Does Atmospheric NO3 Deposition Alter Actinobacterial Abundance and Community Composition in a Northern Hardwood Forest Ecosystem?

Atmospheric nitrogen deposition can alter the cycling of carbon in forest ecosystems by slowing the microbially mediated decay of plant detritus, leading to the accumulation of organic matter in surface soil and the greater leaching of dissolved organic carbon (DOC) to ground and surface waters. However, we presently do not understand the microbial mechanisms affected by atmospheric nitrogen deposition that regulate these biogeochemical responses. Actinobacteria are one of the few groups of saprotrophic soil microorganisms which degrade lignin, uniquely producing soluble polyphenolics which can accumulate in the soil. The overall objective of this study was to examine the impact of atmospheric NO3 - deposition on actinobacterial community composition and subsequent effects on soil carbon cycling. To address this objective, actinobacterial community structure was quantified in a large-scale field study in which atmospheric NO3 - deposition has been experimentally increased for over a decade. Actinobacterial abundance was assessed using quantitative PCR of 16S rDNA and community composition was assessed though the compilation of clone libraries. Experimental atmospheric NO3 - deposition had no effect on actinobacterial relative abundance in either forest floor or surface mineral soil. However, there were significant differences in community structure and the relative occurrence of key lignin degrading actinobacteria families. Specifically, Streptomycetaceae and Micromonosporaceae, decreased in occurrence under experimental NO3 - deposition in the surface soil, whereas the occurrence of Streptomycetaceae in the forest floor increased under experimental NO3 - deposition. Changes in the actinobacterial community composition appear to be one mechanism contributing to the ecosystem-level biogeochemical changes in response to increased nitrate deposition.Master of ScienceNatural Resources and EnvironmentUniversity of Michiganhttp://deepblue.lib.umich.edu/bitstream/2027.42/60560/3/SDEFigure4.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/60560/2/SDEFigure3.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/60560/1/SDEThesis8_11_08.pd

Dispersal limitation and the assembly of soil Actinobacteria communities in a long‐term chronosequence

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90536/1/ECE3_210_sm_suppmat.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/90536/2/ece3.210.pd

Vignette 14: Eelgrass Wasting Disease

Rising seawater temperatures can increase the risk of disease outbreaks in many taxa. Pathogens are potentially the ultimate keystone species in that their small biomass can have massive impacts that ripple through ecosystems. Disease outbreaks can be particularly damaging when they affect ecosystem engineers, such as seagrasses. Outbreaks of wasting disease in seagrasses are one of a myriad of stressors associated with declining temperate and tropical seagrass meadows around the globe. Levels of eelgrass wasting disease are high in the San Juan Islands and Puget Sound. These increasing levels of disease are a threat to sustainability of eelgrass meadows, our most valuable marine habitat

Deeper habitats and cooler temperatures moderate a climate-driven seagrass disease

Eelgrass creates critical coastal habitats worldwide and fulfills essential ecosystem functions as a foundation seagrass. Climate warming and disease threaten eelgrass, causing mass mortalities and cascading ecological impacts. Subtidal meadows are deeper than intertidal and may also provide refuge from the temperature-sensitive seagrass wasting disease. From cross-boundary surveys of 5761 eelgrass leaves from Alaska to Washington and assisted with a machine-language algorithm, we measured outbreak conditions. Across summers 2017 and 2018, disease prevalence was 16% lower for subtidal than intertidal leaves; in both tidal zones, disease risk was lower for plants in cooler conditions. Even in subtidal meadows, which are more environmentally stable and sheltered from temperature and other stressors common for intertidal eelgrass, we observed high disease levels, with half of the sites exceeding 50% prevalence. Models predicted reduced disease prevalence and severity under cooler conditions, confirming a strong interaction between disease and temperature. At both tidal zones, prevalence was lower in more dense eelgrass meadows, suggesting disease is suppressed in healthy, higher density meadows. These results underscore the value of subtidal eelgrass and meadows in cooler locations as refugia, indicate that cooling can suppress disease, and have implications for eelgrass conservation and management under future climate change scenarios

A tale of two sea stars: recovery (ochre star) or endangerment (sunflower star) following the 2014 epidemic

During the summers of 2013 and 2014, populations of sea stars along the west coast from Alaska to Mexico were decimated by the sea star wasting disease (SSWD) epizootic. Two of the most highly affected species along this range are Pisaster ochraceus (the ochre star), the most common intertidal species, and Pycnopodia helianthoides (the sunflower star), the most common subtidal species, both of which are endemic to the western coast of the U.S. For the ochre star, in the San Juan Islands of Washington State, we measured high case fatality rates associated with disease prevalence over 90% during the summer of 2014. Low levels of disease were observed in the summers of 2015, 2016, and 2017. Population levels following the epizootic remain stable but small, and shifted in size structure from larger to smaller stars. At one site, a dramatic increase in both juvenile and adult ochre stars occurred in 2017, giving hope for future recovery. In contrast, the most common subtidal species, the sunflower star, also suffered catastrophic mortality in 2014. However, in this case, Citizen Science Monitoring in all oceanographic basins of the Salish Sea through 2017 shows an extraordinary decimation of this species, with no sign of recovery three years after the SSWD epizootic. Extremely low population size of sunflower stars raises concern about the capacity of this species to recover, as well as to resist other stochastic events in the future

Atmospheric N deposition alters connectance, but not functional potential among saprotrophic bacterial communities

The use of co‐occurrence patterns to investigate interactions between micro‐organisms has provided novel insight into organismal interactions within microbial communities. However, anthropogenic impacts on microbial co‐occurrence patterns and ecosystem function remain an important gap in our ecological knowledge. In a northern hardwood forest ecosystem located in Michigan, USA, 20 years of experimentally increased atmospheric N deposition has reduced forest floor decay and increased soil C storage. This ecosystem‐level response occurred concomitantly with compositional changes in saprophytic fungi and bacteria. Here, we investigated the influence of experimental N deposition on biotic interactions among forest floor bacterial assemblages by employing phylogenetic and molecular ecological network analysis. When compared to the ambient treatment, the forest floor bacterial community under experimental N deposition was less rich, more phylogenetically dispersed and exhibited a more clustered co‐occurrence network topology. Together, our observations reveal the presence of increased biotic interactions among saprotrophic bacterial assemblages under future rates of N deposition. Moreover, they support the hypothesis that nearly two decades of experimental N deposition can modify the organization of microbial communities and provide further insight into why anthropogenic N deposition has reduced decomposition, increased soil C storage and accelerated phenolic DOC production in our field experiment.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/111976/1/mec13224.pd

Tipping the balance: the impact of eelgrass wasting disease in a changing ocean

Infectious disease has the potential to cause devastating damage to valuable marine organisms and habitats. Eelgrass wasting disease (EGWD), caused by the pathogenic protist Labyrinthula zosterae (LZ), has caused mass die-offs in Zostera marina at regional and global scales. Despite this, little is known about the host-pathogen interaction or disease drivers in the Salish Sea. To determine the regional impact of EGWD, we measured summer prevalence and severity in the San Juan Islands, Padilla Bay, Hood Canal, South Puget Sound, and Willapa Bay. We used cultures and quantitative PCR to verify results, measuring LZ load in lesioned tissue from multiple sites. EGWD was present at all 16 sites surveyed, with prevalence ranging from 80% disease prevalence. Recent data suggest water temperature increases the virulence of LZ, indicating possible climate sensitivity. At our sites, water temperatures influenced both EGWD prevalence and severity, suggesting environmental conditions and climate change could impact the eelgrass-LZ relationship and lead to increased virulence. We ran a three-week controlled experiment to examine the impact of LZ infection on eelgrass shoots over time. We exposed half the eelgrass shoots to LZ infection and sampled shoots at seven time points. All exposed shoots showed signs of infection. EGWD severity and lesion number increased through time, corresponding with a measurable decrease in leaf and root growth and increased phenols. Our results show EGWD is widespread in Washington state eelgrass beds and suggests that EGWD severity is positively correlated with water temperature. Furthermore, EGWD has a detrimental effect on eelgrass health, potentially contributing to decreased density and meadow declines. While levels of EGWD in the field are variable, we identified four sites that are experiencing high prevalence. Further research is needed to understand the conditions leading to EGWD outbreaks

Characterizing host-pathogen interactions between Zostera marina and Labyrinthula zosterae

Introduction Seagrass meadows serve as an integral component of coastal ecosystems but are declining rapidly due to numerous anthropogenic stressors including climate change. Eelgrass wasting disease, caused by opportunistic Labyrinthula spp., is an increasing concern with rising seawater temperature. To better understand the host-pathogen interaction, we paired whole organism physiological assays with dual transcriptomic analysis of the infected host and parasite. Methods Eelgrass (Zostera marina) shoots were placed in one of two temperature treatments, 11° C or 18° C, acclimated for 10 days, and exposed to a waterborne inoculation containing infectious Labyrinthula zosterae (Lz) or sterile seawater. At two- and five-days post-exposure, pathogen load, visible disease signs, whole leaf phenolic content, and both host- and pathogen- transcriptomes were characterized. Results Two days after exposure, more than 90% of plants had visible lesions and Lz DNA was detectable in 100% percent of sampled plants in the Lz exposed treatment. Concentrations of total phenolic compounds were lower after 5 days of combined exposure to warmer temperatures and Lz, but were unaffected in other treatments. Concentrations of condensed tannins were not affected by Lz or temperature, and did not change over time. Analysis of the eelgrass transcriptome revealed 540 differentially expressed genes in response to Lz exposure, but not temperature. Lz-exposed plants had gene expression patterns consistent with increased defense responses through altered regulation of phytohormone biosynthesis, stress response, and immune function pathways. Analysis of the pathogen transcriptome revealed up-regulation of genes potentially involved in breakdown of host defense, chemotaxis, phagocytosis, and metabolism. Discussion The lack of a significant temperature signal was unexpected but suggests a more pronounced physiological response to Lz infection as compared to temperature. Pre-acclimation of eelgrass plants to the temperature treatments may have contributed to the limited physiological responses to temperature. Collectively, these data characterize a widespread physiological response to pathogen attack and demonstrate the value of paired transcriptomics to understand infections in a host-pathogen system

Simulated Atmospheric N Deposition Alters Fungal Community Composition and Suppresses Ligninolytic Gene Expression in a Northern Hardwood Forest

High levels of atmospheric nitrogen (N) deposition may result in greater terrestrial carbon (C) storage. In a northern hardwood ecosystem, exposure to over a decade of simulated N deposition increased C storage in soil by slowing litter decay rates, rather than increasing detrital inputs. To understand the mechanisms underlying this response, we focused on the saprotrophic fungal community residing in the forest floor and employed molecular genetic approaches to determine if the slower decomposition rates resulted from down-regulation of the transcription of key lignocellulolytic genes, by a change in fungal community composition, or by a combination of the two mechanisms. Our results indicate that across four Acer-dominated forest stands spanning a 500-km transect, community-scale expression of the cellulolytic gene cbhI under elevated N deposition did not differ significantly from that under ambient levels of N deposition. In contrast, expression of the ligninolytic gene lcc was significantly down-regulated by a factor of 2–4 fold relative to its expression under ambient N deposition. Fungal community composition was examined at the most southerly of the four sites, in which consistently lower levels of cbhI and lcc gene expression were observed over a two-year period. We recovered 19 basidiomycete and 28 ascomycete rDNA 28S operational taxonomic units; Athelia, Sistotrema, Ceratobasidium and Ceratosebacina taxa dominated the basidiomycete assemblage, and Leotiomycetes dominated the ascomycetes. Simulated N deposition increased the proportion of basidiomycete sequences recovered from forest floor, whereas the proportion of ascomycetes in the community was significantly lower under elevated N deposition. Our results suggest that chronic atmospheric N deposition may lower decomposition rates through a combination of reduced expression of ligninolytic genes such as lcc, and compositional changes in the fungal community

Disease surveillance by artificial intelligence links eelgrass wasting disease to ocean warming across latitudes

Ocean warming endangers coastal ecosystems through increased risk of infectious disease, yet detection, surveillance, and forecasting of marine diseases remain limited. Eelgrass (Zostera marina) meadows provide essential coastal habitat and are vulnerable to a temperature-sensitive wasting disease caused by the protist Labyrinthula zosterae. We assessed wasting disease sensitivity to warming temperatures across a 3500 km study range by combining long-term satellite remote sensing of ocean temperature with field surveys from 32 meadows along the Pacific coast of North America in 2019. Between 11% and 99% of plants were infected in individual meadows, with up to 35% of plant tissue damaged. Disease prevalence was 3× higher in locations with warm temperature anomalies in summer, indicating that the risk of wasting disease will increase with climate warming throughout the geographic range for eelgrass. Large-scale surveys were made possible for the first time by the Eelgrass Lesion Image Segmentation Application, an artificial intelligence (AI) system that quantifies eelgrass wasting disease 5000× faster and with comparable accuracy to a human expert. This study highlights the value of AI in marine biological observing specifically for detecting widespread climate-driven disease outbreaks.This work was supported by the National Science Foundation (awards OCE-1829921, OCE-1829922, OCE-1829992, OCE-1829890). This is contribution 104 from the Smithsonian's MarineGEO and Tennenbaum Marine Observatories Network.Peer reviewe