The Impact of Colonizer Plants on Bacterial Community Structure and Function in Early Successional Soils of a Glacial Forefield

Through litter inputs, root exudates, and the resulting changes in soil chemistry, plants directly interact with the soil microbial community. Recent research on plant-microbe interactions suggests that soil microbial community structure and function play an integral role in plant community succession through both positive and negative feedbacks; yet, plant-microbe dynamics along a successional gradient have not been well-studied. My study in the recently exposed soils of the Mendenhall Glacier forefield near Juneau, AK, USA examined the development of microbial communities in coordination with the establishment of the first plants. The Mendenhall Glacier features a perhumid climate, with moist soils throughout the year, and nearby vegetation that serves as a propagule source, facilitating relatively rapid plant colonization. I sampled soils under two different plant species (alder, Alnus sinuata and spruce, Picea sitchensis) and from unvegetated areas. All samples were gathered within a single transect of soils that had been exposed for 6 years. For each sample site soil pH, organic carbon (C), available nitrogen (N), bioavailable (Olsen) Phosphorus (P), microbial biomass C, and nitrogen fixation rates were determined. My research shows specific vegetation type differences in bacterial community structure and the general enrichment of α-Proteobacteria in vegetated soils. Soil nutrient and carbon pools did not correlate with bacterial community composition. Interestingly, although pH did not significantly vary by vegetation type, it was the only parameter that correlated with bacterial community structure. My study revealed a significant correlation between nitrogen fixation rates and bacterial community composition, a feedback with potentially important impacts for the ecology of these environments. Vegetation type explained more variation in differences in bacterial communities than pH, suggesting that plant acidification of soils only partly drive broad shifts in bacterial communities. Plant species-specific differences in bacterial community structure may also relate to the chemical composition of litter and root exudates. Additionally, plant carbon inputs in general likely enhance asymbiotic N-fixer function in these relatively new soils where nitrogen limitations may stifle bacterial growth. My study provides insights into how colonizer plants drive changes in bacterial community structure and function in a glacial forefield, altering bacterial succession and ecosystem development

Microbes as engines of ecosystem function: When does community structure enhance predictions of ecosystem processes?

Microorganisms are vital in mediating the earth\u27s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: \u27When do we need to understand microbial community structure to accurately predict function?\u27 We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology

Microbes as engines of ecosystem function : When does community structure enhance predictions of ecosystem processes?

FUNDING This work was supported by NSF grant DEB-1221215 to DN, as well as grants supporting the generation of our datasets as acknowledged in their original publications and in Supplementary Table S1. ACKNOWLEDGMENT We thank the USGS Powell Center ‘Next Generation Microbes’ working group, anonymous reviews, Brett Melbourne, and Alan Townsend for valuable feedback on this project.Peer reviewedPublisher PD

Toward a Generalizable Framework of Disturbance Ecology Through Crowdsourced Science

© 2021 Graham, Averill, Bond-Lamberty, Knelman, Krause, Peralta, Shade, Smith, Cheng, Fanin, Freund, Garcia, Gibbons, Van Goethem, Guebila, Kemppinen, Nowicki, Pausas, Reed, Rocca, Sengupta, Sihi, Simonin, Słowiński, Spawn, Sutherland, Tonkin, Wisnoski, Zipper and Contributor Consortium.Disturbances fundamentally alter ecosystem functions, yet predicting their impacts remains a key scientific challenge. While the study of disturbances is ubiquitous across many ecological disciplines, there is no agreed-upon, cross-disciplinary foundation for discussing or quantifying the complexity of disturbances, and no consistent terminology or methodologies exist. This inconsistency presents an increasingly urgent challenge due to accelerating global change and the threat of interacting disturbances that can destabilize ecosystem responses. By harvesting the expertise of an interdisciplinary cohort of contributors spanning 42 institutions across 15 countries, we identified an essential limitation in disturbance ecology: the word ‘disturbance’ is used interchangeably to refer to both the events that cause, and the consequences of, ecological change, despite fundamental distinctions between the two meanings. In response, we developed a generalizable framework of ecosystem disturbances, providing a well-defined lexicon for understanding disturbances across perspectives and scales. The framework results from ideas that resonate across multiple scientific disciplines and provides a baseline standard to compare disturbances across fields. This framework can be supplemented by discipline-specific variables to provide maximum benefit to both inter- and intra-disciplinary research. To support future syntheses and meta-analyses of disturbance research, we also encourage researchers to be explicit in how they define disturbance drivers and impacts, and we recommend minimum reporting standards that are applicable regardless of scale. Finally, we discuss the primary factors we considered when developing a baseline framework and propose four future directions to advance our interdisciplinary understanding of disturbances and their social-ecological impacts: integrating across ecological scales, understanding disturbance interactions, establishing baselines and trajectories, and developing process-based models and ecological forecasting initiatives. Our experience through this process motivates us to encourage the wider scientific community to continue to explore new approaches for leveraging Open Science principles in generating creative and multidisciplinary ideas.This research was supported by the U.S. Department of Energy (DOE), Office of Biological and Environmental Research (BER), as part of Subsurface Biogeochemical Research Program’s Scientific Focus Area (SFA) at the Pacific Northwest National Laboratory (PNNL). PNNL is operated for DOE by Battelle under contract DE-AC06-76RLO 1830

Patterns and Processes Underlying Soil Microbial Community Succession

Given the vast diversity of microorganisms and their relevance for environmental and human health, there remains a need to better understand the patterns and processes that fundamentally underlie the structure and function of microbial communities through space and time. In particular, soil bacterial communities are vital to ecosystems and agriculture as they largely control soil fertility, plant community dynamics, and global biogeochemical cycles. To this aim, my dissertation work builds understandings regarding the development of soil microbial communities and their function. First, I demonstrate the paramount role of nutrient limitation in controlling the assembly of autotrophic microbial communities through succession (Chapter 2), based on a nutrient manipulation experiment. This work shows that nitrogen (N) and phosphorous (P) fertilization act as a major control on microbial community succession. In Chapter 3, I examine the connections between environmental, community, and functional properties of microbes in post-fire successional soils. This work builds empirical evidence that relationships between resource environment and ecosystem function shift in relative strength across succession. This work also suggests the role of rRNA operon copy number as a trait that varies across succession and may serve future research in describing processes of microbial community assembly that connect environment, trait, and function. In Chapter 4, I continue to examine plant-microbe interactions, assessing how post-fire revegetation processes may drive post-fire secondary succession with implications for ecosystem function. This work also reveals that the abiotic context of the post-fire landscape may impact when and to what extent biotic factors, such as plant-microbe interactions, matter in structuring microbial communities and their function. The Appendix provides additional research that describes plant-microbe interactions in succession, assessing how the plant root environment may select for particular bacteria in early succession that range in generalist to specialist character. Overall, my work builds knowledge on the controls that may underlie changes in microbial community structure and function through succession, spanning a variety of scales including traits, communities, and ecosystem processes. My work advances our knowledge of how microbial communities assemble through succession and the resulting patterns in their composition and function, which can have immense implications for humans to ecosystems

Soil bacterial community structure remains stable over a five-year chronosequence of insect-induced tree mortality

Extensive tree mortality from insect epidemics has raised concern over possible effects on soil biogeochemical processes. Yet despite the importance of microbes in biogeochemical processes, how soil bacterial communities respond to insect-induced tree mortality is largely unknown. We examined soil bacterial community structure (via 16S rRNA pyrosequencing) and community assembly processes (via null deviation analysis) along a five-year chronosequence (substituting space for time) of bark beetle-induced tree mortality in the southern Rocky Mountains, USA. We also measured soil microbial biomass and soil chemistry, and used in situ experiments to assess inorganic nitrogen mineralization rates. We found that bacterial community structure and assembly―which was strongly influenced by stochastic processes―were largely unaffected by tree mortality despite increased soil ammonium (NH4+) pools and reductions in soil nitrate (NO3-) pools and net nitrogen mineralization rates after tree mortality. Linear models suggested that microbial biomass and bacterial phylogenetic diversity are significantly correlated with nitrogen mineralization rates of this forested ecosystem. However, given the overall resistance of the bacterial community to disturbance from tree mortality, soil nitrogen processes likely remained relatively stable following tree mortality when considered at larger spatial and longer temporal scales—a supposition supported by the majority of available studies regarding biogeochemical effects of bark beetle infestations in this region. Our results suggest that soil bacterial community resistance to disturbance helps to explain the relatively weak effects of insect-induced tree mortality on soil N and C pools reported across the Rocky Mountains, USA

Oligotrophic wetland sediments susceptible to shifts in microbiomes and mercury cycling with dissolved organic matter addition

Recent advances have allowed for greater investigation into microbial regulation of mercury toxicity in the environment. In wetlands in particular, dissolved organic matter (DOM) may influence methylmercury (MeHg) production both through chemical interactions and through substrate effects on microbiomes. We conducted microcosm experiments in two disparate wetland environments (oligotrophic unvegetated and high-C vegetated sediments) to examine the impacts of plant leachate and inorganic mercury loadings (20 mg/L HgCl2) on microbiomes and MeHg production in the St. Louis River Estuary. Our research reveals the greater relative capacity for mercury methylation in vegetated over unvegetated sediments. Further, our work shows how mercury cycling in oligotrophic unvegetated sediments may be susceptible to DOM inputs in the St. Louis River Estuary: unvegetated microcosms receiving leachate produced substantially more MeHg than unamended microcosms. We also demonstrate (1) changes in microbiome structure towards Clostridia, (2) metagenomic shifts toward fermentation, and (3) degradation of complex DOM; all of which coincide with elevated net MeHg production in unvegetated microcosms receiving leachate. Together, our work shows the influence of wetland vegetation in controlling MeHg production in the Great Lakes region and provides evidence that this may be due to both enhanced microbial activity as well as differences in microbiome composition

Soil bacterial community structure remains stable over a 5-year chronosequence of insect-induced tree mortality

Extensive tree mortality from insect epidemics has raised concern over possible effects on soil biogeochemical processes. Yet despite the importance of microbes in nutrient cycling, how soil bacterial communities respond to insect-induced tree mortality is largely unknown. We examined soil bacterial community structure (via 16S rRNA gene pyrosequencing) and community assembly processes (via null deviation analysis) along a 5-year chronosequence (substituting space for time) of bark beetle-induced tree mortality in the southern Rocky Mountains, USA. We also measured microbial biomass and soil chemistry, and used in situ experiments to assess inorganic nitrogen mineralization rates. We found that bacterial community structure and assembly-which was strongly influenced by stochastic processes-were largely unaffected by tree mortality despite increased soil ammonium ([Formula: see text]) pools and reductions in soil nitrate ([Formula: see text]) pools and net nitrogen mineralization rates after tree mortality. Linear models suggested that microbial biomass and bacterial phylogenetic diversity are significantly correlated with nitrogen mineralization rates of this forested ecosystem. However, given the overall resistance of the bacterial community to disturbance from tree mortality, soil nitrogen processes likely remained relatively stable following tree mortality when considered at larger spatial and longer temporal scales-a supposition supported by the majority of available studies regarding biogeochemical effects of bark beetle infestations in this region. Our results suggest that soil bacterial community resistance to disturbance helps to explain the relatively weak effects of insect-induced tree mortality on soil N and C pools reported across the Rocky Mountains, USA

Interspecific Plant Interactions Reflected in Soil Bacterial Community Structure and Nitrogen Cycling in Primary Succession

Past research demonstrating the importance plant–microbe interactions as drivers of ecosystem succession has focused on how plants condition soil microbial communities, impacting subsequent plant performance and plant community assembly. These studies, however, largely treat microbial communities as a black box. In this study, we sought to examine how emblematic shifts from early successional Alnus viridus ssp. sinuata (Sitka alder) to late successional Picea sitchensis (Sitka spruce) in primary succession may be reflected in specific belowground changes in bacterial community structure and nitrogen cycling related to the interaction of these two plants. We examined early successional alder-conditioned soils in a glacial forefield to delineate how alders alter the soil microbial community with increasing dominance. Further, we assessed the impact of late-successional spruce plants on these early successional alder-conditioned microbiomes and related nitrogen cycling through a leachate addition microcosm experiment. We show how increasingly abundant alder select for particular bacterial taxa. Additionally, we found that spruce leachate significantly alters the composition of these microbial communities in large part by driving declines in taxa that are enriched by alder, including bacterial symbionts. We found these effects to be spruce specific, beyond a general leachate effect. Our work also demonstrates a unique influence of spruce on ammonium availability. Such insights bolster theory relating the importance of plant–microbe interactions with late-successional plants and interspecific plant interactions more generally

Rapid Shifts in Soil Nutrients and Decomposition Enzyme Activity in Early Succession Following Forest Fire

While past research has studied forest succession on decadal timescales, ecosystem responses to rapid shifts in nutrient dynamics within the first months to years of succession after fire (e.g., carbon (C) burn-off, a pulse in inorganic nitrogen (N), accumulation of organic matter, etc.) have been less well documented. This work reveals how rapid shifts in nutrient availability associated with fire disturbance may drive changes in soil enzyme activity on short timescales in forest secondary succession. In this study, we evaluate soil chemistry and decomposition extracellular enzyme activity (EEA) across time to determine whether rapid shifts in nutrient availability (1–29 months after fire) might control microbial enzyme activity. We found that, with advancing succession, soil nutrients correlate with C-targeting β-1,4-glucosidase (BG) EEA four months after the fire, and with N-targeting β-1,4-N-acetylglucosaminidase (NAG) EEA at 29 months after the fire, indicating shifting nutrient limitation and decomposition dynamics. We also observed increases in BG:NAG ratios over 29 months in these recently burned soils, suggesting relative increases in microbial activity around C-cycling and C-acquisition. These successional dynamics were unique from seasonal changes we observed in unburned, forested reference soils. Our work demonstrates how EEA may shift even within the first months to years of ecosystem succession alongside common patterns of post-fire nutrient availability. Thus, this work emphasizes that nutrient dynamics in the earliest stages of forest secondary succession are important for understanding rates of C and N cycling and ecosystem development