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Data from: Abiotic and biotic context dependency of perennial crop yield

Cite this dataset

McKenna, Thomas (2020). Data from: Abiotic and biotic context dependency of perennial crop yield [Dataset]. Dryad.


Perennial crops in agricultural systems can increase sustainability and the magnitude of ecosystem services, but yield may depend upon biotic context, including soil mutualists, pathogens and cropping diversity. These biotic factors themselves may interact with abiotic factors such as drought. We tested whether perennial crop yield depended on soil microbes, water availability and crop diversity by testing monocultures and mixtures of three perennial crop species: a novel perennial grain (intermediate wheatgrass—Thinopyrum intermedium-- that produces the perennial grain Kernza®), a potential perennial oilseed crop (Silphium intregrifolium), and alfalfa (Medicago sativa). Perennial crop performance depended upon both water regime and the presence of living soil, most likely the arbuscular mycorrhizal (AM) fungi in the whole soil inoculum from a long term perennial monoculture and from an undisturbed native remnant prairie. Specifically, both Silphium and alfalfa strongly benefit from AM fungi. The presence of native prairie AM fungi had a greater benefit to Silphium in dry pots and alfalfa in wet pots than AM fungi present in the perennial monoculture soil. Kernza did not benefit from AM fungi. Crop mixtures that included Kernza overyielded, but overyielding depended upon inoculation. Specifically, mixtures with Kernza overyielded most strongly in sterile soil as Kernza compensated for poor growth of Silphium and alfalfa. This study identifies importance of soil biota and the context dependence of benefits of native microbes and the overyielding of mixtures in perennial crops.


Experiment location

The pot experiment was conducted in the west campus greenhouse at the University of Kansas in Lawrence, Kansas U.S.A.  Greenhouse temperature controls were set to allow a temperature range of 65 to 85 °F and no supplemental lighting was used.

Soil inoculum

Pots (7 L) were partially filled with a steam sterilized (twice at 174 ° F) 50:50 sand:soil  mixture. The nutrient content of the sterilized soil was 15.8 ppm phosphorus via Melich extraction and 26.55 ppm nitrate (NO3-N) and 5.8 ppm ammonium (NH4-N) via KCl extractions. One of four soil inoculum was added (280 cm3 total, 4% by volume), and then the pots were filled the rest of the way with the sterile sand:soil mixture. Each inoculum consisted of two components (140 cm3 each): live whole soil and live prairie AM fungi (LWLF), live whole soil and sterilized prairie AM fungi (LWSF), sterile whole soil and live prairie AM fungi (SWLF), or sterile whole soil and sterile prairie AM fungi (SWSF). The small volume of inoculum was used to minimize potential differences in abiotic properties among the inoculum, which may be due to soil conditioning effects or nutrient release after sterilization [54].

The whole soil was collected from long-term (established in 2002) monoculture plots of intermediate wheatgrass (T. intermedium) at The Land Institute in Salina, KS as part of the Agroecology Research Trials (38.767690°, -97.572539°). We chose to use a soil community with a history of long-term soil conditioning by T. intermedium, without disturbance (no tillage), to test T. intermedium-specific pathogens and mutualists (i.e. AM fungi), which have been shown to be important in mediating overyielding in perennial systems [37]. Whole soil was collected from the top 10 cm, sieved (1 cm), and stored at 4°C for less than one week prior to inoculating the experiment.

The prairie AM fungi inoculum was isolated and cultured from a native Kansas remnant prairie (39.044991°, -95.191569°) with Oska silty clay loam and Pawnee clay loam soil types [55]. Undisturbed remnant prairies contain unique AM fungi communities not found in highly disturbed agricultural systems [16], and studies have shown differential responses of plant species to fungi isolated from remnant prairies relative to disturbed fungi [6]. In a previous experiment, alfalfa and Silphium were shown to be highly responsive to AM fungi [7]. This inoculum was used to test the differential responsiveness of the crop communities to the whole soil and prairie AM fungi inoculum. The prairie AM fungi inoculum consisted of seven AM fungi species with high spore abundance at the time of sampling: Scutellospora dipurpurescens, Gigaspora gigantea, Funneliformis mosseae, Funneliformis geosporum, Glomus mortonii, Rhizophagus diaphanous, and Claroideoglomus claroideum. Each species of AM fungi was cultured independently on native prairie plants for one growing season in a sterilized 50:50 sand:soil mixture (10.15 ppm P via Melich extraction, 7.375 ppm NO3-N, 22.2 ppm NH4-N via KCl extractions) under greenhouse conditions (see [56] for a detailed description of isolation and culturing). A community mixture of these cultures was homogenized and used as our native AM fungi treatment ("LF" for living cultures). All biota from the live whole soil and live fungi were sterilized via autoclaving (2 X 60 minutes at 121°C) to create the sterile whole soil (SW) and sterile AM fungi (SF) treatments so that each pot had similar additions of whole soil and cultured fungal inoculum, whether living or dead. The sterilized SWSF inoculum was used to test the responsiveness of the crop communities in the absence of soil biota.

Crop community

Six crop communities were designed to test overyielding that included all possible combinations of monoculture and biculture plantings for the three perennial crop species, Silphium integrifolium (henceforth referred to as Silphium or S), Medicago sativa (henceforth referred to as alfalfa or A) and Thinopyrum intermedium (henceforth referred to as Kernza or K). Any combination of two letters represents a biculture (i.e. KA represents a Kernza/alfalfa biculture plant community). Kernza and Silphium seeds were obtained from The Land Institute’s breeding program, and The Land Institute granted permission for seed use.  Alfalfa (Kansas Common variety) seeds were purchased from a commercial supplier. Silphium seeds were cold moist stratified two months prior to germination. Alfalfa was inoculated with commercially produced rhizobia (Exceed Superior Legume Inoculant for alfalfa/true clover, Visjon Biologics, Wichita Falls, TX, USA). Seeds of all plant species were germinated and grown for one week at the end of March in 2018 on a sterilized (2 X autoclaved as above) sand:soil mixture. We planted four conspecific seedlings (one week old) into each pot for monocultures, and two conspecific plants were planted diagonally from each other in each biculture.

Water availability

Pots were randomized via split block where half the block was well-watered, and the other half was given a drought treatment. All plants were well-watered for 18 days before drought treatments were applied by watering twice daily for two minutes (266.7 ml/day) via a drip irrigation emitter to prevent splashing of soil microbes. On day 19, drought pots were watered twice per day every other day for 1 minute (133.3 ml/day), while well-watered pots received no change in water volume for the duration of the experiment. The full experiment design included 7 replicates of each crop community, water regime, and inoculation combination (2 levels of water treatment x 6 levels of crop community x 4 levels of inoculum x 7 replicates = 336 pots).

Data collection

Crops were grown for 8 weeks, and then aboveground biomass was collected by cutting at 4 cm above the soil surface line, separated to species, dried at 60° C, and weighed. Crops were allowed to regrow an additional 5 weeks and a second harvest was performed. A second harvest was conducted to assess the context dependency of biotic and abiotic effects on crop regrowth, as aboveground biomass of perennial systems may be cut multiple times in one growing season [4,22]. Ten plants out of 1344 (0.7%) died before the second harvest. These plants were recorded as 0.0 g at harvest 2.

After the second harvest, root tissues were collected from a subset (4 blocks) of the monoculture pots to confirm AM fungal colonization. Root subsamples from each pot were cleared and stained with Trypan Blue.  Hyphae and arbuscules were counted using the magnified intersections method [57].  The results from the root analysis showed that the presence of AM fungal hyphae and arbuscules was greater in monoculture pots with live soil inoculum (LWLF, LWSF, and SWLF) than in pots inoculated with sterile whole soil and sterile prairie AM fungi (SWSF) (See supporting information for detailed results; Table S1; Figs. S1 – S3).  The mean hyphal and arbuscule presence for the sterile inoculum (SWSF) was close to zero.

Usage notes

H1 is Harvest 1

H2 is Harvest 2

bio is biomass of each crop species

avg is the average yield per individual

Potbio is the total pot biomass for each harvest

Totalpotbio is the total biomass across the experiment (Harvest 1 plus Harvest 2)


Malone Family Foundation Land Preservation Trust/Perennial Agriculture Project

National Science Foundation, Award: DEB‐1556664, DEB-1738041, OIA 1656006

Malone Family Foundation Land Preservation Trust/Perennial Agriculture Project