News & Media
Microbial diversity influences nitrogen cycling in rivers
Seasonal changes affect microbiome communities, genes, and subsurface biogeochemical pathways differently
DOE researchers investigated the role of microbial genetic diversity in two major subsurface biogeochemical processes: nitrification and denitrification. Results show that across different seasons only a few microbe species, namely Nitrosoarchaeum, carry out nitrification functions—demonstrating high resistance to environmental change. However, denitrification genes, which are more broadly distributed in the community, displayed a variety of diversity patterns and abundance dynamics—demonstrating greater microbial interactions as conditions change.
There is little research connecting microbiomes at the genetic level to hydrobiogeochemical modeling. This research helps broaden collective knowledge for a better understanding of the pathways affected by environmental changes. For example, under extreme environmental conditions an entire biochemical pathway could be altered or eliminated if a single step has low genetic diversity such that its loss could not be replaced.
The Pacific Northwest National Laboratory research team, led by Bill Nelson, found that major environmental processes—specifically nitrification and denitrification—are maintained through a variety of diversity strategies. Historically, the bulk of biogeochemical research has focused on microbial communities at the organismal level. But this research focused on the importance of genetic distribution and diversity.
In their recent PLoS ONE paper, the researchers discuss the roles microbes play in ecological functions; the novelty of the genetic makeup of these microbes; and future research opportunities to determine which organisms are genetically expressing nitrogen cycling functions.
The novelty of this study comes from examining the temporal dynamics of diversity at the gene level. To evaluate all genes in the nitrification and denitrification pathways, novel Hidden Markov Models (HMMs) were developed that can recognize the broad diversity found in environmental samples. They found that while different environmental conditions impair microbiome growth and the gene expression of some populations, at the same time, it can stimulate others. High biodiversity at the organism or genetic level creates more resiliency, and the microbiome community can respond more rapidly to environmental changes.
Bill Nelson, Pacific Northwest National Laboratory, William.Nelson@pnnl.gov
This research was supported by the U.S. Department of Energy (DOE), Office of Biological and Environmental Research (BER), as part of the Subsurface Biogeochemical Research Scientific Focus Area (SFA) at Pacific Northwest National Laboratory (PNNL).
W.C. Nelson, E.B. Graham, A.R. Crump, S.J. Fansler, E.V. Arntzen, D.W. Kennedy, J.C. Stegen, “Distinct temporal diversity profiles for nitrogen cycling genes in a hyporheic microbiome”. PLoS ONE 15(1) e0228165 (2020). [DOI: 10.1371/ journal.pone.0228165]
Peeking Into the Lives of Soil Microbiomes
SoilBox provides in-depth imaging and characterization of soil microbial communities in their native environments.
To better characterize the vast diversity of soil microbes and their interactions, DOE researchers developed a high-tech simulated soil core called SoilBox. This 16.7-centimeter-deep box allows researchers to visualize soil microbes’ complex interactions using different imaging methods and facilitating, for the first time, visualization of the soil microbiome’s organization and community metabolism. Furthermore, SoilBox provides a tool for researchers to observe how soil microbial communities respond to environmental changes and perturbations.
The complexity of soil makes spatial imaging of soil microbial communities challenging. Using SoilBox, researchers can now visualize the diversity and metabolic
landscape of the soil microbiome under different environmental conditions, such as soil moisture and temperature. Understanding the basic biology of the soil microbiome is necessary for understanding how native soil systems respond to environmental perturbations such as drought, lack of nutrients, and fire.
Soil-dwelling microbes are key players in the overall health of soil ecosystems, performing critical functions like carbon and nutrient cycling. The interplay between the soil microbiome and the soil it inhabits is a dynamic relationship heavily influenced by factors such as soil acidity, organic content, and temperature. The size and distribution of soil particles also affects many soil characteristics, adding to the already complex challenge of accurately describing structure-function relationships of soil microbial communities.
To address the difficulties of studying the soil microbiome in its native state and at a microscale resolution, a team of researchers from Pacific Northwest National Laboratory, led by Arunima Bhattacharjee and Chris Anderton, developed SoilBox. This system represents a soil ecosystem by simulating an ~12-cm-deep soil core; several windows facilitate molecular and optical imaging measurements that are crucial to understanding the nuanced interactions between the soil microbiome and its environment. This novel imaging capability allows scientists to study the dynamic landscape of soil microbial communities as they relate to environmental changes, including nutrient cycling.
This work overcomes the challenge of visualizing the diversity of soil microbial communities in the complex and ever-changing environment of soil. SoilBox will be used in the near future to investigate soil microbial community dynamics.
Chris Anderton, Pacific Northwest National Laboratory, email@example.com
This research was supported by the Department of Energy (DOE) Office of Biological and Environmental Research (BER) and is a contribution of the Scientific Focus Area "Phenotypic response of the soil microbiome to environmental perturbations." Pacific Northwest National Laboratory (PNNL) is operated for the DOE by Battelle Memorial Institute under Contract DE-AC05-76RLO1830. A portion of the research was performed using EMSL, the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility sponsored by BER and located at PNNL.
A. Bhattacharjee et al.,“Visualizing microbial community dynamics via a controllable soil environment.” mSystems 5, 1:e00645-19 (2020). https://doi.org/10.1128/mSystems.00645-19.
Protecting climate-sensitive soil ecosystems
Review paper summarizes the effects of climate change on soil microorganisms and the ecosystem services they provide, and evaluates potential mitigation measures.
Researchers from Pacific Northwest National Laboratory reviewed the current state of knowledge about the impacts of climate change on soil microorganisms in different climate-sensitive soil ecosystems. They also examined the possibilities of using soil microorganisms to store carbon or inoculate plants to help mitigate the negative consequences of climate change. Based on their review, the authors recommend an integrated approach that combines beneficial properties of soil microorganisms with sustainable soil management practices to support plant production, maintain a clean water supply, sustain biodiversity, store carbon, and increase resilience in the face of a changing climate.
The effects of climate change on soil microbial communities have potentially large consequences for Earth's soil ecosystems and the beneficial services that soil microbiomes provide. This review highlights the need to connect the fine-scale details arising from microbiome studies to the landscape-scale resolution of many Earth system climate models in the search for climate change mitigation measures.
On Earth’s terrestrial surface, the soil microbiome cycles nutrients to sustain plant and animal life. While this microbial community is innately connected to environmental conditions, impacts on the soil microbiome due to climate change vary depending on the ecosystem. Different aspects of climate change impact soil microbial communities and their important ecosystem functions, such as cycling of carbon and supporting plant growth. But the molecular details of soil biochemical reactions responsible for these key functions are largely unknown.
Researchers synthesized existing knowledge of climate change impacts across a range of soil environments—permafrost, forests, grassland, wetlands, and deserts—to examine how the microbiome responds. They looked at microbial changes coinciding with different climate change variables including increases in carbon dioxide levels, temperatures, drought, flooding, and fires. Their review showed that microbial physiology largely determines the ability of soil ecosystems to adapt, and that some microbiomes may be suitable for climate change mitigation measures such as carbon sequestration and promoting plant growth. The review sets the stage for future research on soil microbiomes and challenges to overcome in order to connect to larger-scale predictive models of climate change.
Janet Jansson, Lab Fellow, firstname.lastname@example.org
Kirsten Hofmockel, Earth Scientist, email@example.com
This research was supported by the Department of Energy Office of Biological and Environmental Research (BER) Genomic Science Program and is a contribution of the Scientific Focus Area "Phenotypic response of the soil microbiome to environmental perturbations." PNNL is operated for DOE by Battelle Memorial Institute under Contract DE-AC05-76RLO1830. A portion of the research was performed using the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility sponsored by BER and located at PNNL.
Nutrient-Hungry Peatland Microbes Reduce Carbon Loss Under Warmer Conditions
Enzyme production in peatlands reduces carbon lost to respiration under future high temperatures.
As atmospheric temperatures and carbon dioxide concentrations rise, photosynthesis by plants is expected to increase, leading to more photosynthate released by roots to the soil microbial community. Researchers from Pacific Northwest Northwest National Laboratory and Iowa State University examined the response of boreal peatland soils under future high temperatures. The team found that the peatland’s soil microbial communities allocated more carbon to enzyme production in search of phosphorus as temperatures climbed. This diversion of carbon resources could reduce future carbon losses by microbial respiration from the peatland.
As boreal peatlands face warmer and drier conditions, it is expected that more carbon will be lost from these carbon-rich soils through increased microbial activity. This study showed that enhanced respiration and concomitant loss of carbon is potentially constrained by nutrient demands of the microorganisms. This tradeoff may help the peatland ecosystem retain soil carbon as temperatures warm.
Root exudates are carbon compounds, such as sugars and organic acids, which are easily consumed by soil microorganisms. With a warming climate, science suggests that increased photosynthesis by plants could lead to more photosynthate released as root exudates to the soil microbial community. To examine this question, researchers used laboratory incubations to control both temperature and moisture and simulate belowground substrate additions under an accelerated growing season. Results showed that with a moderate increase in temperature, the addition of common root exude compounds in peatlands initially increased carbon lost through microbial respiration above those treatments receiving water only. However, when pushed to future expected high temperatures, additional exudate compounds dampened the amount of additional carbon respired as compared to treatments receiving water only. This reduction in respiration suggests the microorganisms allocated carbon compounds to enzyme production to mine for limited resources instead of respiring carbon. The data also support the idea that boreal peatland microbial communities maintain a more narrow range in function, measured as respiration, across a range in climate conditions. A wide climatic niche in addition to reallocation of carbon resources dampens the magnitude of change in carbon respiration with increasing temperatures.
Biological and Environmental Scienes Directorate
This material is based upon work supported by the US Department of Energy, Office of Science, Office of Biological and Environmental Research, Terrestrial Ecosystem Science (TES) Program, under grant ER65430 to Iowa State University.
Diversity and Function Within Soil Microbial Communities
How spatial structures of soil microorganisms change across years and seasons, reveal the ecological impact of varying management practices.
The microbial communities within the loose, friable aggregations of organic and mineral components in soil are highly organized spatially, shaped in part by the structure of the soil itself. A recent paper by senior author Kirsten Hofmockel of Pacific Northwest National Laboratory, and two coauthors, examines the spatio-temporal dynamics of microbial communities within soil aggregates. Their aim was to gauge the impact of changes in environmental factors, plant phenology, and aggregate turnover, to understand how varying management practices affect the ecology of soil microbial communities.
Analyzing microaggregates in soil can help researchers better understand the potential diversity and functioning of soil microbial communities. This information is vital in the development of a predictive understanding of soil ecosystem responses to climatic events and environmental change. In addition, land management services can use this data to enhance biodiversity and soil ecosystem services.
Greater biodiversity across all trophic levels can benefit many ecosystems. Biodiversity creates more resilience to abiotic stressors, increases ecosystem services, and promotes sustainability. Within soil systems microbial diversity alone maintains nutrient cycling, impacts plant productivity, enhances drought tolerance, and determines soil health and fertility.
However, the ecological sources of microbial biodiversity, including niche space partition, are not clearly defined at a microbial scale. The Hofmockel study, conducted with lead author Racheal Upton of Iowa State University and Elizabeth Bach of Colorado State University, helps close that knowledge gap by investigating how the spatial structure of microorganisms is vital to understanding the impact of microbial ecology on ecosystem and biogeochemical services.
Historically, researchers have examined microbial diversity in soils at ecosystem or landscape scales. This study, however, shows the importance of scaling such studies to a microbially relevant level. The researchers chose soil aggregate fractions as a way to represent that needed microbially relevant scale.
Over years and seasons, soil aggregate turnover means that soil microbial habitats are dynamic over time. The researchers used data from soil aggregate fractions in three different bioenergy management systems to investigate seasonal and annual changes in discrete microbial communities.
Such research is pertinent to evaluating how different management practices impact spatially discrete microbial communities in soil. Management practices that increase plant diversity across growing seasons, the authors demonstrate, influence soil aggregate habitats and therefore increase microbial diversity.
For other researchers, the study underscores the importance of including both spatial and temporal dynamics in their investigations in order to fully understand microbial community assembly and persistence in soil.
Pacific Northwest National Laboratory
U.S. Department of Energy, award number DESC0010775.
R.N. Upton, E.M. Bach, K.S. Hofmockel. “Spatio-temporal microbial community dynamics within soil aggregates.” Soil Biology and Biochemistry 132 (2019) 58-68.
Drought Spells Changes for Soil Microbes
Researchers found that soil drying altered metabolic pathways within soil microbial communities.
Researchers at the U.S. Department of Energy’s Pacific Northwest National Laboratory and Kansas State University found that soil drying significantly affected the structure and function of soil microbial communities.
A warming Earth is predicted to result in increased drought extent and intensity in the highly fertile and productive grasslands of the central United States. These soils store large reserves of carbon. The decrease in soil moisture due to drought has largely unknown consequences on soil carbon cycling and other key biogeochemical cycles carried out by soil microbiomes. Researchers at the U.S. Department of Energy’s Pacific Northwest National Laboratory and Kansas State University found that soil drying significantly affected the structure and function of soil microbial communities. This included shifts in expression of specific metabolic pathways, such as those leading toward the production of compounds that build up within cells to keep microbes alive during drought.
This study demonstrates the application of a multi-omics approach to decipher details of the soil microbial community’s metaphenomic response to environmental change. The approach should apply to studies of other complex microbial systems as well. This research supports the Genomic Science mission by revealing fundamental principles that guide the interpretation of the genetic code into functional proteins, metabolic pathways, and the metabolic/regulatory networks underlying the systems biology of microbial communities. Advancing fundamental knowledge of these systems will enable understanding of the role of biological systems in the environment and how environmental change affects soil microbial communities.
Warming temperatures are causing shifts in precipitation patterns in the central grasslands of the United States, with largely unknown consequences on the collective physiological responses of the soil microbial community, i.e., the metaphenome. In this study, researchers used an untargeted omics approach to determine the soil microbial community’s metaphenomic response to soil moisture and to define specific metabolic signatures of the response. Specifically, they aimed to develop the technical approaches and metabolic mapping framework necessary for future systematic ecological studies.
The research team collected soil from three locations at a field station in Kansas, incubated the samples for 15 days under dry or wet conditions, and compared them to field-moist controls. The team determined the microbiome response to wetting or drying through 16S rRNA amplicon sequencing, metatranscriptomics, and metabolomics. Researchers then assessed the resulting shifts in taxa, gene expression, and metabolites. Soil drying resulted in significant shifts in both the composition and function of the soil microbiome, such as changes in metabolic pathways that lead toward the production of sugars and other osmoprotectant compounds. By contrast, few changes occurred after wetting. The team used the combined metabolic and metatranscriptomic data to generate metabolite-reaction networks to determine the metaphenomic response to soil moisture transitions, such as generation of trehalose under dry conditions. Using this approach, researchers showed that despite the high complexity of the soil habitat, it is possible to generate insight into the effect of environmental change on the soil microbiome and its physiology and functions, thus laying the groundwork for future, targeted studies.
Pacific Northwest National Laboratory
This research was supported by the Department of Energy Office of Biological and Environmental Research (BER) and is a contribution of the Scientific Focus Area “Phenotypic response of the soil microbiome to environmental perturbations.” This research was also supported by Environmental Molecular Sciences Laboratory (EMSL) open call proposal number 48784, Dissecting and Deciphering of the Soil Microbiome. EMSL is a U.S. Department of Energy (DOE) Office of Science user facility sponsored by the DOE’s Office of Biological and Environmental Research and located at PNNL. A portion of the research was conducted using PNNL Institutional Computing (PIC) resources and partially supported by the Microbiomes in Transition Initiative under the Laboratory Directed Research and Development Program at PNNL. PNNL is a multiprogram national laboratory operated by Battelle for the U.S. DOE under contract DE-AC05-76RL01830.
T. Roy Chowdhury, J.- Y. Lee, E.M. Bottos, C.J. Brislawn, R.A. White III, L.M. Bramer, J. Brown, J.D. Zucker, Y.-M. Kim, A. Jumpponen, C.W. Rice, S.J. Fansler, T.O. Metz, L.A. McCue, S.J. Callister, H.-S. Song, J.K. Jansson, “Metaphenomic Responses of a Native Prairie Soil Microbiome to Moisture Perturbations.” mSystems 4(4), e00061-19 (2019). [DOI: 10.1128/mSystems.00061-19]
Predicting Neighbor-Dependent Microbial Interactions
A new microbial network inference method reliably predicts interactions dependent on neighboring organisms
Soil microbial communities are made of networks of interacting species that dynamically reorganize in a changing environment. Understanding how such microbiomes are organized in nature is important for designing or controlling them in the future. Meanwhile, soil ecologists know well that some microbial interactions change because of neighboring species—so-called context-dependent interactions. Yet no theoretical framework, until now, has been available to address this phenomenon. In a new paper, researchers from PNNL’s computational biology and bioinformatics group proposed a method that reliably predicts how the modulation of interactions occurs in microbial communities subject to membership changes. The method, called minimal interspecies interaction adjustment (MIIA), addresses the problem of such context-dependent microbial interactions by accurately predicting dramatic shifts in microbial control of carbon and nitrogen cycles in the environment.
By providing unprecedented predictions of neighbor-dependent interactions, the new computational method significantly improves our understanding of microbial network reorganization. This method will also enable the rational design and engineering of microbial consortia and natural communities.
Microbial community dynamics in soil and other habitats involve nonlinear interspecies interactions, so these dynamics are notoriously difficult to predict. Yet understanding how such microbiomes are organized in nature is necessary for designing them (such as for biofuel production) and for controlling them—for example, as a way to assure that soils do not emit too much carbon into the Earth’s atmosphere. Meanwhile, ecologists know that interactions in microbial communities are influenced by neighboring species. Until now, however, there has been no theoretical framework for predicting such context-dependent microbial interactions.
The research was motivated by the following fundamental ecological questions: How are interspecies interactions modulated by shifts in community composition and species populations? And to what extent can interspecies relationships observed in simple cultures be translated into complex communities?
The researchers addressed these questions by demonstrating that MIIA enables microbial interactions in binary cultures to be translatable into complex communities. The researchers also demonstrated the utility of this method in designing and engineering microbial consortia. In this regard, they found that microbial interactions can be significantly modulated when perturbed by a small number of neighboring species—but that the level of modulation diminishes as the number of new neighboring species increases.
This work, the authors say, can also be applied to questions of community ecology beyond microbes. It may provide a theoretical platform for better understanding all biological interaction systems, including human interactions.
PNNL Principal Investigator
Pacific Northwest National Laboratory
This research was supported by the U.S. Department of Energy (DOE) Office of Biological and Environmental Research (BER), as part of Foundational Scientific Focus Area (SFA), Soil Microbiome SFA, and Subsurface Biogeochemistry Research (SBR) SFA at the Pacific Northwest National Laboratory (PNNL).
H-S. Song, J-Y. Lee, S. Haruta, W.C. Nelson, D-Y. Lee, S.R. Lindemann, J.K. Fredrickson, and H.C. Bernstein,”Minimal Interspecies Interaction Adjustment (MIIA): Inference of Neighbor-Dependent Interactions in Microbial Communities,” Frontiers in Microbiology (2019). [DOI: 10.3389/fmicb.2019.01264]