Source: PENNSYLVANIA STATE UNIVERSITY submitted to
DETERMINING THE FACTORS GUIDING MICROBIOME TRANSFER BETWEEN SOILS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
1016233
Grant No.
(N/A)
Cumulative Award Amt.
(N/A)
Proposal No.
(N/A)
Multistate No.
(N/A)
Project Start Date
Jul 1, 2018
Project End Date
Jun 30, 2023
Grant Year
(N/A)
Program Code
[(N/A)]- (N/A)
Recipient Organization
PENNSYLVANIA STATE UNIVERSITY
208 MUELLER LABORATORY
UNIVERSITY PARK,PA 16802
Performing Department
Plant Pathology & Environmental Microbiology
Non Technical Summary
It has long been known that microorganisms in the soil contribute to soil health and plant growth. However, it is only recently that we have been able to profile the extremely diverse microbial assemblages that live in soil, using new high-throughput sequencing technologies. Since many soil functions (e.g. rate of decomposition) cannot be tied to a single microorganism, and microorganisms function differently within a system than they do in isolation, it is important to be able to test the function of entire microbial assemblages. To date, there are not effective procedures for predictably transferring an entire microbial assemblage from one soil to the next, which makes it impossible to reproduce experimental results through time or in different research labs. We aim to determine 1) approaches for transferring microbial assemblages between soils, 2) storage conditions that allow us to preserve microbial assemblages in the lab for long periods of time, and 3) whether the functional attributes of a microbial assemblage (e.g. rate of decomposition) are transferrable, or will instead remain difficult to predict.
Animal Health Component
50%
Research Effort Categories
Basic
50%
Applied
50%
Developmental
0%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
1020110107050%
1024099107050%
Knowledge Area
102 - Soil, Plant, Water, Nutrient Relationships;

Subject Of Investigation
4099 - Microorganisms, general/other; 0110 - Soil;

Field Of Science
1070 - Ecology;
Goals / Objectives
Objective 1: Determine the method(s) most appropriate for transferring microbiomes from different soil types. Success will be evaluated based on similarity to the natural source, and repeatability for future studies.Objective 2: Determine the optimal storage conditions for soil microbiomes to allow for biobanking of microbiomes, and for repeatability of experiments between labs and through time.Objective 3. Determine whether microbiome functional traits (i.e. group traits) are transferrable.
Project Methods
Objective 1. We will compare sustained contact of source microbiomes with recipient soils to direct soil transfers at various dilutions, an approach commonly used to date in the literature. We assume that one of the factors leading to poor replication of the source microbiome in low-dilution microbiome transfers is that the introduced microorganisms only have a single opportunity to colonize the sterile recipient soil. Microbiomes will remain in contact across wide-pore filters, allowing for successive recolonization attempts over multiple weeks. We will compare microbiome profiles using 16S rRNA gene and fungal ITS amplicon sequencing, and will estimate soil substrate transfer through 15N and 13C isotope tracking.Objective 2. We have collected a variety of agricultural soils from across Pennsylvania through the PSU Extension network, and have stored these under various conditions (e.g. different temperatures, and with or without cryopreservatives). We will re-introduce the microbiomes from these soils to multiple sterile soil types, and assess which storage approaches led to the best retention of diversity, and replication of the parent microbiomes, across all collected soils.Objective 3. We will assess whether functional microbiome traits such as CO2 production and plant growth can be replicated as we transfer microbiomes from one soil to another. CO2 output will be assayed through high-throughput plate assays such as MicroResp, whereas plant growth will be determined through trait measurement, including height and dry

Progress 10/01/19 to 09/30/20

Outputs
Target Audience:Scientific community and Pennsylvania farmers Changes/Problems:Main delay is in publishing the described Bell et al. paper due to extreme childcare responsibilities during covid. This is my next priority, and should be sent off in the next month or two. What opportunities for training and professional development has the project provided?A postdoc and two graduate students are working on these projects. How have the results been disseminated to communities of interest?Publications and presentations to both farmers and the academic community What do you plan to do during the next reporting period to accomplish the goals?Complete described manuscripts: Bell et al. Hidden communitites within communities: minimal overlap in microbial composition between source and recipient environments. Yates et al. Rapid modification of bacterial niche breadth and functioning through conditioning in novel soils. King et al. Both targeted and random selection of root-associated microbiomes can enhance Brassica rapa biomass in the presence and absence of added salt. Grandinette et al. Yes, it is fine to autoclave your soils for microbiome transfer experiments.

Impacts
What was accomplished under these goals? Objective 1. Project in which we collected soils from across PA and have used to inoculate recipient soils is still pending submission. Some aspects delayed due to covid interruptions, and we are integrating new data obtained from a collaboration with General Automation Lab Technologies (GALT) Inc. They are sequencing thousands of isolates cultivated from these soils to determine whether switching microbiomes between environments has an impact on cultivable diversity. Another project, described last year, in which we are looking at how soil amendments impact microbial colonization from different sources, was submitted several months ago, and has now been resubmitted with revisions to Environmental Microbiology. Objective 2. A key component of microbiome reproduction is our ability to sterilize soils and achieve predictable recolonization. As described last year in our goals, we completed a project that looked at the impact of different sterilization approaches on microbiome composition and found that there is little difference between autoclaving and gamma irradiation. In fact, the main difference is that gamma irradiation is less effective at initial clearing soils. We are preparing this paper now. Objective 3. A postdoc in my group is completing the writing and analysis for a paper on microbiome selection from high biomass Brassica rapa. This shows that while microbiome divergence is consistent and predictable, plant growth advantages due to microbiome selection are hard to predict (planned for submission this fall). A grad student of mine has also shown that transferring bacterial isolates between soils and conditioning them within those soils impacts their ability to survive, as well as their performance (relative resource use and respiration).

Publications

  • Type: Journal Articles Status: Awaiting Publication Year Published: 2020 Citation: Malik RJ, Trexler RV, Eissenstat DM, Bell TH. In press. Bark decomposition shifts soil microbial assemblages, while a home-field advantage is detected for white oak. Biogeochemistry.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Bell TH, Trexler RV, X Peng, M Huntemann, A Clum, B Foster, B Foster, S Roux, K Palaniappan, N Varghese, S Mukherjee, TBK Reddy, C Daum, A Copeland, NN Ivanova, NC Kyrpides, C Pennacchio, EA Eloe-Fadrosh, MA Bruns. 2020. Metatranscriptomic and 16S rRNA gene analysis of a cyanobacterial soil-surface consortium with and without a diverse underlying soil microbiome. Microbiology Resource Announcements 9: e01361-19.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Trexler RV, Bell TH. 2019. Testing sustained soil-to-soil contact as an approach for limiting the abiotic influence of source soils during experimental microbiome transfer. FEMS Microbiology Letters 366: fnz228.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Bell TH. 2020. Can we manipulate soil microbiomes? Colorado State University, Fort Collins, CO, USA. (virtual presentation)
  • Type: Conference Papers and Presentations Status: Other Year Published: 2019 Citation: Bell TH. 2019. The invisible and essential inhabitants of soil. PASA Advanced Farmer Gathering: Collaborating to Improve Your Workforce and Your Soil. Harrisburg, PA, USA. (presentation)


Progress 10/01/18 to 09/30/19

Outputs
Target Audience:Academics working at the interface of agriculture and microbially-related biotechnology; farmers and particularly organic farmers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Ph.D. student, Laura Kaminsky, has worked on this project. Additionally, two undergraduate assistants contributed to the project. How have the results been disseminated to communities of interest?Presented at academic meetings and a PASA-sponsored grower event. What do you plan to do during the next reporting period to accomplish the goals?Complete described manuscripts. Bell et al. Hidden communities within communities: minimal overlap in microbial composition between source and recipient environments Kaminsky et al. Soil amendments impact the ability to detect the source of microbial colonizers. Test soil sterilization approaches and determine consistency of microbiome assembly under each scenario, as well as the reliability of sterilization Autoclaved soils + wild microbiome inoculant Autoclaved soils + washing + wild microbiome inoculant Gamma irradiated soils + wild microbiome inoculant Gamma irradiated soils + washing + wild microbiome inoculant Autoclaved soils + synthetic community inoculant (i.e. 20 defined cultivated strains) Autoclaved soils + washing + synthetic community inoculant Gamma irradiated soils + synthetic community inoculant Gamma irradiated soils + washing + synthetic community inoculant Assess composition through 16S + ITS sequencing Assess sterility through plating of sterilized soil at different time points

Impacts
What was accomplished under these goals? Objective 1. Finished collecting data for colonization of two recipient soils from twenty sources. Have performed extensive analyses of these data, which has been presented at conferences. Are preparing a manuscript for submission in the next few months. Overall, we found that microbiome composition in recipient soils varied based on source, and that signatures of the source soil (e.g. low vs. high pH) were detectable in recipient soil microbiomes. We also collected data for a related project that looks at the interaction between source soil, amendments in recipient soils (nutrient addition, salt addition), and microbial colonization. We have completed initial analyses of these data, and my student Laura Kaminsky is leading the writing and analysis of a publication for this project.In this project, we observed that recipient soil treatment had a much larger impact on microbial composition in recipient soils than did the source of the microbiome. Objective 2. As part of the first project (colonization of two recipients from twenty sources), we looked at colonization depending on storage conditions. This has been analyzed entirely, and showed that, in general, the use of no additives during frozen storage led to the highest diversity transfer into new soils. These data will be published alongside those described for Obj. 1. Objective 3. Nothing pursued on this objective this year.

Publications

  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Kaminsky et al. 2019. The Inherent Conflicts in Developing Soil Microbial Inoculants. Trends in Biotechnology 37: 140-151.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Kaminsky et al. 2019. Factoring Ecological, Societal, and Economic Considerations into Inoculant Development. Trends in Biotechnology 37: 572-573.
  • Type: Other Status: Published Year Published: 2019 Citation: Kaminsky and Bell. 2019. Microbial inoculants for agricultural soils: potential and challenges. Penn State Extension https://extension.psu.edu/
  • Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Bell TH. 2018. Microbial colonization of soils: implications for agriculture and experimental systems. International Phytobiomes Conference, Montpellier, France.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2019 Citation: Bell TH. 2019. Microbial source and recipient environments: interactions impact microbial establishment and function. 3rd Microbiome Movement - AgBioTech Summit, Raleigh, NC.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2019 Citation: Bell TH. 2019. Microbial invasion in agriculture: harder to stop it or to make it happen? American Phytopathological Society  Northeast Division Meeting, State College, PA.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2019 Citation: Bell TH and Kaminsky L. 2019. Can we enhance microbial contributions to regenerative ag systems? Regenerative Grazing from the Ground Up  PASA sponsored, Wernersville, PA.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2019 Citation: Bell TH. 2019. Getting there and staying there: microbial establishment in heterogeneous soils. USDA Animal and Plant Health Inspection Service, Beltsville, MD.


Progress 07/01/18 to 09/30/18

Outputs
Target Audience:In this reporting period, I communicated work through both scientific presentations (presenting at Wild and Tamed Phytobiomes Symposium and invited talks at Cornell and University of Illinois) and talks to ag professionals (Keystone Crop and Soils Conference). Changes/Problems:None so far as this is a new project. What opportunities for training and professional development has the project provided?Both a Ph.D. student and undergraduate assistant worked on initiating the microcosms and processing the samples. I will present on this work at the International Phytobiomes Conference in December. How have the results been disseminated to communities of interest?As mentioned, they have been discussed at a variety of conferences, and this will continue into next year. What do you plan to do during the next reporting period to accomplish the goals?Next year we expect to complete analysis for the first stages of Objectives 1 and 2 and submit a publication on these efforts.

Impacts
What was accomplished under these goals? Objective 1. We ran a long-term incubation, extracted DNA, and sent samples for sequencing.We ran a long-term incubation, extracted DNA, and sent the recipient soil samples for sequencing. These were two sterilized soil types, targeted to maximize differences in soil parameters, that were colonized by different microbial sources. We have now received some of the data from Genome Quebec.We have now received some of the data from Genome Quebec. We also ran a pilot study in which we colonized the same sterile soil with microbes from various forest and ag soils, and looked at C metabolism profiles among the colonizers. Interestingly, colonizing microbiomes metabolized different C sources similarly to long-term microbiomes in ag soils. This suggests that agriculture selects for traits observed in rapidly growing microorganisms. Objective 2. This is integrated with what is described in 1. We tested methods associated with different storage types. Storage was initiated in 2017. Objective 3. Nothing pursued on this objective this year.

Publications

  • Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Bell and Kaminsky. 2018. One crop, many partners: finding ways to understand the importance of microorganisms in the soil. Keystone Crop and Soil Conference, Harrisburg, PA.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Bell. 2018. Storage and reproduction of microbiomes. Wild and Tamed Phytobiomes, University Park, PA
  • Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Bell. 2018. Exploring the potential for microbiome manipulation in agricultural soils and experimental systems. University of Illinois, Urbana-Champaign.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Bell. 2018. Learning to manipulate microbiomes: creating model systems and managing microbes in agriculture. Cornell University, Ithaca, NY.