Progress 06/01/21 to 05/31/22
Outputs
Target Audience:Target audience is colleague scientists who are studying microbial traits in soil communities Changes/Problems:We have been awarded an EMSL and JGI user proposal to test new approaches for the metabolic flux analysis technique that was used in this NIFA project. We will use the same soil as used for the metagenome and metatranscriptome study (agricultural soil) to test whether incorporation of position-specific 13C-labeled glucose can be determined using high precision metabolomics, proteomic and lipidomic techniques What opportunities for training and professional development has the project provided?Two PhD students were employed on this project. One is slated to graduate in the spring of 2022, while the other student still has at least one year to go before graduation. Additionally, the approaches to analyze metagenomes and metatranscriptomes have been communicated to other interested students within our lab. How have the results been disseminated to communities of interest?Yes, the results of research have been disseminated via international journals. What do you plan to do during the next reporting period to accomplish the goals?The next reporting period will be short as the project is finished (money-wise). The thesis of one student and submission of several other papers are expected to occur in the next period
Impacts
What was accomplished under these goals?
goal 1) we discovered that the metabolic pathways used to process glucose differ between soils. Some soils are dominated by Embden-Meyerhof-Parnas glycolysis, while others are dominated either by Entner-Doudoroff and/or pentose phosphate pathways. We also developed theory on how the biochemical and carbon use efficiencies of communities are related, and that in general biochemical effficiencies in soil communities is high. We also developed a method using position-specific PLFA analysis that allowed us to demonstrate experimentally that differences in metabolic flux patterns and biochemical efficiency exists within an intact soil microbial community. goal 2) We observed large changes in gene-expression of the N cycling genes in response to a glucose addition. We furthermore demonstrated large responses for especially, but not limited to, the N transporters. We also show changes in various other metabolic modules and life history traits in response to a sugar addition. Finally, we have analyzed, using public datasets how genomic traits in soils vary, correlate to ecosystem properties such as soil pH and C:N ratio, and differ from relationships between genomic traits for ocean, high temperature and host-associated environments. These differences in genomic traits are most likely a response to selection pressures in the soil environment, but may to an unknown degree also be caused by community assembly processes. Additionally, we showed that gene-expression of soil communities responds rapidly (30 min) to a heat shock, where especially the heat shock chaperone proteins increase in abundances.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Dijkstra P, Martinez A, Thomas SC, Seymour CO, Wu W, Dippold MA, Megonigal JP, Schwartz E, Hungate BA (2022) On maintenance and metabolisms in soil microbial communities. Plant and Soil. doi: 10.1007/s11104-022-05382-9.
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Chuckran PF, Fofanov V, Hungate BA, Morrissey EM, Schwartz E, Walkup J, Dijkstra P (2021a) Rapid Response of Nitrogen Cycling Gene Transcription to Labile Carbon Amendments in a Soil Microbial Community. mSystems 6. doi: 10.1128/mSystems.00161-21
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Chuckran PF, Hungate BA, Schwartz E, Dijkstra P (2021c) Variation in genomic traits of microbial communities among ecosystems. FEMS Microbes 2. doi: 10.1093/femsmc/xtab02010.1101/2021.04.05.438506
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Wu W, Dijkstra P, Dippold MA (2020) 13C analysis of fatty acid fragments by gas chromatography mass spectrometry for metabolic flux analysis. Geochimica et Cosmochimica Acta 284: 92-106. doi: https://doi.org/10.1016/j.gca.2020.05.032.
- Type:
Journal Articles
Status:
Other
Year Published:
2022
Citation:
Neri U, Wolf YI, Roux S, Camargo AP, Lee B, Kazlauskas D, Chen IM, Ivanova N, Allen LZ, Paez-Espino D, Bryant DA, Bhaya D, Consortium RVD, Krupovic M, Dolja VV, Kyrpides NC, Koonin EV, Gophna U (2022) A five-fold expansion of the global RNA virome reveals multiple new clades of RNA bacteriophages. bioRxiv: 2022.2002.2015.480533. doi: 10.1101/2022.02.15.480533.
|
Progress 06/01/17 to 05/31/22
Outputs
Target Audience:
Nothing Reported
Changes/Problems:This is the Final Report and no changes are reported What opportunities for training and professional development has the project provided?The project has provided research opportunities for two PhD students, and within the context of the laboratory, opportunities for other students to familiarize themselves with the technqiues of metagenome and metatranscriptome analyses. How have the results been disseminated to communities of interest?Yes. The project has yielded nine published publications, four publications in review and at least one in preparation. It is likely that the dataset generated in this project will be re-utilized to analyze other aspects of microbial functioning in the near future. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
In this project, we have studied how microbial metabolism respond to a change in carbon availability. We have applied two new tools to study microbial responses: 1) metabolic flux analysis (using position-specific labeled glucose to identify the activities of the glycolysis, TCA cycle, pentose phosphate pathway, entner-doudoroff pathway and biochemical efficiency - Dijkstra et al 2011 - SBB 2011, 43: 1848-1857), and 2) metagenomes and metatranscriptomes. We applied these techniques to agricultural, rangeland and forest soils. Using a forest soil, we showed that the biochemical efficiency of microbes is high, and not affected by a large glucose addition (Geyer et al 2019). This high biochemical efficiency under varying C additions is contrasted with the response of the C use efficiency, which is strongly affected. This demonstrates that especially microbial turnover (grazing, predation) and perhaps allocation is affected by C addition. The differences between biochemical efficiency and C use efficiency is further explored in Dijkstra et al (2022). Using a forest, rangeland and marsh soil, we showed for the first time that the activity of the main metabolic pathways of the central C metabolic network varies across biomes: we observed high activity of glycolysis in a anoxic marsh soil, high activity of the pentose phosphate pathway in a rangeland soil, and a mix of activities of pentose phosphate and Entner-Doudoroff pathway in a high elevation forest soil (Dijkstra et al 2022). Furthermore, we argued that the high activity of the pentose phosphate and Entner-Doudoroff pathway is related to oxidative or nitrosative stress, and a stress that is absent in the anoxic methane produce marsh soil (Martinez et al, in review). We used metagenomics and metatranscriptomics to describe microbial metabolism in response to a change in C availability. We showed that 1) especially the N cycling processes exhibited a strong response, and 2) responses in gene-expression occurred already 8h after glucose addition (Chuckran et al 2021). The metatranscriptome data was strong enough to reveal detailed aspects of transcriptional regulation. In a follow-up paper (Dijkstra et al in prep), we describe the response of the metabolic processes of energy generation, biosynthesis, degradation, DNA and RNA replication, and ribosome functioning to a change in C availability. We found strong evidence that, already 24h after glucose addition, a shift in ecophysiology (as evidenced by changes in gene-expression) occurs that suggest a shift between exponential and stationary phase. These observations are important because they contradict current theoretical thinking in soil ecology that assumes that under conditions of low and high C availability, microbial metabolism is inefficient and slow. The publicly available metagenome and metatranscriptome data generated in this study has been used by the science community to generate two other publications: one on the occurrence of RNA viruses in natural microbial communities (including soil) (Neri et al 2022), and a second on the identification of new protein families (Pavlopoulos et al, in review). These publications demonstrate the importance of public availability of these large and valuable datasets. Using publicly available metagenomes of microbial communities in oceans, hot springs, animal gut and soil, we analyzed the relationship between GC content and genome size. Our observations of these genomic traits in oceans and hot springs confirms patterns observed for individual species in the past - a positive relationship between GC content and genome size. However, in soil ecosystems, a negative relation was observed (Chuckran et al 2021b). In a follow-up, a more detailed analysis was made of 398 metagenomes collected by the NEON consortium across agricultural, forest and grassland soils across the US. The observations confirmed the negative relationship of GC content and genome size: agricultural soils grouped together with desert and grassland soils as having small genome size and high GC-content. Precipitation, soil pH and soil C:N ratio correlated with these genomic traits, suggesting that community assembly processes and/or evolutionary forces influence genome size and GC content. In the broader context of NIFA efforts to provide innovative solutions to US farmers, ranchers and foresters, correct understanding of the microbial processes underlying soil C and N health is essential for developing new approaches of soil management and innovative solutions to problems. Our results provide deep understanding of processes of soil C stabilization and de-stabilization with the ultimate goal of providing techniques to manage soil C for the purpose of economic and environmental health of managed soil ecosystems.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Chuckran PF, Fofanov V, Hungate BA, Morrissey E, Schwartz E, Walkup J, and Dijkstra P (2021a) Rapid response of nitrogen cycling gene transcription to labile carbon amendments in a soil microbial community. mSystems 6:e00161-21. https://doi.org/10.1128/mSystems.00161-21.
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Chuckran, P.F., Hungate, B.A., Schwartz, E., and Dijkstra, P (2021b) Variation in genomic traits of microbial communities. FEMS Microbes, 2, 2021, xtab020. https://doi.org/10.1093/femsmc/ xtab020.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Geyer, K.M., Dijkstra, P., Sinsabaugh, R. and Frey, S.D. (2019) Clarifying the interpretation of carbon use efficiency in soil through methods comparison. Soil Biology and Biochemistry 128, 79-88.
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Chuckran, P.F., Huntemann, M., Clum, A., Foster, B., Foster, B., Roux, S., Palaniappan, K., Varghese, N., Mukherjee, S., Reddy, T.B.K., Daum, C., Copeland, A., Ivanova, N.N., Kyrpides, N.C., del Rio, T.G., Eloe-Fadrosh, E.A., Morrissey, E.M., Schwartz, E., Fofanov, V., Hungate, B. and Dijkstra, P. (2020) Metagenomes and metatranscriptomes of a glucose-amended agricultural soil. Microbiology Resource Announcements 9(44), e00895-20. doi: 10.1128/MRA.00895-20.
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2022
Citation:
Chuckran PF (2022). A multi-omics approach to assessing growth, stress, and disturbance in soil microbial communities. PhD Northern Arizona University.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Dijkstra, P., Martinez, A., Thomas, S.C., Seymour, C.O., Wu, W., Dippold, M.A., Megonigal, J.P., Schwartz, E. and Hungate, B.A. (2022) On maintenance and metabolisms in soil microbial communities. Plant and Soil 476, 385396.
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Wu W, Dijkstra P, Dippold MA, 2020. 13C analysis of fatty acid fragments by gas chromatography mass spectrometry for metabolic flux analysis. Geochim Cosmochim Acta 284: 92-106.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Yang W, Yao L, Zhu M, Li C, Li S, Wang B, Dijkstra P, Liu Z and Zhu B (2022) Replacing urea-N with Chinese milk vetch (Astragalus sinicus L.) mitigates CH4 and N2O emissions in rice paddy. Agriculture, Ecosystems & Environment 336, 108033.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Neri, U, Wolf, YI, Roux S et al. (2022). Expansion of the global RNA virome reveals diverse clades of bacteriophages. Cell (2022), https://doi.org/10.1016/j.cell.2022.08.023.
- Type:
Journal Articles
Status:
Awaiting Publication
Year Published:
2022
Citation:
Wu, W, Dijkstra, P, Hungate BA, Shi L and Dippold, MA In situ diversity of metabolism and carbon use efficiency among soil bacteria. Science Advances (in press).
- Type:
Journal Articles
Status:
Under Review
Year Published:
2022
Citation:
Chuckran PF, Flagg C, Propster J, Rutherford WA, Sieradzki E, Blazewicz SJ, Hungate BA, Pett-Ridge J, Schwartz E, Dijkstra P. Edaphic controls on genome size and GC content of bacteria in soil microbial communities. (In review Soil Biology and Biochemistry).
- Type:
Journal Articles
Status:
Under Review
Year Published:
2022
Citation:
Martinez, A, Megonigal, JP, Hungate, BA and Dijkstra P. Microbial central carbon metabolism in a tidal freshwater marsh and an upland mixed conifer soil under oxic and anoxic conditions. (In review FEMS microbiology).
- Type:
Journal Articles
Status:
Under Review
Year Published:
2022
Citation:
Pavlopoulos, GA, Baltoumas, FA, Liu S, et al. Discovery, diversity and distribution of functional dark matter through global metagenomics. In Review (Nature)
- Type:
Journal Articles
Status:
Other
Year Published:
2022
Citation:
Dijkstra, P, Chuckran PF, Hungate BA, Pett-Ridge J, Schwartz E. Microbial metabolism during a feast-famine event (in prep).
|
Progress 06/01/20 to 05/31/21
Outputs
Target Audience:Target Audience 1) researchers focused on soil management, soil health and utilization of crop residues, winter crops, mulches, and fertilization to improve soil C and N sequestration Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Several other students are now using publicly available metagenomes and metatranscriptomes to test specific hypotheses related to soil microbial functioning using python and R scripts developed in this project. For example, one study will look at N cycling genes and gene expression across a large range of ecosystems. These studies all will specifically include agricultural soils at the request of this research team. How have the results been disseminated to communities of interest?Some results have been published, some are in progress. Students have participated in poster presentations at conferences (online only) What do you plan to do during the next reporting period to accomplish the goals?We are wrapping up publications, initiating new collaboration, and sifting through the data to target new opportunities for achieving insight into the question of how microbes respond to a change in C and N availability
Impacts
What was accomplished under these goals?
We are continuing with the analysis of the metagenomes and metatranscriptomes that were generated in this project: A paper is published in Microbiome Resources Announcements describing the experiment and publicly available dataset consisting of 29 metagenomes and metatranscriptomes. This paper describes the experimental procedures and provides details of treatments and related metadata. We already received several requests from other research groups for permission to use the data. The importance of this paper is to stimulate a wider collaborative analysis of these valuable research products. A paper has been accepted (mSystems), describing how soil N cycling genes and gene-expression, and its interaction with C metabolism, respond to a sudden increase in C availability. This work shows, for the first time, how soil microbes' primary metabolism responds to a rapid shift in C availability and reveals a biochemically consistent view on soil processes that differs from current whole system thinking. This research is importance because it addresses a central aspect of soil health: managing soil for C and N availability. It also shows that the modern tools of metagenomes and metatranscriptomes are powerful in helping understand soil health at a foundational biochemical level. A paper on genome streamlining is submitted to the journal Microbiome (available on BioRxiv). This paper shows that the average genome size in agricultural soils is relatively small and GC-rich, similar to cold and hot deserts, and contrasting soils from forests and grasslands. This research involved an analysis of 128 metagenomes and collaboration with several research groups. A second paper on the topic of genome streamlining is in preparation. This work continues analysis of genome streamlining processes in soil ecosystems using more than 400 metagenomes from NEON (the National Ecological Observatory Network). This study suggests that selection for C and N availability played an important role in genomic streamlining in soil ecosystems. This data is used to request further funding from various agencies (DOE, NSF). This research is important because with the selection for smaller genome size, traits such as less stable and shorter proteins and an impaired DNA repair system are observed in other model plant and microbial systems. A paper is in preparation describing gene-expression of inorganic nutrient transporters. In collaboration with several other research groups, we describe the gene-expression profiles of these transporters in response to a glucose addition and compare it to gene-expression profiles for a range of soil and aquatic ecosystems. The gene abundance and gene-expression patterns are very similar across ecosystems, including agricultural soils. Surprisingly, transcript abundances for iron transporters are consistently high in soil, freshwater and marine ecosystems. There are two exceptions: after increasing C availability and in a marine habitat with highly abundant nitrifying Thaumarcheota, especially ammonium, nitrate/nitrate and urea transporters are abundant. This research has important consequences for thinking about nutrient resource limitations and fertilization during decomposition of C-rich plant materials as part of soil management. A paper on contrasting activities of the cyclic pentose phosphate pathway in mineral upland and marsh soil was submitted but rejected. This paper is now adapted for publication in the journal Soil Biology and Biochemistry. The importance of this research is that this is the first time we show that the organization of the central C metabolic processes (glycolysis, pentose phosphate pathway, TCA cycle) differs between soil ecosystems. In both soil, the efficiency of the metabolic processes (respiration versus biosynthesis) is high.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Chuckran, P.F., Huntemann, M., Clum, A., Foster, B., Foster, B., Roux, S., Palaniappan, K., Varghese, N., Mukherjee, S., Reddy, T.B.K., Daum, C., Copeland, A., Ivanova, N.N., Kyrpides, N.C., del Rio, T.G., Eloe-Fadrosh, E.A., Morrissey, E.M., Schwartz, E., Fofanov, V., Hungate, B. and Dijkstra, P. (2020) Metagenomes and metatranscriptomes of a glucose-amended agricultural soil. Microbiology Resource Announcements 9(44), e00895-20. doi: 10.1128/MRA.00895-20.
- Type:
Journal Articles
Status:
Accepted
Year Published:
2021
Citation:
Chuckran, PF, Fofanov V, Hungate BA, Morrissey E, Schwartz E, Walkup J, and Dijkstra P. (2021) Rapid response of nitrogen cycling gene transcription to labile carbon amendments in a soil microbial community. mSystems. (Accepted).
- Type:
Journal Articles
Status:
Other
Year Published:
2021
Citation:
Chuckran, P.F., Hungate, B.A., Schwartz, E., and Dijkstra, P. Marine, soil, hot-spring, and host-associated environments reveal unique selection pressures on genomic features of bacteria in microbial communities. Submitted to Microbiome.
|
Progress 06/01/19 to 05/31/20
Outputs
Target Audience:The target audience targeted consisted of students, faculty of this and other universities through lecture, seminar, poster presentations and conversations. More and more we are having conversations about our research outside of our discipline (with bioinformatic sciences). Changes/Problems:The role of transcription factors is much less clear than hypothesized. On the other hand, our ability to describe and interpret basic metabolic responses to changes in C and N availability are much better than expected. Our focus will now be on describing functional responses, and identifying suitable gene targets for primer development. What opportunities for training and professional development has the project provided?Two PhD students are trained in advanced method of soil microbial ecology, specifically metabolic flux analysis and shotgun sequencing analyses. Additionally, within our group, an increased interest by other PhD pstudents, not affiliated with this effort, will stimulate further analysis of data produced in this project and other publicly available datasets. How have the results been disseminated to communities of interest?Preliminary results have been presented to small groups of collegues at Northern Arizona University, UC Berkeley, and various DOE institutions. Two papers describing the datasets (Chuckran et al) and results of the N cycling genes and transcripts (Chuckran et al) are in advanced stage of preparation, while three more manuscripts are in development (Martinez et al, Dijkstra et al). What do you plan to do during the next reporting period to accomplish the goals?Further analysis of the responses of transcription factors, and integrated metabolic responses will be based on this dataset.
Impacts
What was accomplished under these goals?
DNA and RNA is sequenced, reads were assembled and annotated and are now being analyzed. Analysis has focused on three aspects of microbial functioning: 1) genes and transcripts associated with N cycling, 2) genes and transcripts associated with C cycling, and 3) genes and transcripts associated with transcription factors. Seven papers are in advanced stage of preparation: 1) Metagenomes and metatranscriptomes of a glucose-amended agricultural soil, 2) Response of gene-expression of N cycling processes and transcription controls to a change in C availability (Pete Chuckran first author), 3) Genome streamlining in terrestrial, aquatic and extreme environments (Pete Chuckran first author), 4) Respiration and gene-expression in response to a change in C availability (Paul Dijkstra et al first author), 5) Relating growth rates to genomic traits in soil microbial communities (Junhui Liu first author), 6) Responses of microbial biochemical efficiency in response to combined substrate additions (Ayla Martinez first author), and 7) Contrasting activities of the cyclic pentose phosphate pathway in mineral soil and freshwater sediment (Ayla Martinez first author). We developed python and R code that allows us to automatically download annotated datasets from the JGI website and process the data. We have 16,100 samples of annotated data available for samples as diverse as microbial communities from cattle intestines to agricultural fertilizer experiments, to forests around the globe. This database will serve as a backdrop to put our results of microbial responses to stress in a global context. A paper was published by Professor Bo Zhu, a visiting Associate Professor from the College of Agronomy, Yangtze University, Hubei Province, Central China (Nie et al 2019), and two more papers are in preparation.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
1- Nie J, Yi LO, Xu H, Liu Z, Zeng Z, Dijkstra P, Koch GW, Hungate BA, and Zhu B 2019. Leguminous cover crop Astragalus sinicus enhances grain yields and nitrogen use efficiency through increased tillering in an intensive double-cropping rice system in Southern China. Agronomy 2019, 9, 554; doi:10.3390/agronomy9090554
|
Progress 06/01/18 to 05/31/19
Outputs
Target Audience:The target audience targeted consisted of students, faculty of this and other universities through lecture, seminar, poster presentations and conversations Changes/Problems:There is a large amount of publicly available data that we are analyzing as part of this project. This was not foreseen in the project descritpion but is an important opportunity to accelerate the research What opportunities for training and professional development has the project provided?We trained one faculty member (Dijkstra), two graduate students (Chuckran and Propster), and three undergraduates how to use Python and R and become familiar with accessing data from the online metagenome and metatranscriptome database, including the data related to this project How have the results been disseminated to communities of interest?We have presented our data on microbial stress responses and metagenome and metatranscriptome analyses in the form of seminars to the lab group, as part of meetings with collaborating projects, and through talks and poster at conferences, and seminars at other universities What do you plan to do during the next reporting period to accomplish the goals?In the next few months, the information on metatranscriptomes will become available. We will combine that data with data on metagenomes and compare the results with other publicly available studies. We have in place the structure to easily compare large numbers of metagenomes across agricultural experiment and non-managed ecosystems
Impacts
What was accomplished under these goals?
Pete Chuckran successfully prepared DNA and RNA for sequencing. Sequencing and analysis is done by DOE-JGI. Analyses of metagenomes is complete, annotation of metatranscriptomes is in progress. We are currently analyzing our data with the help of three undergraduates, master student and PI, focusing on genes from regulatory network (sigma factors and transcription factors), N and P cycle, extracellular enzymes, and the central C metabolic network. An undergraduate student, Ryan Lancione, in collaboration with Dijkstra, Fofanov, and Chuckran, analyzed the abundances of sigma factors related to bacterial stress responses in existing datasets available on the NCBI website. 30 TB of data of ~650 datasets of metagenomes and metatranscriptomes were analyzed. The results are very comparable (with exception of Sigma E) and give us confidence that JGI IMG annotated data will be reproducible. We developed python and R code that allowed us to 1) automatically download annotated datasets from the JGI website and process the data. We have 16,100 samples of annotated data available for samples as diverse as microbial communities from cattle intestines to agricultural fertilizer experiments, to forests around the globe. This database will serve as a backdrop to put our results of microbial responses to stress in a global context. A second graduate student hired by the project is investigating the metabolic flux patterns and biochemical efficiency of microbes living in soil. For the first time, she observed significant differences between pentose phosphate pathway activities between a grassland soil and a salt marsh. Very little is known about the fundamental processes of the central C metabolic network in microbial communities, and our results from previous results always indicated high biochemical efficiencies and high pentose phosphate pathway activity. We are using this data to compare information on the metabolic network activities with the relative abundances of genes and transcripts in our metagenomes and metatranscriptomes. Professor Bo Zhu, a visiting Associate Professor from the College of Agronomy, Yangtze University, Hubei Province, Central China, has worked on trace gas release from incorporated crop residues on the relationships between N2O production, nitrogen use efficiency, inorganic and organic fertilizer. His stay at our department was funded by the China Scholarship Council. Although his greenhouse experiment failed to demonstrate N2O production, he contributed to the demonstrating pentose phosphate pathway activity differences. We have had three undergraduate researchers work on measurements of the central C metabolic network activities and three working on analyzing data from our metagenome study using python and R scripts. Methodologies developed in this USDA project will also be applied in the other projects, for example to look for responses to drought or as part of the study into metabolic processes.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Geyer KM, Frey SD, Dijkstra P, Sinsabaugh R. 2019. Clarifying the interpretation of carbon use efficiency estimates in soil through methods comparison. Soil Biology and Biochemistry 128: 79-88
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Dijkstra P, Martinez A, Chuckran P 2018. Modeling Soil Metabolism Using Position-Specific 13C-Labeled Substrates and Omics . American Geophysical Union Dec 10-14, 2018 (invited talk)
Dijkstra P, Chuckran P, Schwartz E, Fofanov V, Hungate BA. Baseline Metabolic Capabilities in Microbial Communities: A Cross Ecosystem Study of Metatranscriptomes. FY 2018 NIFA Water and Soils Annual Project Directors Meeting Oct 1-3, 2018. Newark, Delaware. (Poster presentation)
|
Progress 06/01/17 to 05/31/18
Outputs
Target Audience:
Nothing Reported
Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?1- Training of one master student (Pete Chuckran) in extraction, purification and quantification of DNA and RNA from soil 2- Training of one undergraduate (Ryan Lancione) in bioinformatics and database analysis 3- Development of protocols for database analyses of metagenomes and metatranscriptomes using multiple publicaly available datasets How have the results been disseminated to communities of interest?Results of the metagenome and metatranscriptome analyses have been presented in various (invited) talks and poster presentations. Work on metabolic efficiency and fundamental questions related to soil microbial metabolism has been presented in various invited talks, and in one submitted paper. What do you plan to do during the next reporting period to accomplish the goals?1- We will (have already started to) study the response of the microbial growth, metabolism and biochemical efficiency, and transcriptional networks to large fluctuations in C and N availability. as a side-project, we will also study how a temperature shock (from 20 to 60 degrees C for 30 min) affects transcriptional networks. In exchange for this side-project, samples generated in both experiments will be analyzed and bioinformaticallyt processed by the JGI as part of an award to Dijkstra and collaborators. Most of next year will be spent on analysis of thes datasets. 2- as part of these initial exps, we will study in detail the microbial dynamics and metabolic efficiencies of these communities. 3- Dr Bo Zhu will study trace gas production and N use efficiency under inorganic and organic fertilizer treatments in rice. We will conduct parallel experiments with using a dryland crop species, and collect DNA and RNA to study microbial stress responses 4- Work on the relative abundances of sigmas and other transcriptional regulatory factors will be wrapped up, and summarized in a publication.
Impacts
What was accomplished under these goals?
1- Pete Chuckran was trained to do soil DNA and RNA extractions. He optimized the methods, and based on the DNA/RNA amount extracted, we chose the soil type to be used in this experiment (Soil from the Organic Crop Livestock Fields (OCLF) experiment at West Virginia University (https://organic.wvu.edu/). Pete is paid of the USDA grant starting Jan 2018. 2- Starting Jan 2018, Ryan Lancione, and undergraduate researcher, analyzed, in collaboration with Dijkstra, Fofanov, and Chuckran, the relative abundances of sigma factors related to bacterial stress responses in publicly available metagenomes and metatranscriptomes (NCBI website). 30 TB of data of ~650 metagenomes and metatranscriptomes were analyzed. In parallel, analysis using the JGI IMG public database was conducted by Dijkstra and Chuckran. These analyses give us a baseline to which we can match the temporal changes in transcription networks in our experiments. 3- In December 2017, Bo Zhu, a visiting Associate Professor from the College of Agronomy, Yangtze University, Hubei Province, Central China, expressed interest in working with us on the relationships between N2O production, nitrogen use efficiency, inorganic and organic fertilizer. His stay at our department, starting April this year, is funded by the China Scholarship Council, but will provide us with opportunities to combine experimentation on trace gas production, N use efficiency, and microbial stress responses.
Publications
- Type:
Journal Articles
Status:
Submitted
Year Published:
2018
Citation:
Geyer KM, Frey SD, Dijkstra P, Sinsabaugh R. Clarifying the interpretation of carbon use efficiency estimates in soil through methods comparison. Submitted to Soil Biology and Biochemistry
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2017
Citation:
Invited talk: Dijkstra P, Mau R, Schwartz E, Koch B, Marks J, Caporaso G, van Gestel N, McHugh T, Morrissey E, van Groenigen KJ, Liu C, Price L, Orr G, Baldrian P, and Hungate BA. Frontiers in Microbial Ecology: Growth and Metabolism in Soil. BIOGEOMON - 9th International Symposium on Ecosystem Behavior. Aug 20-24 2017. Litomyal, Czech Republic
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2017
Citation:
Invited talk: Dijkstra P. Microbial Biosynthesis and Energy Metabolism in Soil. Soil Science Society of America Meeting, October 22-25 2017. Tampa, FL
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2018
Citation:
Invited talk: Dijkstra P, Martinez A, Chuckran P, van Groenigen KJ, Schwartz E, Hungate BA, Fofanov V. Microbial Energetics Through a Mist of Maintenance. European Geophysical Union, April 5-13 2018. Vienna, Austria
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2017
Citation:
Poster: Dijkstra P, Koch BJ, Pett-Ridge J, Blazewicz S, Mayali X, Hofmockel K, Schwartz E, Morrissey EM, Orr G, Baldrian P, Hungate BA. Studying Microbial Stress in Soil Ecosystems. Multi-omics for Microbiomes EMSL integration 2017 Conference Aug 1-3. Pasco, WA.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2018
Citation:
Poster: Dijkstra P, Chuckran P, Schwartz E, Fofanov V, Hungate BA. Analysis of Microbial Stress Responses in Soil Using Metagenomes and Metatranscriptomes. FY 2017 Project Directors Annual Meeting for AFRI Water for Agriculture, AFRI Foundational-Biology Natural Resources and Environment (BNRE), National Integrated Water Quality (NIWQP), and NSF/NIFA Water Sustainability and Climate (WSC) Programs from January 29-31, 2018. Washington, DC.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2018
Citation:
Poster: Dijkstra P, Chuckran P, Schwartz E, Fofanov V, Pett-Ridge J, Hungate BA. Analysis of Microbial Stress Responses in Soil Using Metagenomes and Metatranscriptomes. 2018 Genomic Sciences Program Annual Principal Investigator (PI) Meeting, Feb 22-25, 2018. Washington, DC.
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