Source: PENNSYLVANIA STATE UNIVERSITY submitted to NRP
IS THERE A ROLE FOR MICROBIAL MANAGEMENT IN ORGANIC AGRICULTURE?
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
OTHER GRANTS
Reporting Frequency
Annual
Accession No.
1020468
Grant No.
2019-51106-30196
Cumulative Award Amt.
$500,000.00
Proposal No.
2019-03513
Multistate No.
(N/A)
Project Start Date
Sep 1, 2019
Project End Date
Aug 31, 2023
Grant Year
2019
Program Code
[112.E]- Organic Transitions
Recipient Organization
PENNSYLVANIA STATE UNIVERSITY
408 Old Main
UNIVERSITY PARK,PA 16802-1505
Performing Department
Plant Path & Env Microbiology
Non Technical Summary
Many organic farmers understand that soil microorganisms are important for soil function, but are unsure how to effectively manage microbial populations. Soil microorganisms are increasingly important as farmers transition to organic agriculture, as microbial services need to replace benefits that would otherwise have been provided by chemical inputs. For example, microorganisms can transform nutrients from forms that are unavailable to plants to forms that are available to plants, which limits the need for fertilizer additions.Attempts to directly manage microorganisms are common in organic agriculture. Popular approaches include the development of compost that is expected to contain beneficial microorganisms, Korean natural farming, and the application of live microbial products obtained commercially. This latter approach in particular is growing in popularity. For example, a substantial majority of organic farmers in Ohio used microbial products in 2014, which was more than twice the proportion measured in 2009.However, microbial communities are incredibly diverse and complex, and to the farmer, invisible. This invisibility makes it hard for farmers to benchmark potential solutions, leaving them without a real framework for microbial management, and thus, no clear consensus on which approaches to apply. In this project, we will examine how soil type and farming practices interact with both passive and active microbial management, in collaboration with farmer partners, and within a long-term organic farming project at Penn State.Our Research Objectives are to:1) Determine how location, existing management, and microbial re-seeding impact microbial colonization of soils. This will help farmers to understand the impact of including diverse plants in or around production areas on microbial diversity, and will also validate the impact of additional management treatments that they are using.2) Link the establishment of OMRI-certified microbial products to soil traits, and determine whether on-farm conditioning can enhance product survival. Microbial products have a long history of unpredictable effectiveness, and we aim to advance understanding of where products will be effective and why.3) Evaluate the sensitivity of soil respiration, a widely used metric for microbial health, to microbial composition. Many organic farmers pay to assess soil respiration, with the assumption that it reflects soil biological health; however, respiration readings are confounded by differences in soil characteristics. We aim to determine how sensitive this assay is to microbiological differences, and benchmark this against two other potential metrics of soil biological activity.Our Extension Objectives are to work with farmers to understand the role of soil microorganisms in organic agriculture through annual meetings and farmer conferences, and make lasting contributions to their decision-making through Extension publications that communicate our results and reveal the breadth of microbial management used by organic farmers.We believe that providing empirical guidance on microbial management is going to help organic and transitioning farmers assess the risks and rewards of investing in this area.
Animal Health Component
40%
Research Effort Categories
Basic
40%
Applied
40%
Developmental
20%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
1020110107050%
1020110110350%
Knowledge Area
102 - Soil, Plant, Water, Nutrient Relationships;

Subject Of Investigation
0110 - Soil;

Field Of Science
1103 - Other microbiology; 1070 - Ecology;
Goals / Objectives
Our long-term research goals are to:Understand the role of microbial management in soils undergoing organic transition.Establish how and when to use OMRI-certified microbial products to predictably increase economic benefits to organic farmers.Determine microbial contributions to common soil health metrics.Translate and extend what we learn to empower organic farmers to manage soil microbiomes to meet their goals.Our research in this project aims to answer the following questions:How do location, existing management, and microbial re-seeding impact "natural" microbial colonization of soils?Can we enhance the predictability with which OMRI-certified microbial products establish and function in soils?To what extent does changing soil microbial composition impact a commonly used metric of soil microbial health?Our extension objectives in this project are to:Work with farmers to develop a mutual understanding of the role of soil microbes in organic agriculture through annual meetings and presentations at farmer conferences.Make lasting contributions to farmer decision-making by producing Extension publications that A) communicate our results and B) reveal the breadth of microbial management approaches that are used by farmers in our region.
Project Methods
O1: How do location, existing management, and microbial re-seeding impact "natural" microbial colonization of soils?At each of 5 participating farms, we will work with farmers to establish replicate transects of 'microbial traps' on production land that increase in distance from a bordering forest patch. This will also be done at a long-term organic field site at Penn State. To create the microbial traps, soil will initially be collected from a long-term organically managed field site at Penn State that is managed by Co-PI Kaye, to standardize the abiotic conditions that microbes will colonize. Collected soil will be sterilized, and will then receive 1 of 4 treatments: 1) no additives; 2) sterile compost; 3) incorporation of 1% forest soil from neighboring forest patch; and 4) farmer-determined treatment.Each treatment will be allocated to ~18 μm nylon mesh bags, which allow most microorganisms to enter or exit freely. Traps will be half buried before planting in Year 1 of the project, with one surface exposed to air, to allow rain and dew to act as microbial sources. Traps will be collected at 4 and 16 months post-installation, and microbiome composition assessed (high-throughput sequencing of bacterial and fungal DNA markers). The metabolic capacity of soils closest to and furthest from the forest will be assessed with the MicroResp assay.We also aim to identify the active colonizing microbial pool associated with different long-term organic cover crop treatments at Penn State. Duplicate microbial traps will be introduced to 4 replicate plots for each of 12 long-term cover crop treatments that vary in cover crop diversity. We will collect traps 4 and 16 months after burial to assess microbiome composition.O2: Can we enhance the predictability with which OMRI-certified microbial products establish and function in soils?i) Test association between optimal pH and resource preferences of microbial products and compatibility with recipient soilsWe will screen bacteria from OMRI-certified products intended for soil application, to assess tolerance to different abiotic conditions. For each product, we will determine the pH range tolerated by the organism in culture and the organism's optimal pH. Next, we will assess bacterial growth in sterilized soils collected from organic land at Penn State and from our farmer partners. Growth in each soil will be benchmarked after 2 and 4 weeks against a control in which the original soil microbiome is re-introduced. Growth will be assessed by 1) DNA extraction and quantification, and 2) respiration, using MicroResp. We will also assess resource use by each product, to determine which soil C sources are likely to support growth in soil.Based on initial screening, we will select 3 products that differ most in pH tolerance and C metabolism, and perform on-farm trials to determine how product survival relates to soil traits when other microbes are present. At each site, we will pool 10 evenly spaced subsamples of the top 15 cm of soil. A portion of the pooled soil will be analyzed for soil traits, while the rest will be added to open-top 16-qt plastic storage boxes, to serve as experimental units. At each site, we will assess survival of our three isolates, each in three replicate boxes, and will include three control boxes with no product added. In parallel, we will repeat this setup, but allow our farmer partners to incorporate a soil nutrient management treatment.We will collect soil samples from each experimental unit directly post-inoculation, and at 1 week, 1 month, and 3 months after product addition. We will extract DNA from each sample and perform qPCR to assess the persistence of the added bacteria relative to the control, using primers specific to each strain.ii) Determine whether on-farm conditioning of microbial products can increase survivability in those soilsThe 'ichip' is an easily constructed device, used to cultivate previously uncultivable microorganisms. Here, we will apply a modified version of this device, not to capture bacteria, but to facilitate product adaptation to particular soils. Nine devices for each product will be buried at each participating farm pre-planting in Year 1. We aim to collect at least three intact replicates per site 12 months after installation, with others left for potential longer term sampling.After collection, we will introduce adapted and initial products to non-sterile farm soils, and track survival at 1 week, 1 month, and 3 months post-addition as described in the previous section. We will identify the farm soil that induced the largest increase in survival, and these adapted products will be selected for metatranscriptomic comparison to the initial products. Adapted products will be introduced to microcosms containing sterile and non-sterile versions of the farm soil they were adapted to, as will the initial product. Microcosms will incubate for 2 weeks, after which we will extract RNA, which will prepared and pooled for a single Illumina HiSeq run. These data will demonstrate how each product changed to better survive in the environment.O3: To what extent does changing soil microbial composition impact a commonly used metric of soil microbial health?In this Objective, we will test the sensitivity of soil respiration to changes in microbial composition across soil types. In parallel, we will determine the sensitivity of two other low-cost assays of soil microbial activity.Soils for this Objective will be solicited through a collaboration with PASA, in association with the large Soil Health Benchmark Study they have run since 2016.We will collect 6 soils that vary widely in abiotic characteristics, with a focus on a broad range of soil pH and organic matter, factors known to shape soil microbial composition. Each collected soil will be split in two, with one portion sterilized to eliminate all biological content. Part of the sterile portion will be sent for physicochemical analysis, to determine soil traits after sterilization. The non-sterilized portions will be used as inoculum to reintroduce microbiomes to each sterile soil.Sterile recipient soils will be distributed to laboratory microcosms, and we will re-introduce microbiomes to each soil from the ten sources of inoculum, by burying the non-sterile source soils within nylon bags. We will allow colonization from each inoculum source for either 1 week or 16 weeks. Inoculum introductions will be timed so that nylon bags are added to one-week microcosms after fifteen weeks of colonization in the twelve-week microcosms. Following colonization, nylon bags will be removed, and microbial growth continued for eight weeks to allow communities to stabilize. DNA will be extracted from a small soil sample in each microcosm, and quantified. We will then normalize microbial biomass by adding sterile soil as needed to each sample, to ensure differences in respiration relate to composition.From extracted DNA, we will assess microbiome composition. This will allow us to assess microbial richness in each microcosm, and confirm differences in community composition based on inoculum source. Total soil respiration will be assessed using MicroResp. For total respiration, each microcosm soil will be amended with water only, and CO2output will be compared to a sterile control for that soil type. We will also use MicroResp to assess relative metabolism of two pools of C sources (labile vs. recalcitrant) by each microbiome in each soil. Finally, we will assess decomposition of two litter types from a long-term organic cropping system at Penn State. Corn and soybean litter will be dried and weighed, and buried separately in each microcosm soil in fine-mesh litter bags for 4 months. Decomposition will be assessed by comparing final and initial dry weights.

Progress 09/01/19 to 08/31/23

Outputs
Target Audience:Our target audience includedfarmers who use organic practices, farmers with interest in organic practices, agricultural practitioners (esp. those involved in the microbial products industry), and academics with a focus on microbial ecology and/or agricultural management. We also had specific close interactions with a number of organic and transitioning farmers in Pennsylvania, with whom we established on-farm projects. Our close interaction with farmers has ensured that our work has direct relevance to the farming community and has also allowed us to understand the wide range of microbial management practices in Pennsylvania, as well as the wide range of perceived benefits and challenges of microorganisms in agriculture. Trainees were also a target audience, and the project has provided training opportunities for undergraduates, graduates, and a postdoctoral fellow. Changes/Problems:We made a few changes through this project, some due to COVID-related disruptions. The largest of these is that we did not ultimately perform large-scale respiration assessments in collaboration with Pasa Sustainable Agriculture, despite some initial movement on this project. Unfortunately, the logistics and personnel assignments became too challenging and we decided to put more effort and emphasis on our other project objectives. A somewhat related study was published by another group in 2020 (https://www.nature.com/articles/s41467-020-17502-z), which also nudged us towards pursuing other goals. What opportunities for training and professional development has the project provided?Overall, this project has provided extensive direct training for one undergraduate student (Helen Senerchia), one graduate student (Laura Kaminsky), and one postdoctoral associate (William King). Two other graduate students also became involved, working on our deployment of microbial traps in the long-term cover crop experiments that are ongoing at Penn State (Sarah Richards and Lily Cao). Our Extension work also incorporated three other graduate students (Sarah Isbell, Mara Cloutier, Suzanne Fleishman) who were involved in developing written Extension materials. Trainees on this project were engaged in a range of original research projects, both in-field and in-lab, and were involved in communication with farmers from across the state. Additionally, Laura Kaminsky engaged heavily in farmer recruitment and communication through our dispersed on-farm project, so gained substantial experience in network building. All trainees had opportunities to develop written materials, both for the academic community and for farmer partners. Laura Kaminsky won a dissertation award for her work on this project. How have the results been disseminated to communities of interest?Results have been disseminated through farmer conferences (e.g. PASA Meeting, Stroud series), interfacing with on-farm partners, Extension articles (e.g. eOrganic), scientific conferences, and academic publications. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Research Objective 1 - Showed that the pool of microbial colonizers is more limited when soils have been disturbed through added nutrients or salt accumulation (as can occur in high tunnel systems), with mostly generalist microorganisms surviving (Kaminsky et al. 2020. Environmental Microbiology). - Deployed microbial traps along farm transects and showed that our ability to detect differences by location and land use type is substantially increased through the use of microbial traps that focus on collection of colonizing microbes (King et al. 2022. ISME Communications) - Deployment of corn litter in litter bags across the Cover Crop Cocktail plots appeared to show limited differences in decomposition based on plot type. - Demonstrated that rediversification of microbiomes in soil can restore at least some functions of interest, such as nitrogen cycling, with corresponding changes in functional gene composition (King et al. 2023. Environmental Microbiome). - Deployed microbial traps throughout a long-term cover crop experiment, which we sampled over two years. The biggest observed difference in microbial colonizer pools was between fallow and cover crop inclusion, although other differences were observed between cover crop types when grouped at broader levels (Richards et al. In prep). - Showed that very small-scale differences in location across root systems impact microbial function and root metabolites. This further supports conclusions from this project that small-scale differences in management may have important impacts on microbial processes. Data from that were funded by EMSL, but postdoc time to write and analyze those complementary data was funded by this project. (King et al. 2023. Plant, Cell, and Environment) Research Objective 2 - Using two commonly sold and OMRI-certified microbial products that perform a clear and known function in soils (Actinovate and MegaPhos), we developed systems for in situ adaptation of microbial products and seeded these with the targeted products. These were deployed across the farms of on-farm partners and collected after 3, 10, and 24 months of in-field conditioning. We observed both generalized and site-specific evolution, suggesting that farm-specific adaptation of microbial products may be possible (Kaminsky et al. In prep). - Developed primers that specifically detect the bacterial species in MegaPhos, allowing us to assess its survival in experimental soils and evaluate in-soil survival (Kaminsky et al. 2021. Applied Soil Ecology). - Showed soil-specific adaptation of microbes that changed through time; however, the most substantial genomic shifts were related to in-culture growth, an unavoidable part of the microbial product pipeline. In-culture growth especially had a major influence on the in-soil survival of microbial products (Kaminsky et al. In prep). Research Objective 3 - In collaboration with Franklin Egan and Sara Nawa from PASA, we collected soils from their Soil Health Benchmarks project, which were targeted for use in this Objective. COVID restrictions impaired our ability to move ahead on this Objective in a number of ways. We ultimately moved away from these project objectives to focus on more promising avenues. Extension Objective 1 - Developed and maintained an on-farm network of farmers for this project. Provided them with sequencing and interpretation of soils from their farms, including detailed factsheets developed by L Kaminsky. - In preparing for Res. Obj. 2, L Kaminsky performed a screening of 9 commonly sold microbial products for organic farmers and found that four did not even contain the marketed organism. Although not a robust and replicated study, we have used this as a point of caution in presentations to farmers about the potential of microbial products. - Presentations at PASA annual meeting as well as other soil health series. Extension Objective 2 - We published two written products for eOrganic, focused on assessment and management of in-soil microbes. - Another article was published through Penn State Extension.

Publications


    Progress 09/01/21 to 08/31/22

    Outputs
    Target Audience:Our target audience includes farmers who use organic practices, farmers with interest in organic practices, agricultural practitioners (esp. those involved in the microbial products industry), and academics with a focus on microbial ecology and/or agricultural management. We also have specific close interactions with a number of organic and transitioning farmers in Pennsylvania, with whom we established on-farm projects. Our close interaction with farmers has ensured that our work has direct relevance to the farming community and has also allowed us to understand the wide range of microbial management practices in Pennsylvania, as well as the wide range of perceived benefits and challenges of microorganisms in agriculture. The project has provided training opportunities for undergraduates, graduates, and a postdoctoral fellow. Changes/Problems: We chose to invest more heavily in research objectives 1 and 2, due to promising results and the goals of the people we had available to the project. We decided not to further pursue research objective 3 as our original timeline and workforce was disrupted too heavily by COVID. PI Bell has moved to a new position at the University of Toronto, so this grant is now managed by previous Co-PI Jason Kaye. What opportunities for training and professional development has the project provided?Overall, this project has provided extensive direct training for one undergraduate student (Helen Senerchia), one graduate student (Laura Kaminsky), and one postdoctoral associate (William King). In the past year, two other graduate students have become involved, working on our deployment of microbial traps in the long-term cover crop experiments that are ongoing at Penn State (Sarah Richards and Lily Cao). Our ongoing Extension work has also incorporated three other graduate students (Sarah Isbell, Mara Cloutier, Suzanne Fleishman) who were involved in developing written Extension materials. In the past year: Laura Kaminsky: Heavily involved in both the research and Extension aspects of this project. Laura has helped in recruiting and maintaining our on-farm network, and connected with these partners multiple times through the year, providing them with data-based factsheets. She has also developed and given Extension presentations on microbial products (Ext. Obj. 1 and 2). Leads the project related to on-farm conditioning of microbial products as well as microbial survival under different soil conditions and has performed extensive work in this area, resulting in one publication and a thesis award in the past year (Res. Obj. 2). William King: Heavily involved in developing projects related to assessing microbial recolonization in soils (Res. Obj. 1). Has published multiple articles on this in the past year, while working in his new position at Cornell, and showed that restoring microbial function through microbiome reintroduction is possible. Sarah Richards and Lily Cao: Collection and analysis of data related to microbial trap deployment in a long-term cover crop experiment at Penn State (Res. Obj. 1). Sarah Isbell, Mara Cloutier, Suzanne Fleishman: Publication of Extension article on microbial management that was previously not reported. How have the results been disseminated to communities of interest?Results have been disseminated through farmer events (e.g. Farming for Success Field Day), Extension publications, and academic papers. What do you plan to do during the next reporting period to accomplish the goals?Res Obj. 1 - Complete data analysis and publication of microbial traps in long-term cover crop project. Res. Obj. 2 - Complete two publications related to microbial adaptation under different soil and culture conditions. Res. Obj. 3 - We have decided not to pursue this objective further. Ext Obj. 1 - Nothing planned, but will consider invitations to speak at farmer-facing events. Ext. Obj. 2 - Nothing planned, but will consider opportunities for Extension papers if there is student interest.

    Impacts
    What was accomplished under these goals? Res Obj. 1: How do location, existing management, and microbial re-seeding impact "natural" microbial colonization of soils? Microbial trap transect project was completed and published, showing variability in active microbial colonizers across land use types, but also at very local scales. We performed a controlled experiment of microbiome reintroduction, building on previous work that had suggested this could not "rescue" microbial function in soils. With some technical adjustments in our design (mostly, choice of soils, microbial dilutions, and incubation time), we show the opposite, that certain functions can be rescued through microbiome introductions. We now have two seasons of data on the impact of cover crop mixtures on active microbial colonizers. These are currently being analyzed and we expect a publication in the coming year. Res. Obj. 2: Can we enhance the predictability with which OMRI-certified microbial products establish and function in soils? All data has been collected and much of the data has been analyzed. LM Kaminsky won a Penn State dissertation award for this work and defended her thesis at the end of 2022. She showed soil-specific adaptation of microbes that changed through time; however, the most substantial genomic shifts were related to in-culture growth, an unavoidable part of the microbial product pipeline. LM Kaminsky published a paper on the primers used to assess in-soil survival and showed differential survival of introduced microbes across soil type. We expect two other papers to be published in the next year...these are close to completion, as they were both included in LM Kaminsky's thesis. Res. Obj. 3: To what extent does changing soil microbial composition impact a commonly used metric of soil microbial health? - After consultation with PASA, we opted to not pursue this objective further and to concentrate our effort on our other objectives. Ext. Obj. 1: Work with farmers to develop a mutual understanding of the role of soil microbes in organic agriculture through annual meetings and presentations at farmer conferences. LM Kaminsky presented at the Farming for Success field day hosted by Penn State, speaking on the topic of microbial products. Ext. Obj. 2: Make lasting contributions to farmer decision-making by producing Extension publications that A) communicate our results and B) reveal the breadth of microbial management approaches that are used by farmers in our region. We added one additional Extension publication (not previously reported), summarizing our previous contributions on this topic for farmers.

    Publications

    • Type: Journal Articles Status: Published Year Published: 2023 Citation: King WL, Richards SC, Kaminsky LM, Bradley B, Kaye J, Bell TH. 2023. Leveraging microbiome rediversification for the ecological rescue of soil function. Environmental Microbiome 18: 7.
    • Type: Other Status: Published Year Published: 2021 Citation: Borrelli K, Bell TH, Isbell S, Fleishman S, Kaminsky L, Cloutier M. 2021. Understanding and Managing Soil Microbes. Penn State Extension https://extension.psu.edu/understanding-and-managing-soil-microbes
    • Type: Other Status: Other Year Published: 2022 Citation: Kaminsky LM. 2022. Invited speaker on microbial products. Farming for Success Field Day, hosted by Penn State
    • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Bell TH. 2022. How directed evolution in complex environments can reshape bacterial niche breadth. Canadian Society of Microbiologists Conference, Guelph, ON, Canada.
    • Type: Journal Articles Status: Published Year Published: 2021 Citation: King W, Kaminsky LM, Gannett M, Thompson G, Kao-Kniffin J, Bell TH. 2021. Soil salinization accelerates microbiome stabilization in iterative selections for plant performance. New Phytologist 234: 2101-2110.
    • Type: Journal Articles Status: Published Year Published: 2022 Citation: King WL, Kaminsky LM, Richards SC, Bradley BA, Kaye JP, Bell TH. 2022. Farm-scale differentiation of active microbial colonizers. ISME Communications 2: 39.
    • Type: Journal Articles Status: Published Year Published: 2022 Citation: Kaminsky LM, Bell TH. 2022. Novel primers for quantification of Priestia megaterium populations in soil using qPCR. Applied Soil Ecology 180: 104628.


    Progress 09/01/20 to 08/31/21

    Outputs
    Target Audience:Our target audience includes farmers who use organic practices, farmers with interest in organic practices, agricultural practitioners (esp. those involved in the microbial products industry), and academics with a focus on microbial ecology and/or agricultural management. We also have specific close interactions with a number of organic and transitioning farmers in Pennsylvania, with whom we have established on-farm projects. Our close interaction with farmers ensures that our work has direct relevance to the farming community and has also allowed us to understand the wide range of microbial management practices in Pennsylvania, as well as the wide range of perceived benefits and challenges of microorganisms in agriculture. The project also provides training opportunities for undergraduates, graduates, and a postdoctoral fellow. Changes/Problems:- We are just getting truly back to full capacity and re-evaluating where we are. RO3 has stayed on the backburner as we have prioritized other work. - We may need to look at recruiting changes, as the postdoc on the project may have other career opportunities starting in January. What opportunities for training and professional development has the project provided?This project has provided direct training for one undergraduate student (Helen Senerchia), one graduate student (Laura Kaminsky), and one postdoctoral associate (William King). Our ongoing Extension work has also incorporated three other graduate students so far (Sarah Isbell, Mara Cloutier, Suzanne Fleishman) who were involved in developing written Extension materials. Helen Senerchia: Continued to develop our farmer survey, but has now moved to another position. Looking to move this project to other personnel.(Ext. Obj. 2). Laura Kaminsky: Heavily involved in both the research and Extension aspects of this project. Laura has helped me in recruiting our on-farm network, and connects with these partners multiple times through the year. In addition to establishing research projects on their farms, she has taken samples for them which she then processed for sequencing and/or PLFA analysis. She translated those data into factsheets for the farmers to help them understand the outputs, as well as providing annual project updates (Ext. Obj. 1). Has also contributed to Extension presentations and is developing written and video-based Extension materials (Ext. Obj. 1 and 2). Leads the project related to on-farm conditioning of microbial products as well as microbial survival under different soil conditions (Res. Obj. 2). Has completed and published a project that looks at how soil conditions impact natural microbial recolonization (Res. Obj. 1). William King: Heavily involved in developing projects related to assessing microbial recolonization in soils (Res. Obj. 1). Has developed various on-farm assessment systems to assess recolonization of soils and litter, including the ability to determine how the latter impacts litter decomposition. Further, the litter-based project is nested within the long-term Cover Crop Cocktail project at Penn State, which also helps in building a larger interdisciplinary knowledge base around cover cropping in organic systems (Res. Obj. 1). Published an article focused on factors impacting in-field microbial product success (Res. Obj. 2). Suzanne Fleishman, Mara Cloutier, Sarah Isbell: Contributing to the writing of two articles published in eOrganic. How have the results been disseminated to communities of interest?Results have been disseminated through farmer conferences (e.g. PASA Meeting, Stroud series), Extension articles (e.g. eOrganic), and academic publications. What do you plan to do during the next reporting period to accomplish the goals?Res Obj. 1 - Analysis of sequences from microbial re-introduction project and corn decomposition project. - Submission of manuscript focused on microbial recolonization across transects. - Deployment, sequencing, and analysis of microbial traps in cover crop treatments, in collaboration with a colleague who will look at changes in root composition at the same sites. Res. Obj. 2 - Continued sequence analysis of adapted MegaPhos and Actinovate strains, including publication of comparison between whole genome, 100-isolate mix, and metagenome sequencing approaches. - Complete conditioning of MegaPhos to multiple physical soil environments and performing sequencing to assess adaptation. - Complete publication of in situ adaptation method. Res. Obj. 3 - Re-assess approach for this objective. Potentially advance as originally planned, but will discuss with colleagues who may have related objectives to see if we can do this in a higher impact way. Ext Obj. 1 - Present at upcoming Keystone Crop and Soils Conference and plan for at least one other oral presentation. - Continued discussion/collaboration with on-farm partners. Ext. Obj. 2 - Focus on completing and deploying farmer survey.

    Impacts
    What was accomplished under these goals? Res Obj. 1: How do location, existing management, and microbial re-seeding impact "natural" microbial colonization of soils? - Microbial trap transects that were set up by W King had DNA extracted, bacterial and fungal communities sequenced, and many analyses performed. We have a working draft of this paper and these results are guiding our upcoming work. - Corn litter deployed in cover crop treatments was assessed for decomposition and DNA was extracted and sequenced. Analyses for differences in microbial composition by treatment are ongoing. - For controlled experiment, looking at microbial re-introductions, DNA is extracted and sequenced and accessory analyses (N mineralization and enzyme assays) have been performed. Analyses are ongoing. - We are deploying soil microbial traps throughout the long-term cover crop treatments to look at how cover crops influence active microbial pools. A collaborator is helping us to compare these data to root growth, to determine how these two metrics relate in soil. Res. Obj. 2: Can we enhance the predictability with which OMRI-certified microbial products establish and function in soils? - Additional samplings of field-deployed microbial adaptation devices plys additional sequencing - Have performed numerous genome-level analyses on initial MegaPhos sequencing and are sequencing for Actinovate now. Identified numerous mutant genes, some of which appear to be involved in nutrient acquisition. - It appears the soil conditions may be more important than deployment location, so we are now modifying the incubation soil type to determine how that impacts product adaptation. Res. Obj. 3: To what extent does changing soil microbial composition impact a commonly used metric of soil microbial health? - Due to various COVID challenges and interesting results from the other research aims, we have not made substantial progress on this aim in the past year. We are evaluating the best path forward. Ext. Obj. 1: Work with farmers to develop a mutual understanding of the role of soil microbes in organic agriculture through annual meetings and presentations at farmer conferences. - Continue to managean on-farm network of farmers for this project. Providethem with annual project updates, as well as in-person interaction. - Presentations at PASA annual meeting as well as two other soil health series. Ext. Obj. 2: Make lasting contributions to farmer decision-making by producing Extension publications that A) communicate our results and B) reveal the breadth of microbial management approaches that are used by farmers in our region. - Two publications in eOrganic, focused on demistifying soil microbes and talking about the potential for microbial management in organic ag.

    Publications

    • Type: Other Status: Published Year Published: 2021 Citation: Kaminsky L, Cloutier M, Fleishman S, Isbell S, Borrelli K, Bell TH. 2021. Soil microbes in organic crop production systems 101. eOrganic http://eorganic.org/node/34601
    • Type: Other Status: Published Year Published: 2021 Citation: Isbell S, Fleishman S, Cloutier M, Kaminsky L, Borrelli K, Bell TH. 2021. Management of soil microbes on organic farms. eOrganic http://eorganic.org/node/34646
    • Type: Journal Articles Status: Published Year Published: 2021 Citation: King W, Bell TH. 2021. Can dispersal be leveraged to improve microbial inoculant success? Trends in Biotechnology doi.org/10.1016/j.tibtech.2021.0.
    • Type: Conference Papers and Presentations Status: Other Year Published: 2021 Citation: Bell TH, Kaminsky LM, Richards S. 2021. The present and future of boosting soil health through microbial management. Stroud Water Research Center, Avondale, PA, USA.
    • Type: Conference Papers and Presentations Status: Other Year Published: 2021 Citation: Bell TH. 2021. Potential for management in the soil microbiome. Crops Conference Series.
    • Type: Conference Papers and Presentations Status: Other Year Published: 2021 Citation: Bell TH and Kaminsky LM. 2021. Harnessing soil biology for healthy crops. Pasa Sustainable Agriculture Conference, virtual.


    Progress 09/01/19 to 08/31/20

    Outputs
    Target Audience:Our target audience includes farmers who use organic practices, farmers with interest in organic practices, agricultural practitioners (esp. those involved in the microbial products industry), and academics with a focus on microbial ecology and/or agricultural management. We also have specific close interactions with a number of organic and transitioning farmers in Pennsylvania, with whom we have established on-farm projects. Our close interaction with farmers ensures that our work has direct relevance to the farming community and has also allowed us to understand the wide range of microbial management practices in Pennsylvania, as well as the wide range of perceived benefits and challenges of microorganisms in agriculture. The project also provides training opportunities, for undergraduates, graduates, and a postdoctoral fellow. Changes/Problems:- As mentioned, we could not initiate microbial recolonization transects with our on-farm partners due to COVID restrictions. Depending on our results from initiating this project at the PSU farm, we will decide on the value of pursuing this in the coming year. - Delay in initiating controlled experiments for Res. Obj. 3, again due to COVID restrictions on lab access. Expect to initiate these in the coming year. - Sequencing services have been incredibly slow this year. We hope this picks up in the next few months, or we could have unexpected delays in data generation for the project. What opportunities for training and professional development has the project provided?This project has provided direct training for one undergraduate student (Helen Senerchia), one graduate student (Laura Kaminsky), and one postdoctoral associate (William King). Our ongoing Extension work has also incorporated three other graduate students so far (Sarah Isbell, Mara Cloutier, Suzanne Fleishman) who have been involved in developing written Extension materials. Helen Senerchia: Has been involved in putting together our survey on microbial managementthat we hope to distribute to farmers next year. Helen was involved in creating questions, organizing the survey, transcribing our survey to RedCap, and working through IRB approvals (Ext. Obj. 2). Laura Kaminsky: Heavily involved in both the research and Extension aspects of this project. Laura has helped me in recruiting our on-farm network, and connects with these partners multiple times through the year. In addition to establishing research projects on their farms, she has taken samples for them which she then processed for sequencing and/or PLFA analysis. She translated those data into factsheets for the farmers to help them understand the outputs (Ext. Obj. 1). Has also contributed to Extension presentations and is developing written and video-based Extension materials (Ext. Obj. 1 and 2). Leads the project related to on-farm conditioning of microbial products as well as microbial survival under different soil conditions (Res. Obj. 2). Has completed and published a project that looks at how soil conditions impact natural microbial recolonization (Res. Obj. 1). William King:Heavily involved in developing projects related to assessing microbial recolonization in soils(Res. Obj. 1). Has developed various on-farm assessment systems to assess recolonization of soils and litter, including the ability to determine how the latter impacts litter decomposition. Further, the litter-based project is nested within the long-term Cover Crop Cocktail project at Penn State, which also helps in building a larger interdisciplinary knowledge base around cover cropping in organic systems(Res. Obj. 1). Suzanne Fleishman, Mara Cloutier, Sarah Isbell: Contributing to the writing of two eOrganic articles on microbial assessment and management that we expect to submit in December 2020. How have the results been disseminated to communities of interest?Results have mostly been disseminated through a pair of farmer conferences last winter and a research publication, as well as research-focused talks. In addition, we have had direct conversations with our on-farm partners regarding project progress and results. What do you plan to do during the next reporting period to accomplish the goals?Res Obj. 1 - Collection and sequencing of samples from field deployments. Analysis of how soil conditions and distance from forest and/or cover crop treatments influenced microbial colonization. - Functional assessment of controlled experiments to determine how microbial reintroductions influence soil function. - Assess value of on-farm deployments for this project with farmer partners. Res Obj. 2 - Analysis of sequences generated to assess microbial adaptation through on-farm conditioning. - Collection of long-term on-farm samples for this project (likely collection at 16 or 18 months). - Validation of developed qPCR probes for MegaPhos as well as testing of in-soil persistence. - Attempt to develop qPCR probes for Actinovate (this has so far been a challenge). - Determine subset of field-conditioned Actinovate samples for sequencing and assessment of on-farm adaptation. Res Obj. 3 - Expect to initiate respiration experiments with soils collected through PASA collaboration. Ext Obj. 1 - Along with L Kaminsky, I will present on our work at the PASA Conference in January. We also expect to present at 1-2 research meetings, depending on what conferences look like for next year. - Continued discussion and collaboration with on-farm partners. Ext Obj. 2 - Submission and publication of two eOrganic articles focused on microbial assessment and microbial management in organic farming systems. - Publication of L Kaminsky video on microbial assessment. - Deployment of farmer survey to assess integration and perceptions of microbial management in Pennsylvania.

    Impacts
    What was accomplished under these goals? Res Obj. 1:How do location, existing management, and microbial re-seeding impact "natural" microbial colonization of soils? - L Kaminsky published a paper looking at how soil conditions interact with microbial sources to shape microbial colonization (Kaminsky et al. 2020). This paper showed that the pool of colonizers is more limited when soils have been disturbed through added nutrients or salt accumulation (as can occur in high tunnel systems), with mostly generalist microorganisms surviving. - Initially we had planned to set up transects for assessing microbial recolonization at each on-farm location, but due to COVID restrictions early in the year, we adapted this to be performed exclusively at the PSU Russell Larson Ag Center. Microbial traps were deployed across multiple transects by W King, collected at two time points, and DNA is being extracted for future sequencing. Microbial regrowth in farm soil appears to be slower than in forest soil. - W King deployed corn litter in litter bags throughout the Cover Crop Cocktail plots at the long-term organic site at the Russell Larson Ag Center in order to assess the impact of cover crops on litter colonization and decomposition. These will be collected in December to assess decomposition and microbial composition. - W King also initiated a controlled experiment which aims to look at how microbial reintroductions influence soil functioning. This will incubate for the next ~3 months, so we expect results within the next year. Res. Obj. 2:Can we enhance the predictability with which OMRI-certified microbial products establish and function in soils? - Identified two commonly sold and OMRI-certified microbial products that contain the marketed organism and that perform a clear and known function in soils (Actinovate and MegaPhos). - Developed systems for in situ adaptation of microbial products and seeded these with the targeted products. - Systems deployed to farms of on-farm partners and two organic-certified land at Russell Larson Agricultural Center at PSU. Collected after 3 and 10 months of in-field conditioning, with 1-2 more sets of units still deployed in the field. - To assess genomic change, we sequenced the ancestral and conditioned products for MegaPhos in 3 ways: 1) single collected isolates, 2) pools of 100 isolates, and 3) soil metagenomes. We will compare these approaches to determine which is ideal for assessing in situ adaptation. - L Kaminsky has developed primers that specifically detect the MegaPhos strain, allowing her to assess its survival in experimental soils. This will allow us to perform differential survival assays over the next year to see whether on-farm conditioning impacts in-soil survival. Res. Obj. 3:To what extent does changing soil microbial composition impact a commonly used metric of soil microbial health? - In collaboration with Franklin Egan and Sara Nawa from PASA, we collected soils from their Soil Health Benchmarks project, which will be used in this Objective. COVID restrictions have impaired our ability to move ahead on this Objective in a number of ways, including lab shutdowns through June, restrictions to one person at a time now, and slow sequencing from providers. Ext. Obj. 1: Work with farmers to develop a mutual understanding of the role of soil microbes in organic agriculture through annual meetings and presentations at farmer conferences. - Developed and maintained an on-farm network of farmers for this project. Provided them with sequencing and interpretation of soils from their farms, including detailed factsheets developed by L Kaminsky. - In preparing for Res. Obj. 2, L Kaminsky performed a screening of 9 commonly sold microbial products for organic farmers and found that four did not even contain the marketed organism. Although not a robust and replicated study, we use this as a point of caution in presentations to farmers about the potential of microbial products. Ext. Obj. 2: Make lasting contributions to farmer decision-making by producing Extension publications that A) communicate our results and B) reveal the breadth of microbial management approaches that are used by farmers in our region. - We have prepared the bulk of a survey that will be used to assess microbial management strategies and perceptions in Pennsylvania. We hope to distribute this in the next year. - We have made substantial progress on two written products for eOrganic, which we expect to submit in December. - L Kaminsky developed a video explaining common metrics for microbial assessment, which she is editing for publication through Penn State Extension.

    Publications

    • Type: Conference Papers and Presentations Status: Other Year Published: 2019 Citation: Bell, T.H., & Kaminsky, L. (2019). "Can we enhance microbial contributions to regenerative ag systems?," Regenerative Grazing From The Ground Up, Pennsylvania Association for Sustainable Agriculture, Spring Creek Farm - Wernersville, PA.
    • Type: Conference Papers and Presentations Status: Other Year Published: 2019 Citation: Bell, T.H. (2019). "The invisible and essential inhabitants of soil," PASA Advanced Farmer Gathering: Collaborating to Improve Your Workforce and Your Soil, Pennsylvania Association for Sustainable Agriculture, Harrisburg, PA.
    • Type: Conference Papers and Presentations Status: Other Year Published: 2019 Citation: Kaminsky, L., Peoples, T., & Bell, T.H. (2019). "Characterizing the primary microbial colonizers of soil," Microbiome Center Networking Event, Penn State, University Park, PA.
    • Type: Journal Articles Status: Published Year Published: 2020 Citation: Kaminsky, L., Esker, P., & Bell, T.H. (2020) Abiotic conditions outweigh microbial origin during bacterial assembly in soils. Environmental Microbiology doi:10.1111/1462-2920.15322.
    • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Bell, T.H. (2020). "Can we manipulate soil microbiomes?," Colorado State University, Fort Collins, CO (virtual).