Source: UNIVERSITY OF NEBRASKA submitted to NRP
THE ROLE OF PLANT ROOT EXUDATES IN SHAPING SOIL MICROBIAL COMMUNITY COMPOSITION AND THE INFLUENCE THAT HAS ON NUTRIENT CYCLING AND NITROGEN USE
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
Reporting Frequency
Annual
Accession No.
1022979
Grant No.
2020-67019-31796
Cumulative Award Amt.
$749,812.00
Proposal No.
2019-08314
Multistate No.
(N/A)
Project Start Date
Jul 1, 2020
Project End Date
Jun 30, 2025
Grant Year
2020
Program Code
[A1402]- Agricultural Microbiomes in Plant Systems and Natural Resources
Recipient Organization
UNIVERSITY OF NEBRASKA
(N/A)
LINCOLN,NE 68583
Performing Department
Agronomy and Horticulture
Non Technical Summary
The leaching of nitrates from agricultural soils due to fertilizer application is clearly a problem in many parts of the United States. In California, nitrate in groundwater is a health risk for about 250,000 people in the Tulare Lake Basin and Salinas Valley. In Iowa, the Des Moines water district is spending millions of dollars to remove nitrates in water coming from the Raccoon and Des Moines rivers. The effects of nitrates and also phosphate may be visualized in the dead zone that forms around the Mississippi River delta in the gulf of Mexico. To maintain productive agricultural systems the application of fertilizer is essential, but it will be important to find multiple solutions to reduce the nitrate contamination of ground and surface waters. Nitrification inhibitors may contribute to reducing nitrification. However using plants that exude natural products that inhibit nitrifying bacteria is a more environmentally friendly and is more economical for farmers and may be more effective than the application of inhibitors.The rhizosphere is the key region where plant roots interact with soils and microbes to acquire essential minerals and water. Soil ecosystems contain one of the most diverse arrays of microbial species that are free living or live in association with plant roots and their rhizosphere. The characterization of the nitrifying microbes in soils and the opportunity for biological nitrification inhibition through root exudates has the potential to increase the nitrogen use efficiency of agroecosystems in the United States by either using sorghum in rotations or by engineering maize to produce exudates that inhibit nitrification. This biological solution has the potential to reduce nitrate leaching on over 100 million acres of farmland where maize is being grown. The reduction in nitrate leaching will reduce the negative impact that fertilizers have on waterways and drinking water.The rhizosphere and the soil around the roots are the major regions from where plants acquire essential minerals and water. The rhizosphere contains many different root exuded metabolites including carbon compounds, hormones, amino acids and other small molecules. Research on how root exudates influence the soil microbiome has the potential to reduce the environmental footprint of commercial agriculture and to increase the economic efficiency of crop production through reductions in fertilizer. Little is known about how plant root exudates influence the function of the soil microbiome and the effect this has on environmental processes such as nutrient cycling. The goal of this project is to elucidate how the sorghum root exudates sorgoleone and strigolactone influence the rhizosphere and soil microbial communities and how this may enhance nutrient use efficiency and yield.Sorgoleone is the major root exudate that has been shown to be a biological nitrification inhibitor, but its role in shaping the soil microbiome or in reducing the loss of nitrogen from field based agroecosystems has not been determined. Strigolactone is an important root exudate and plant hormone induced by phosphorus and nitrogen deficiency and acts as a signal for mycorrhizal fungi and parasitic plants, but it's impact on the bacterial, archaeal and fungal microbiomes and on nutrient use efficiency has not been determined. This project will focus on how root exudates shape microbial community composition and soil functional properties with emphasis on nitrification and nitrogen use efficiency.
Animal Health Component
10%
Research Effort Categories
Basic
90%
Applied
10%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
1025210110035%
2010110102035%
2064099106030%
Goals / Objectives
Aim 1: Determine the dynamics across two seasons of sorgoleone exudation and how that alters nitrification rates and nitrifying bacteria and archaea in the rhizosphere and in the soil outside of the rhizosphere.Aim 2: Determine whether sorgoleone alters the rate of nitrogen leaching in soil.Aim 3: Directly test the effect of sorgoleone on field soil microcosms to determine how sorgoleone alters the microbial community composition, nitrification potential and ammonia monooxygenase (amoA) gene abundance.Aim 4: Characterize transgenic plants for changes in strigolactone exudation and test how exudation of strigolactone from sorghum roots alters bacterial, archaeal, and fungal communities in the endosphere, rhizosphere and soil, and determine how these lines perform and acquire nitrogen in the field.
Project Methods
Aim 1 - Determine the dynamics across two seasons of sorgoleone exudation and how that alters soil nitrification rates and the abundance of nitrifying bacteria and archaea in the rhizosphere and in the soil outside of the rhizosphere. In the summers of 2020 and 2021, the wild type sorghum and two RNAi events will be planted in replicated plots (eight replicates per sorghum line). As a control, nitrapyrin will be added to another eight plots where the wild type is being grown. Nitrapyrin is a chemical nitrification inhibitor that is used in commercial agriculture. There will also be four unplanted plots. Each plot (36 total) will consist of four rows and will be of sufficient length to ensure that the intensive sampling can be done without excessive disruption to the plots for accurate estimates of leaching as described in Aim 2. The sorghum rhizosphere and the soil near roots will be sampled on a weekly basis during the season starting four weeks after germination, and will continue for about 10 weeks and will cease several weeks before the grain is harvested. Plants will be excavated from all plots from the outer two of the four rows. The inner two rows will not be sampled during the season but will be used to estimate the per plot grain yield at the end of the season. Soils will be stored at 4oC and analyzed the same week of collection.At each sampling time, 36 rhizosphere, 36 soil near root samples and 36 soil cores will be collected. These samples will then be used for analysis using digital droplet PCR (ddPCR), which will provide information about absolute abundance of the amo genes.PCR primer sets will be synthesized to quantify the amo gene (ammonia monooxygenase) in bacteria and archaea in soil. There have been a number of different primers used over the years for ammonia oxidizing archaea (AOA) and for ammonia oxidizing bacteria (AOB).Aim 2: Determine whether sorgoleone significantly alters the rate of nitrogen leaching in soil.Nitrate leaching will be measured using anion resin bags buried one meter below the soil surface prior to planting. The top one meter of soil contains over 90% of the roots of maize which should be similar to sorghum. Five resin filled bags will be placed in each plot. These bags will be placed in the center of the plots under the two rows of sorghum that will not be sampled during the season. The resin bags will contain 100 mls of Purolite A-400 anion exchange resin in a 0.1 X 0.1 meter organza fabric bag and will be buried before planting. All the nitrogen absorbed by the resin in each bag will be assumed to come from leaching of nitrate directly above the bag. 500 mls of 3M KCl will be used to extract the nitrate from the resin after retrieval for a 92% efficiency of nitrate recovery from the resin. A colorimetric microplate technique based on the Greiss reaction will be used to determine the concentration of NO3 -N in all extracts.Aim 3: Directly test the effect of sorgoleone on field soil microcosms to determine how sorgoleone alters the microbial community composition, nitrification potential and amoA gene abundance.Microcosms will also be used in these studies to provide a more controlled environment to test the effects of sorgoleone on changes in the microbial community composition and nitrification potential of the soil. Microcosms have been used widely in a range of studies in soil and water microbiology and their use will help to establish a more direct link between sorgoleone and functional changes in the microbiome such as nitrification. To conduct these experiments, we have a small supply of sorgoleone, but will isolate more as described previously.Soil cores will be brought in from the field at three different times during the growing season. Soil cores will be taken from areas away from roots to ensure that there is no sorgoleone in the soil at the start of these assays. Cores will be from three depths where roots are primarily located. Soils will be sieved and mixed well to ensure uniformity between microcosms. Soil will be maintained at a constant moisture content. Headspace in the jar will be flushed regularly with air and water will be added to keep the moisture content constant. At the start of the experiment three concentrations of sorgoleone will be added to four replicate soil microcosms and soil will be homogenized.Aim 4 - Characterize transgenic plants for changes in strigolactone exudation and test how exudation of strigolactone from sorghum roots alters bacterial, archaeal, and fungal communities in the endosphere, rhizosphere and soil, and determine how well these lines perform and acquire nitrogen in the field.Currently, we have three homozygous edited lines and one has been confirmed to have orabancol exudation abolished beyond levels of detection. Orabancol is the most abundant form of strigolactone exuded by bTX430 sorghum roots. We have characterized the molecular edits in two other lines (SbCCD8b and SbCCD8d-like) (Fig. 7) and now need to determine the exudate profiles in these lines during year 1 of the project. These lines will be grown in the field in years 2 and 3 to test whether they alter the bacterial, archaeal, and fungal microbiomes of the rhizosphere and soil around the roots, change nitrification rates and yields of the sorghum under full and low nitrogen. In this study, the characterization of changes in fungal community composition is particularly important because strigolactone has been shown to act as a signal in mycorrhizal colonization, and microbe communities from different phyla may be interrelated or co-dependent.Evaluation of exudates of SbCC8a, SbCCD8b, and SbCCD8d-like edited lines. The sorghum root exudates will be isolated using a hydroponic system, where plants will be grown up for two weeks in a modified Hoaglands solution and then deprived of nitrogen to stimulate the exudation of strigolactones. After seven days, hydroponic solutions will be collected and put through C18 solid phase extraction columns to concentrate the strigolactone. This will be done for the remaining edited lines for SbCCD8b and the SbCCD8d-like isoforms (described in preliminary results). The samples will then be analyzed using the multiple reaction monitoring (MRM)-based LC-MS/MS methods.The available standards for three strigolactones: strigol, 5-deoxystrigol, and orobanchol will be purchased.Testing for performance, nutrient use efficiency and microbial communities. We will use similar procedures as in Aim 1 to sample the soil but will focus on the root endosphere, rhizosphere, and bulk soil. We will analyze the bacterial and fungal community composition and diversity in wild type sorghum and in the CRISPR/Cas9 lines, which have edited the SbCCD8 genes. This plant material will be grown in full nitrogen soils and in plots where nitrogen has been depleted (low nitrogen) because of reports that indicate strigolactone production is enhanced by low nitrogen conditions and these are the conditions where we may see difference between wild type and the edited lines. Four row plots will be used with eight replicate plots and the two treatments (full nitrogen and low nitrogen). This will be a fully randomized design including 2 - 4 unplanted plots.Endosphere, rhizosphere, and bulk soil will be collected and analyzed in a similar manner to what we have published previously. Since mycorrhizal fungi are also implicated in the acquisition of nitrogen from soils and since strigolactone is an important signal for mycorrhizal colonization, we will use trypan blue staining to quantify the colonization rates in roots. Phenotyping of the plants in the field will be conducted to more fully characterize the differential responses of the SbCCD7 and SbCCD8 edited lines as compared to the wild type under low nitrogen and sufficient nitrogen as described in Aim 1.

Progress 07/01/23 to 06/30/24

Outputs
Target Audience:Our target audience is the scientific community mainly reached through peer-reviewed publications. Changes/Problems:We lost two summers of data for Aim 2 because of the very dry conditions. This year already appears wetting in Nebraska and if it is too dry we will use irrigation to complete experiments for Aims 2 and 3. What opportunities for training and professional development has the project provided?Training of a new postdoc occurred in 2023 as well as on undergraduate student. How have the results been disseminated to communities of interest?Via peer reviewed publications listed previously. What do you plan to do during the next reporting period to accomplish the goals?In 2024 we are committed to finishing the work of Aim 2by doing another field experiment using irrigation as necessary and obtaining data on leaching. Wewill also extend this to capture data for Aim 3 using quantitative PCR to monitor amoA genes, sample soils to measure nitrification potential, and study microbial community structure.

Impacts
What was accomplished under these goals? Aim 1:Completed Aim 2: Determine whether sorgoleone alters the rate of nitrogen leaching in soil. During the summer of 2021 we developed and tested a system to measure leaching of nitrate in large field plots using an anion exchange resin. We buried mesh bags containing resin to a depth of 0.5 meters in the early summer. A subset of bags was extracted from the soil in Sept of 2021 and remained in April 2022. Three genotypes were tested one with high sorgoleone, one with low sorgoleone, and one with high resorcinol which is a lipid related to sorgoleone. Preliminary results suggest that the plots in which sorghum lines were planted with higher levels of sorgoleone in root exudates did show less nitrate leaching. A more comprehensive experiment was planted in June of 2022 to repeat with greater replication of the experiment planted in 2021, but this experiment failed because of the extremely dry conditions. The summer of 2023 was also very dry so an experiment was not attempted. Therefore in 2024 we are committed to finishing this work by using irrigation as necessary and obtaining data on leaching and will also extend this to capture data for Aim 3 using standard quantitative PCR to monitor amoA genes, sample soils to measure nitrification potential, and study microbial community structure. Aim 3: Directly test the effect of sorgoleone on field soil to determine how sorgoleone alters the microbial community composition, nitrification potential and ammonia monooxygenase (amoA) gene abundance. This will be done this summer in our field experiment in 2024. Aim 4: Completed

Publications

  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Hao, J., Y. Yang, S. Futrell, E. Kelly, C. Lorts, B. Nebie, S. Runo, J. Yang , S. Alvarez, J. Lasky and D. Schachtman (2023). "CRISPR/Cas9-mediated mutagenesis of carotenoid cleavage dioxygenase (CCD) genes in sorghum alters strigolactone biosynthesis and plant biotic interactions." Phytobiomes 7:339 - 351.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Hao, J. J., Y. N. Chai, L. D. Lopes, R. A. Ordonez, E. E. Wright, S. Archontoulis and D. P. Schachtman (2021). "The Effects of Soil Depth on the Structure of Microbial Communities in Agricultural Soils in Iowa (United States)." Applied and Environmental Microbiology 87(4): e02673-02620.
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Lopes, L., S. Futrell, E. Wright, G. Danalatos, M. Castellano, T. Vyn, S. Archontoulis and D. Schachtman (2023). "Soil depth and geographic distance modulate bacterial ??diversity in deep soil profiles throughout the US Corn Belt." Molecular Ecology 32:37183732.
  • Type: Journal Articles Status: Published Year Published: 2024 Citation: Chai, Y. N., Y. Qi, E. Goren, D. Chiniquy, A. M. Sheflin, S. G. Tringe, J. E. Prenni, P. Liu and D. P. Schachtman (2024). "Root-associated bacterial communities and root metabolite composition are linked to nitrogen use efficiency in sorghum." mSystems 9(1): e0119023.


Progress 07/01/22 to 06/30/23

Outputs
Target Audience:The target audiencereached by our efforts has mainly been the plant and soil science scientific communities. Dissemination of information has mainly been done through the publication of journal articles. Changes/Problems:The postdoc working on part of the project left to return to his home country in Brazil. Hiring a new postdoc has slowed down some of the work. A new postdoc has been hired and they are now waiting for their visa to work in the USA. What opportunities for training and professional development has the project provided?A postdoc was trained, as well as a technician and several undergraduate. The technician was trained to do field work and basic lab work including DNA extraction, DNA quantification and 16S library construction. The postdoc was trainedto do field work and basic lab work including DNA extraction, DNA quantification, 16S library construction and also the analysis of 16S data. The postdoc also received training in the analysis of 16S data and manuscript writing. How have the results been disseminated to communities of interest?Six refereed manuscript have been or are in the process of being published. What do you plan to do during the next reporting period to accomplish the goals?Complete the data analysis and work being done for aim 2 and initiate and complete the work described in aim 3.

Impacts
What was accomplished under these goals? Aim 1 - This work has been completed and a paper published. Aim 2 - This aim is still ongoing with one season of preliminary data and data from the 2022 season being processed. Resin bags that were left in the field over winter and were excavated several weeks ago. Aim 3 - We are working on the experimental design and will complete this experiment upon arrivalof new postdoc. Aim 4 - This work has now been completed, paper was submitted and we are currently waiting for the publication to appear.

Publications

  • Type: Journal Articles Status: Accepted Year Published: 2023 Citation: Hao, J., Y. Ying Yang, S. Futrell, E. A. Kelly, C. M. Lorts, B. Nebie, S. Steven Runo, J. Jinliang Yang, S. Sophie Alvarez, J. R. Jesse R. Lasky and D. P. Schachtman (2023). "CRISPR/Cas9-mediated mutagenesis of carotenoid cleavage dioxygenase (CCD) genes in sorghum alters strigolactone biosynthesis and plant biotic interactions " Phytobiomes Journal in press.
  • Type: Journal Articles Status: Accepted Year Published: 2023 Citation: Lopes, L., S. Futrell, E. Wright, G. Danalatos, M. Castellano, T. Vyn, S. Archontoulis and D. Schachtman (2023). "Soil depth and geographic distance modulate bacterial ??diversity in deep soil profiles throughout the US Corn Belt." Molecular Ecology In press.
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Lopes, L. D. and D. P. Schachtman (2023). "Rhizosphere and bulk soil bacterial community succession is influenced more by changes in soil properties than in rhizosphere metabolites across a maize growing season " Applied Soil Ecology 189: 104960.
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Lopes, L. D., S. Futrell and D. P. Schachtman (2023). "Root exudate concentrations of indole-3-acetic acid (IAA) and abscisic acid (ABA) affect maize rhizobacterial communities at specific developmental stages " FEMS Microbiology Ecology 99: 1-12.
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Lopes, L., P. Wang, S. Futrell and D. Schachtman (2022). "Sugars and jasmonic acid concentration in root exudates effect maize rhizosphere bacterial communities." Applied and Environmental Microbiology e00971-22.
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Chai, Y. N. and D. P. Schachtman (2022). "Root exudates impact plant performance under abiotic stress." Trends in Plant Science 27(1): 80-91.


Progress 07/01/21 to 06/30/22

Outputs
Target Audience:In this past granting period the target audience was readers of the journal of mSystems (IF=6.5) and Trends in Plant Science (IF=12.5). Citations so far have been from Spain, Scotland, the Netherlands and other countries for the mSystems paper. There have been 241 readers of the manuscript according to Researchgate and 5 citations so far according to Google Scholar. The Trends in Plant Science review we wrote that was published in 2022 has been cited by 12 other manuscripts according to Google Scholar written by scientists in Australia, China and the UK. This review has been read by 202 scientists according to ResearchGate. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?A postdoc, undergraduates and a technician have worked on the project over the years and gained experience in microbial ecology, field approaches to studying nitrification, soil microbes and agronomic parameters. How have the results been disseminated to communities of interest?Mainly through publications in refereed journals. What do you plan to do during the next reporting period to accomplish the goals?Continue working on aim 2 and aim 3 and get the work from aim 4 published.

Impacts
What was accomplished under these goals? Aim 1: Determine the dynamics across two seasons of sorgoleone exudation and how that alters nitrification rates and nitrifying bacteria and archaea in the rhizosphere and in the soil outside of the rhizosphere. This work has beencompleted and the manuscript was published in 2021. The research showed that sorgoleone under field conditions had the strongest impacts on rhizophere soil inhibition of nitrification at specific developmental times during sorghum development. We also found that the soil outside of the rhizosphere did not experience the same type of inhibition of nitrification due to sorgoleone leading to the hypothesis that sorgoleone may not have a significant overall effecton inhibiting nitrification under field conditions. Aim 2:Determine whether sorgoleone alters the rate of nitrogen leaching in soil. During the summer of 2021 we developed and tested a system to measure leaching of nitrate in large field plots using an anion exchange resin. We buried mesh bags containing resin to a depth of 0.5 meters in the early summer. A subset of bags was extracted from the soil in Sept of 2021 and the remained in April 2022. Three genotypes were tested one with high sorgoleone, one with low sorgoleone and one with high resorcinol which is a lipid related to sorgoleone.Preliminary results suggest that the plots in which sorghum lines were planted with higher levels of sorgoleone in root exudatesdid show less nitrate leaching. The bags extracted in April 2022 are currently being analyzed for nitrate levels. A more comprehensive experiment was planted in June of 2022 to repeat with greater replication the experiment planted in 2021. Aim 3:Directly test the effect of sorgoleone on field soil microcosms to determine how sorgoleone alters the microbial community composition, nitrification potential and ammonia monooxygenase (amoA) gene abundance. Nothing to report at this time. Aim 4:Characterize transgenic plants for changes in strigolactone exudation and test how exudation of strigolactone from sorghum roots alters bacterial, archaeal, and fungal communities in the endosphere, rhizosphere and soil, and determine how these lines perform and acquire nitrogen in the field. Field experiments have been conducted on three transgenic lines of sorghum in which three CCD8 genes have been inactived using CRISPR editing.Knockout of the CCD8 genes altered the production of strigolactones, and knockout of CCD8b reduced grain yield and altered the root architecture and sorghum susceptibility to Striga. In addition, changes in root exudation of orobanchol due to the knockout of the CCD8b geneimpactedthe rhizosphere bacterial diversity and community composition. The fungal taxa that were differentially enriched due to changes in the exudation of orobanchol also highlight the role of this plant hormone on plant-microbe interactions. Our findings also shed light on a potentially sustainable and effective approach for parasitic weed management identified in this study. We found that the resistance of one strain of Striga was due to the exudation of orobanchol. This unique experiment was done in collaboration with colleagues at the Penn State University. It highlights that the manipulation of strigolactone production may be a pathway to modifying the resistance of crops to the parasitic plants but because of the plietrophic effects additional work will be required to fine tune this strategy.

Publications

  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Chai, YN, Schachtman, DP (2022) Root exudates impact plant performance under abiotic stress. Trends in Plant Science 27:80-91. https://doi.org/10.1016/j.tplants.2021.08.003
  • Type: Journal Articles Status: Submitted Year Published: 2022 Citation: CRISPR/Cas9-mediated mutagenesis of carotenoid cleavage dioxygenase (CCD) genes affects strigolactone biosynthesis and plant biotic interactions in sorghum Jingjie Hao, Ying Yang, Elizabeth Kelly, Claire M. Lorts, Baloua Nebie, Steven Runo, Jesse R. Lasky, Sophie Alvarez, Stephanie Futrell, Daniel P. Schachtman 2022 New Phytologist


Progress 07/01/20 to 06/30/21

Outputs
Target Audience:Target audience is other scientists and the general public who consider nitrate in ground water important. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?One postdoc and 1 technician has been trained. Dr. Schachtman has gained new knowledge about strigolactone and its impacts of the rhizosphere. New methods have been developed for the analysis of sorgoleone using a mass spectrometer. How have the results been disseminated to communities of interest?One publication so far. What do you plan to do during the next reporting period to accomplish the goals?Continue with Aims 2 in the field next summer and excavate resin bags in current field over the next six months. Continue with Aim 4 and get information on fungal populations followed by a publication.

Impacts
What was accomplished under these goals? Aim 1 -Determine the dynamics across two seasons of sorgoleone exudation and how that alters nitrification rates and nitrifying bacteria and archaea in the rhizosphere and in the soil outside of the rhizosphere. This aimwas completed and the work has been published. Aim 2 -Determine whether sorgoleone alters the rate of nitrogen leaching in soil. Sorghum varieties were tested to find one that had high and low rates of sorgoleone exudation. These varieties were planted in 2021 and three levels of nitrogen were applied. Three bags containing anion exchange resin were buried in each plot. One bag was excavated and will be analyzed for nitrate in Sept 2021. Aim 3 -Directly test the effect of sorgoleone on field soil microcosms to determine how sorgoleone alters the microbial community composition, nitrification potential and ammonia monooxygenase (amoA) gene abundance. no progess Aim 4 -Characterize transgenic plants for changes in strigolactone exudation and test how exudation of strigolactone from sorghum roots alters bacterial, archaeal, and fungal communities in the endosphere, rhizosphere and soil, and determine how these lines perform and acquire nitrogen in the field. The field work has been completed and data analyzed. Work continues in the lab analyzing data and studying the transgenic plant phenotypes.

Publications

  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Wang, P., Chai, Y.N., Roston, R., Dayan, F.E., Schachtman, D.P. (2021) The Sorghum bicolor root exudate sorgoleone shapes bacterial communities and delays network formation, mSystems 6: 10.1128/mSystems.00749-20