodiversity to Ecosystem Function Across Scales, Trophic Levels, and Realms

2021 ◽  
Vol 9 ◽  
Author(s):  
Kyla M. Dahlin ◽  
Phoebe L. Zarnetske ◽  
Quentin D. Read ◽  
Laura A. Twardochleb ◽  
Aaron G. Kamoske ◽  
...  
Keyword(s):  
Ecosystem Function ◽  
Large Scale ◽  
Information Science ◽  
Spatial Scales ◽  
Biodiversity Loss ◽  
Relative Strength ◽  
Trophic Levels ◽  
Aquatic Biodiversity ◽  
Patterns And Processes ◽  
The Impact

Global declines in biodiversity have the potential to affect ecosystem function, and vice versa, in both terrestrial and aquatic ecological realms. While many studies have considered biodiversity-ecosystem function (BEF) relationships at local scales within single realms, there is a critical need for more studies examining BEF linkages among ecological realms, across scales, and across trophic levels. We present a framework linking abiotic attributes, productivity, and biodiversity across terrestrial and inland aquatic realms. We review examples of the major ways that BEF linkages form across realms–cross-system subsidies, ecosystem engineering, and hydrology. We then formulate testable hypotheses about the relative strength of these connections across spatial scales, realms, and trophic levels. While some studies have addressed these hypotheses individually, to holistically understand and predict the impact of biodiversity loss on ecosystem function, researchers need to move beyond local and simplified systems and explicitly investigate cross-realm and trophic interactions and large-scale patterns and processes. Recent advances in computational power, data synthesis, and geographic information science can facilitate studies spanning multiple ecological realms that will lead to a more comprehensive understanding of BEF connections.

scholarly journals How global extinctions impact regional biodiversity in mammals

2011 ◽  
Vol 8 (2) ◽  
pp. 222-225 ◽  
Author(s):  
Shan Huang ◽  
T. Jonathan Davies ◽  
John L. Gittleman
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Diversity ◽  
Spatial Scales ◽  
Spatial Location ◽  
Ecosystem Processes ◽  
Biodiversity Hotspots ◽  
Species Assemblage ◽  
Species Extinction ◽  
History Of ◽  
And Function

Phylogenetic diversity (PD) represents the evolutionary history of a species assemblage and is a valuable measure of biodiversity because it captures not only species richness but potentially also genetic and functional diversity. Preserving PD could be critical for maintaining the functional integrity of the world's ecosystems, and species extinction will have a large impact on ecosystems in areas where the ecosystem cost per species extinction is high. Here, we show that impacts from global extinctions are linked to spatial location. Using a phylogeny of all mammals, we compare regional losses of PD against a model of random extinction. At regional scales, losses differ dramatically: several biodiversity hotspots in southern Asia and Amazonia will lose an unexpectedly large proportion of PD. Global analyses may therefore underestimate the impacts of extinction on ecosystem processes and function because they occur at finer spatial scales within the context of natural biogeography.

scholarly journals Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology

2021 ◽  
Vol 12 ◽  
Author(s):  
Lauren M. Lui ◽  
Erica L.-W. Majumder ◽  
Heidi J. Smith ◽  
Hans K. Carlson ◽  
Frederick von Netzer ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Ecology ◽  
High Throughput Sequencing ◽  
Spatial Scales ◽  
Data Types ◽  
Modeling Framework ◽  
Rapid Acquisition ◽  
Mechanistic Understanding ◽  
And Function

Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.

scholarly journals Rolling a mycobiome down a hill: endophytes in the Taiwanese Cloud Forest

2017 ◽  
Author(s):  
Dan Thomas ◽  
Roo Vandegrift ◽  
Yu-Ming Ju ◽  
Monica Hsieh ◽  
Bitty Roy
Keyword(s):  
Tree Species ◽  
Spatial Scales ◽  
Cloud Forest ◽  
Fungal Endophytes ◽  
Amplicon Sequencing ◽  
Fungal Endophyte ◽  
Core Microbiome ◽  
The Core ◽  
Host Tree Species ◽  
Ecological Importance

AbstractFungal endophytes of plants are ubiquitous and important to host plant health. Despite their ecological importance, landscape-level patterns of microbial communities in plant hosts are not well-characterized. Fungal wood-inhabiting and foliar endophyte communities from multiple tree hosts were sampled at multiple spatial scales across a 25 ha subtropical research plot in northern Taiwan, using culture-free, community DNA amplicon sequencing methods. Fungal endophyte communities were distinct between leaves and wood, but the mycobiomes were highly variable across and within tree species. Of the variance that could be explained, host tree species was the most important driver of mycobiome community-composition. Within a single tree species, “core” mycobiomes were characterized using cooccurrence analysis. These core groups of endophytes in leaves and wood show divergent spatial patterns. For wood endophytes, a more consistent, “minimal” core mycobiome coexisted with the host across the extent of the study. For leaf endophytes, the core fungi resembled a more dynamic, “gradient” model of the core microbiome, changing across the topography and distance of the study.

scholarly journals Bio-GO-SHIP: The Time Is Right to Establish Global Repeat Sections of Ocean Biology

2022 ◽  
Vol 8 ◽  
Author(s):  
Sophie Clayton ◽  
Harriet Alexander ◽  
Jason R. Graff ◽  
Nicole J. Poulton ◽  
Luke R. Thompson ◽  
...  
Keyword(s):  
Optical Sensors ◽  
Large Scale ◽  
New Technologies ◽  
Chemical Properties ◽  
Trophic Levels ◽  
Global Ocean ◽  
Technological Advances ◽  
And Function ◽  
Physical And Chemical ◽  
Ocean Observing

In this article, we present Bio-GO-SHIP, a new ocean observing program that will incorporate sustained and consistent global biological ocean observations into the Global Ocean Ship-based Hydrographic Investigations Program (GO-SHIP). The goal of Bio-GO-SHIP is to produce systematic and consistent biological observations during global ocean repeat hydrographic surveys, with a particular focus on the planktonic ecosystem. Ocean plankton are an essential component of the earth climate system, form the base of the oceanic food web and thereby play an important role in influencing food security and contributing to the Blue Economy. Despite its importance, ocean biology is largely under-sampled in time and space compared to physical and chemical properties. This lack of information hampers our ability to understand the role of plankton in regulating biogeochemical processes and fueling higher trophic levels, now and in future ocean conditions. Traditionally, many of the methods used to quantify biological and ecosystem essential ocean variables (EOVs), measures that provide valuable information on the ecosystem, have been expensive and labor- and time-intensive, limiting their large-scale deployment. In the last two decades, new technologies have been developed and matured, making it possible to greatly expand our biological ocean observing capacity. These technologies, including cell imaging, bio-optical sensors and 'omic tools, can be combined to provide overlapping measurements of key biological and ecosystem EOVs. New developments in data management and open sharing can facilitate meaningful synthesis and integration with concurrent physical and chemical data. Here we outline how Bio-GO-SHIP leverages these technological advances to greatly expand our knowledge and understanding of the constituents and function of the global ocean plankton ecosystem.

scholarly journals Tree diversity increases robustness of multi-trophic interactions

2019 ◽  
Vol 286 (1898) ◽  
pp. 20182399 ◽  
Author(s):  
Felix Fornoff ◽  
Alexandra-Maria Klein ◽  
Nico Blüthgen ◽  
Michael Staab
Keyword(s):  
Trophic Interactions ◽  
Experimental Manipulation ◽  
Tree Diversity ◽  
Trophic Levels ◽  
Community Diversity ◽  
Ecosystem Functions ◽  
Network Analyses ◽  
Biodiversity Change ◽  
Ant Diversity ◽  
Diversity Effects

Multi-trophic interactions maintain critical ecosystem functions. Biodiversity is declining globally, while responses of trophic interactions to biodiversity change are largely unclear. Thus, studying responses of multi-trophic interaction robustness to biodiversity change is crucial for understanding ecosystem functioning and persistence. We investigate plant–Hemiptera (antagonism) and Hemiptera–ant (mutualism) interaction networks in response to experimental manipulation of tree diversity. We show increased diversity at both higher trophic levels (Hemiptera and ants) and increased robustness through redundancy of lower level species of multi-trophic interactions when tree diversity increased. Hemiptera and ant diversity increased with tree diversity through non-additive diversity effects. Network analyses identified that tree diversity also increased the number of tree and Hemiptera species used by Hemiptera and ant species, and decreased the specialization on lower trophic level species in both mutualistic and antagonist interactions. Our results demonstrate that bottom-up effects of tree diversity ascend through trophic levels regardless of interaction type. Thus, local tree diversity is a key driver of multi-trophic community diversity and interaction robustness in forests.

scholarly journals Ecosystem-level effects of large-scale disturbance in kelp forests

2020 ◽  
Vol 656 ◽  
pp. 163-180 ◽  
Author(s):  
KM Norderhaug ◽  
K Filbee-Dexter ◽  
C Freitas ◽  
SR Birkely ◽  
L Christensen ◽  
...  
Keyword(s):  
Large Scale ◽  
Single Species ◽  
Structure And Function ◽  
Trophic Levels ◽  
Kelp Forests ◽  
Ecosystem Structure ◽  
Substantial Impact ◽  
Large Scale Disturbance ◽  
And Function ◽  
Ecosystem Structure And Function

Understanding the effects of ecological disturbances in coastal habitats is crucial and timely as these are anticipated to increase in intensity and frequency in the future due to increasing human pressure. In this study we used directed kelp trawling as a scientific tool to quantify the impacts of broad-scale disturbance on community structure and function. We tested the ecosystem-wide effects of this disturbance in a BACI design using two 15 km2 areas. The disturbance had a substantial impact on the kelp forests in this study, removing 2986 tons of kelp and causing a 26% loss of total kelp canopy at trawled stations. This loss created a 67% reduction of epiphytes, an 89% reduction of invertebrates and altered the fish populations living within these habitats. The effect of habitat loss on fish was variable and depended on how the different species used the habitat structure. Our results show that large-scale experimental disturbances on habitat-forming species have ecological consequences that extend beyond the decline of the single species to affect multiple trophic levels of the broader ecosystem. Our findings have relevance for understanding how increasing anthropogenic disturbances, including kelp trawling and increased storm frequency caused by climate change, may alter ecosystem structure and function.

scholarly journals Age-related environmental gradients influence invertebrate distribution in the Prince Charles Mountains, East Antarctica

2016 ◽  
Vol 3 (12) ◽  
pp. 160296 ◽  
Author(s):  
Paul Czechowski ◽  
Duanne White ◽  
Laurence Clarke ◽  
Alan McKay ◽  
Alan Cooper ◽  
...  
Keyword(s):  
Soil Salinity ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Environmental Gradients ◽  
Spatial Scales ◽  
East Antarctica ◽  
Soil Biodiversity ◽  
Age Related ◽  
Invertebrate Biodiversity ◽  
Terrestrial Biodiversity

The potential impact of environmental change on terrestrial Antarctic ecosystems can be explored by inspecting biodiversity patterns across large-scale gradients. Unfortunately, morphology-based surveys of Antarctic invertebrates are time-consuming and limited by the cryptic nature of many taxa. We used biodiversity information derived from high-throughput sequencing (HTS) to elucidate the relationship between soil properties and invertebrate biodiversity in the Prince Charles Mountains, East Antarctica. Across 136 analysed soil samples collected from Mount Menzies, Mawson Escarpment and Lake Terrasovoje, we found invertebrate distribution in the Prince Charles Mountains significantly influenced by soil salinity and/or sulfur content. Phyla Tardigrada and Arachnida occurred predominantly in low-salinity substrates with abundant nutrients, whereas Bdelloidea (Rotifera) and Chromadorea (Nematoda) were more common in highly saline substrates. A significant correlation between invertebrate occurrence, soil salinity and time since deglaciation indicates that terrain age indirectly influences Antarctic terrestrial biodiversity, with more recently deglaciated areas supporting greater diversity. Our study demonstrates the value of HTS metabarcoding to investigate environmental constraints on inconspicuous soil biodiversity across large spatial scales.

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