EEOB publications September 1 - September 30
Herbivory shapes the rhizosphere bacterial microbiota in potato plants
Antonino Malacrinò, Mingyuan Wang, Sandra Caul, Alison J. Karley, and Alison E. Bennett. 2021. doi:10.1111/1758-2229.12998
Summary
Plant-associated microbiomes assist their host in a variety of activities, spanning from nutrition to defence against herbivores and diseases. Previous research showed that plant-associated microbiomes shift their composition when plants are exposed to stressors, including herbivory. However, existing studies explored only single herbivore-plant combinations, whereas plants are often attacked by several different herbivores, but the effects of multiple herbivore types on the plant microbiome remain to be determined. Here, we first tested whether feeding by different herbivores (aphids, nematodes and slugs) produces a shift in the rhizosphere bacterial microbiota associated with potato plants. Then, we expanded this question asking whether the identity of the herbivore produces different effects on the rhizosphere microbial community. While we found shifts in microbial diversity and structure due to herbivory, we observed that the herbivore identity does not influence the diversity or community structure of bacteria thriving in the rhizosphere. However, a deeper analysis revealed that the herbivores differentially affected the structure of the network of microbial co occurrences. Our results have the potential to increase our ability to predict how plant microbiomes assemble and aid our understanding of the role of plant microbiome in plant responses to biotic stress.
Microbiota Perturbation or Elimination Can Inhibit Normal Development and Elicit a Starvation-Like Response in an Omnivorous Model Invertebrate
Arturo Vera-Ponce de León, Benjamin C. Jahnes, Alejandro Otero-Bravo, Zakee L. Sabree. 2021. mSystems 6:e00802-21. https://doi.org/10.1128/mSystems.00802-21.
ABSTRACT
Omnivorous animals, including humans, harbor diverse, species-rich gut communities that impact their growth, development, and homeostasis. Model invertebrates are broadly accessible experimental platforms that enable linking specific species or species groups to host phenotypes, yet often their specialized diets and distinct gut microbiota make them less comparable to human and other mammalian and gut communities. The omnivorous cockroach Periplaneta americana harbors ;4 102 bacterial genera within its digestive tract and is enriched with taxa commonly found in omnivorous mammals (i.e., Proteobacteria, Bacteroidetes, and Firmicutes). These features make P. americana a valuable platform for identifying microbe-mediated host phenotypes with potential translations to mammals. Rearing P. americana insects under germfree conditions resulted in prolonging development time by ;30% and an up to ;8% reduction in body size along three dimensions. Germfree rearing resulted in downregulation of gene networks involved in growth, energy homeostasis, and nutrient availability. Reintroduction of a defined microbiota comprised of a subset of P. americana commensals to germfree insects did not recover normal growth and developmental phenotypes or transcriptional profiles observed in conventionally reared insects. These results are in contrast with specialist-feeding model insects (e.g., Drosophila), where introduction of a single endemic bacterial species to germfree condition-reared specimens recovered normal host phenotypes. These data suggest that understanding microbe-mediated host outcomes in animals with species-rich communities should include models that typically maintain similarly diverse microbiomes. The dramatic transcriptional, developmental, and morphological phenotypes linked to gut microbiome status in this study illustrates how microbes are key players in animal growth and evolution.
Consequences of changing water clarity on the fish and fisheries of the Laurentian Great Lakes
David B. Bunnell, Stuart A. Ludsin, Roger L. Knight, Lars G. Rudstam, Craig E. Williamson, Tomas O. Höök, Paris D. Collingsworth, Barry M. Lesht, Richard P. Barbiero, Anne E. Scofield, Edward S. Rutherford, Layne Gaynor, Henry A. Vanderploeg, and Marten A. Koops. 2021. Can. J. Fish. Aquat. Sci. https://cdnsciencepub.com/doi/pdf/10.1139/cjfas-2020-0376
Abstract
Human-driven environmental change underlies recent changes in water clarity in many of the world’s great lakes, yet our understanding of the consequences of these changes on the fish and fisheries they support remains incomplete. Herein, we offer a framework to organize current knowledge, guide future research, and help fisheries managers understand how water clarity can affect their valued populations. Emphasizing Laurentian Great Lakes findings where possible, we describe how changing water clarity can directly affect fish populations and communities by altering exposure to ultraviolet radiation, foraging success, predation risk, reproductive behavior, or territoriality. We also discuss how changing water clarity can affect fisheries harvest and assessment through effects on fisher behavior and sampling efficiency (i.e., catchability). Finally, we discuss whether changing water clarity can affect understudied aspects of fishery performance, including economic and community benefits. We conclude by identifying generalized predictions and discuss their implications for priority research questions for the Laurentian Great Lakes. Even though the motivation for this work was regional, the breadth of the review and generality of the framework are readily transferable to other freshwater and marine habitats.
Standardized NEON organismal data for biodiversity research
Daijiang Li, Sydne Record, Eric Sokol, Matthew E. Bitters, Melissa Y. Chen, Anny Y. Chung, Matthew R. Helmus, Ruvi Jaimes, Lara Jansen, Marta A. Jarzyna, Michael G. Just, Jalene M. LaMontagne, Brett Melbourne, Wynne Moss, Kari Norman, Stephanie Parker, Natalie Robinson, Bijan Seyednasrollah, Colin Smith, Sarah Spaulding, Thilina Surasinghe, Sarah Thomsen, Phoebe Zarnetske. link to article.
Abstract
Understanding patterns and drivers of species distributions and abundances, and thus biodiversity, is a core goal of ecology. Despite advances in recent decades, research into these patterns and processes is currently limited by a lack of standardized, high-quality, empirical data that spans large spatial scales and long time periods. The National Ecological Observatory Network (NEON) fills this gap by providing freely available observational data that are: generated during robust and consistent organismal sampling of several sentinel taxonomic groups within 81 sites distributed across the United States; and will be collected for at least 30 years. The breadth and scope of these data provides a unique resource for advancing biodiversity research. To maximize the potential of this opportunity, however, it is critical that NEON data be maximally accessible and easily integrated into investigators’ workflows and analyses. To facilitate its use for biodiversity research and synthesis, we created a workflow to process and format NEON organismal data into the ecocomDP (ecological community data design pattern) format, and available through the ecocomDP R package; we then provided the standardized data as an R data package (neonDivData). We briefly summarize sampling designs and data wrangling decisions for the major taxonomic groups included in this effort. Our workflows are open-source so the biodiversity community may: add additional taxonomic groups; modify the workflow to produce datasets appropriate for their own analytical needs; and regularly update the data packages as more observations become available. Finally, we provide two simple examples of how the standardized data may be used for biodiversity research. By providing a standardized data package, we hope to enhance the utility of NEON organismal data in advancing biodiversity research.
Landscape Features Fail to Explain Spatial Genetic Structure in White-Tailed Deer Across Ohio, USA
Javan M. Bauder, Christine S. Anderson,H. Lisle Gibbs, Michael J. Tonkovich, W. David Walter. 2021. https://doi.org/10.1002/jwmg.22120
ABSTRACT
Landscape features influence wildlife movements across spatial scales and have the potential to influence the spread of disease. Chronic wasting disease (CWD) is a fatal prion disease affecting members of the family Cervidae, particularly white-tailed deer (Odocoileus virginianus), and the first positive CWD case in a wild deer in Ohio, USA, was recorded in 2020. Landscape genetics approaches are increasingly used to better understand potential pathways for CWD spread in white-tailed deer, but little is known about genetic structure of white-tailed deer in Ohio. The objectives of our study were to evaluate spatial genetic structure in white-tailed deer across Ohio and compare the support for isolation by distance (IBD) and isolation by landscape resistance (IBR) models in explaining this structure. We collected genetic data from 619 individual deer from 24 counties across Ohio during 2007–2009. We used microsatellite genotypes from 619 individuals genotyped at 11 loci and haplotypes from a 547-base pair fragment of the mitochondrial DNA control region. We used spatial and non-spatial genetic clustering tests to evaluate genetic structure in both types of genetic data and empirically optimized landscape resistance surfaces to compare IBD and IBR using microsatellite data. Non-spatial genetic clustering tests failed to detect spatial genetic structure, whereas spatial genetic clustering tests indicated subtle spatial genetic structure. The IBD model consistently outperformed IBR models that included land cover, traffic volume, and streams. Our results indicated widespread genetic connectivity of white-tailed deer across Ohio and negligible effects of landscape features. These patterns likely reflect some combination of minimal resistive effects of landscape features on white-tail deer movement in Ohio and the effects of regional recolonization or translocation. We encourage continued CWD surveillance in Ohio, particularly in the proximity of confirmed cases. © 2021 The Wildlife Society. This article has been contributed to by US Government employees and their work is in the public domain in the USA.
The Phylogeographic Shortfall in Hexapods: A Lot of Leg Work Remaining
Jordan D Satler, Bryan C Carstens, Ryan C Garrick, Anahí Espíndola. Insect Systematics and Diversity, Volume 5, Issue 5, September 2021, 1, https://doi.org/10.1093/isd/ixab015
Abstract
In the 21st century, phylogeography has experienced dramatic growth in the data and methods used by the field. Insect (more generally, hexapod) phylogeography has contributed to major advances and many of the influential papers included hexapods as model systems. In this literature review, we: (i) highlight recent phylogeographic work in hexapod systems, and (ii) identify broader trends and critical future steps in the field. We include a summary of useful methodological approaches and identify the methods used to approach different questions asked in phylogeographic studies. An updated summary of the applications that phylogeography has contributed to the field of entomology, including spatial studies, conservation, systematics, pest control, and invasive species, is included to highlight vital work in the field. Special attention is devoted to investigations which seek to use multi-species data to understand community ecological and evolutionary processes. Finally, we overview the main challenges, opportunities, and emerging areas, highlighting the “phylogeographic shortfall” that exists between the number of described hexapod species vs. the number of species that have been the focus of phylogeographic investigation.
Lipid composition of the stratum corneum in different regions of the body of Kuhl's pipistrelle from the Negev Desert, Israel
Alexis Cockley, Alex M.Champagne, Miriam Ben-Hamo, Berry Pinshow, Carmi Korine, Agustí Muñoz-Garcia. 2021. https://doi.org/10.1016/j.cbpa.2021.111074
Abstract
The most superficial epidermal layer in endotherms is the stratum corneum (SC), which is composed of dead corneocytes embedded in a lipid matrix with free fatty acids, cholesterol, ceramides, and cerebrosides; the lipid composition of the SC determines its permeability to water vapor. Lipids that are more polar, have longer hydrocarbon chains, and are less bulky are often packed in more ordered phase states to slow cutaneous evaporative water loss (CEWL); these lipids also resist transitions to more disordered phases at high ambient temperatures (Ta). In bats, wing and tail membranes (wing patagia and tail uropatagium, respectively) allow powered flight, but increase surface area, and hence CEWL, with implications for survival in arid environments. We captured Pipistrellus kuhlii from an arid habitat and measured the lipid composition of the SC of the plagiopatagium in the wing, the uropatagium, and the non-membranous region (NMR) of the body using thin layer chromatography and reversed phase high performance liquid chromatography coupled with atmospheric pressure photoionization mass spectrometry. The patagia contained more cholesterol and shorter-chained ceramides, and fewer cerebrosides than the NMR, indicating that the lipid phase transition temperature in the patagia is lower than in the NMR. Thus, at moderate Ta the lipids in the SC in all body regions will remain in an ordered phase state, allowing water conservation; but as Ta increases, the lipids in the SC of the patagia will more easily transition into a disordered phase, resulting in increased CEWL from the patagia facilitating efficient heat dissipation in hot environments.
CORALLORHIZA MACULATA (ORCHIDACEAE) NEW TO ALASKA AND ITS DISTRIBUTIONAL RELATIONSHIP TO CORALLORHIZA MERTENSIANA
Marlin L. Bowles, John V. Freudenstein, Judy Hall Jacobson. Madroño, 68(2):75-86 (2021).
Abstract
In the Pacific Northwest, the spotted coralroot, Corallorhiza maculata (Raf.) Raf., has been recognized as occurring as far north as central British Columbia, but excluded from the flora of Alaska. The western coralroot, C. mertensiana Bong., reaches its northern range limit in Southeast Alaska, where collections of this sister species may be confused with C. maculata. In 2019-20, we conducted herbarium and field studies that verified eight C. maculata stations in northern Southeast Alaska. Two of these stations are represented by collections made in 2000 and 2007, which were identified as C. mertensiana; 14 C. mertensiana collections had been identified as C. maculata. This confusion may have resulted from nomenclatural changes, as well as rarity of actual C. maculata material. These species differ in morphological features that reflect different breeding systems, and occupy different habitats in Alaska. The Alaska stations of C. maculata represent a 650 km range extension that is disjunct from locations in central British Columbia. These stations occur in a summer-dry climate zone caused by a rainshadow from coastal mountains. We advance the hypothesis that this area provides habitat for populations of C. maculata that represent relics of a floristic migration that occurred during the Xerothermic interval 10-7500 yr BP. In contrast, C. mertensiana is widespread in humid coastal habitats in southeast Alaska, and its distribution is contiguous with more southern coastal populations. Though both species occur in Southeast Alaska, they occupy different climate zones, and their distributions are narrowly allopatric.
Phylogenetic relationships and biogeography of the Hybomys division (Muridae: Murinae: Arvicanthini), rodents endemic to Africa's rainforests
Nelish Pradhan, Ryan W. Norris, Jan Decher, Julian Kerbis Peterhans, Christopher R. Gray, George Bauer, Michael D. Carleton, C. William Kilpatrick. J. of Vertebrate Biology, 70(2):21034.1-26 (2021). https://doi.org/10.25225/jvb.21034
Abstract
The Hybomys division (Muridae: Murinae: Arvicanthini) consists of four genera (Hybomys, Typomys, Dephomys, and Stochomys) endemic to the Guineo-Congolian rainforests of central Africa. Based on sequences from two mitochondrial (Cytb, 12S rRNA) and two nuclear (Rbp3, Ghr) genes, we present a fossil-calibrated molecular phylogeny of the Hybomys division, based on wider taxon and geographic sampling than previously published phylogenies. Species of Typomys formed a clade that was sister to a clade containing Hybomys and the sister genera Dephomys and Stochomys. Hybomys basilii and Hybomys lunaris were recovered as monophyletic, whereas Hybomys univittatus was recovered as polyphyletic and likely consists of at least three species. The divergence between the East African taxon H. lunaris, and the West and Central African taxa of Hybomys is estimated at 3.1 Mya. Based on molecular phylogenies and genetic distances, we infer that forms of Hybomys from both the highlands and lowlands of the Cameroon Volcanic Line, except for H. basilii, should be considered a single species for which Hybomys rufocanus is the oldest available name. As proposed, H. rufocanus would include the named forms badius and eisentrauti as synonyms, as well as populations north of the River Sanaga previously recognized as H. univittatus. Material from nearest the type locality of H. univittatus is sister to H. rufocanus, whereas other specimens currently recognised as H. univittatus from south of the River Ogooue and in the Congo Basin are sister to this H. rufocanus + true H. univittatus clade. Dating estimates place the origin and early diversification of the Hybomys division in the late Miocene, slightly preceding the radiation of most arvicanthine genera that inhabit savannah biomes. The historical biogeography of the Hybomys division appears to be congruent with hypothesized forest refugia, savannah barriers, and aridification cycles of the Neogene and Pleistocene.
A non-native earthworm shifts seed predation dynamics of a native weed
Emilie E. Regnier, Stephen M. Hovick, Jianyang Liu, Steven Kent Harrison, Florian Diekmann. 2021. https://doi.org/10.1111/1365-2664.14034
Abstract
Introduced seed dispersers can shift seed predation dynamics in native species, impacting native plant establishment and spread. We studied the effect of the non-native earthworm, Lumbricus terrestris, on seed loss dynamics in the large-seeded native annual, Ambrosia trifida (giant ragweed), an expanding agricultural weed whose seeds are heavily predated by mice. Lumbricus terrestris may protect seeds against rodent predation by caching them in its burrows from which seedlings can emerge unharmed; however, little is known about the ability of earthworms to compete with rodents for seeds. We investigated this interaction and how environmental factors affected the competitive outcome.
In a 2-year field study, we analysed relative rates of seed removal by earthworms and mice for seeds dispersed at various times in habitats that varied in vegetative cover.
Species-specific responses to environmental conditions drove variation in the share of seeds taken by earthworms versus mice, with earthworms gaining relatively more seeds under warmer, wetter conditions and in low plant cover habitats, and mice obtaining more seeds under colder, drier conditions and in high cover habitats.
Environmental factors also determined which competitor accessed seeds first, and this conferred a competitive advantage that was compounded over time.
Earthworms cached some seeds under all experimental conditions, suggesting that L. terrestris can act mutualistically with giant ragweed in diverse environments.
Synthesis and applications. Our results support the hypothesis that the non-native earthworm Lumbricus terrestris behaves as a seed dispersal mutualist for the native annual giant ragweed by caching its seeds in its burrows, thereby reducing their availability to rodent seed predators. The data also support the view that interactions among the environment and competing seed predators determine the fate of seed pools in response to species-specific environmental preferences. In crop fields where L. terrestris is abundant, additional efforts to prevent giant ragweed seed return may be warranted due to the likelihood that earthworms will increase giant ragweed soil seed pools. Lumbricus terrestris is expanding its range throughout temperate regions and may similarly affect secondary seed dispersal and seed predation dynamics of large-seeded species in other plant communities.
Genomic evidence of an ancient Inland Temperate Rainforest
Megan Ruffley, Megan Smith, Anahi Espindola, Daniel Turck, Niels Mitchell, Bryan Carstens, Jack Sullivan, David Tank. Authorea. September 25, 2021.
DOI: 10.22541/au.163254059.95545414/v1
Abstract
The disjunct temperate rainforests of the Pacific Northwest of North America (PNW) are characterized by late-successional dominant tree species western redcedar (Thuja plicata) and western hemlock (Tsuga heterophylla). The demographics of these species, along with the PNW rainforest ecosystem in its entirety, have been heavily impacted by the geological and climatic changes the PNW has experienced over the last 5 million years, including mountain orogeny and repeated Pleistocene glaciations. These environmental events have ultimately shaped the history of these species, with inland segments potentially being extirpated during the Pleistocene glaciation. Here, we collect genomic data for both species across their ranges in order to develop multiple demographic models, each reflecting a different hypothesis on how the ecosystem dominant species may have responded to dramatic climatic change. Results indicate that inland and coastal populations in both species diverged an estimated ~2.5 million years ago and experienced a decrease in population size during glaciation, with a subsequent population expansion. Importantly, we found evidence for gene-flow between coastal and inland populations during the mid-Holocene. It is likely that intermittent migration in these species has prevented allopatric speciation. In conclusion, the combination of genomic data and population demographic inference procedures involving machine learning establish that populations of the ecosystem dominants Thuja plicata and Tsuga heterophylla persisted in refugia located in both the coastal and inland regions, with populations expanding and contracting in response to glacial cycles with occasional gene-flow.
Functional traits reveal the dominant drivers of long-term community change across a North American Great Lake
James S Sinclair, Michael E Fraker, James M Hood, Kenneth T Frank, Mark R DuFour, Ann Marie Gorman, Stuart A Ludsin. Glob Chang Biol. 2021. doi: 10.1111/gcb.15902.
Abstract
Ecosystems worldwide have been impacted by multiple anthropogenic stressors, yet efforts to understand and manage these impacts have been hindered by difficulties in disentangling relative stressor effects. Theoretically, the actions of individual stressors can be delineated based on associated changes in functional traits and these relationships should be generalizable across communities comprised of different species. Thus, combining trait perspectives with community composition data could help to identify the relative influence of different stressors. We evaluated the utility of this combined approach by quantifying shifts in fish species and trait composition in Lake Erie during the past 50 years (1969-2018) in relation to human-driven changes in nutrient inputs, climate warming, and biological invasions. Species and trait shifts were also compared between two Lake Erie basins, which differ in their environmental and biological characteristics, to identify trait responses that were generalizable across different ecosystems versus those that were context dependent. Our analyses revealed consistent species changes across basins, and shifts in feeding and thermal traits, that were primarily associated with altered nutrient inputs (oligotrophication followed by eutrophication). We found no or inconsistent trait-based evidence for the effects of warming and two invasive fishes. Context-dependent trait responses were also evident; nutrient inputs were related to shifts in species tolerant of turbidity in the shallow, eutrophic western basin, which contrasted to shifts between benthopelagic and benthic species in the deeper central basin. Our results reveal the dominant effects of specific stressors on a large freshwater lake and offer a framework for combining species-based and trait-based approaches to delineate the impacts of simultaneous stressors on communities of perturbed natural ecosystems.