DOI: 10.5061/dryad.sqv9s4n1p
title: Data from: Abiotic and biotic context dependency of perennial crop yield

description: 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.
description: <i>Experiment location</i> 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. <i>Soil inoculum
 </i> 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 cm<sup>3</sup> 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 cm<sup>3
 </sup>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 (<i>T. intermedium</i>) 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 <i>T. intermedium</i>,
 without disturbance (no tillage), to test <i>T.
 intermedium-</i>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 <i>Silphium</i> 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:
 <i>Scutellospora dipurpurescens, Gigaspora gigantea, Funneliformis
 mosseae, Funneliformis geosporum, Glomus mortonii, Rhizophagus diaphanous,
 </i>and<i> Claroideoglomus claroideum</i>. 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. <i>Crop community </i>
 Six crop communities were
 designed to test overyielding that included all possible combinations of
 monoculture and biculture plantings for the three perennial crop species,
 <i>Silphium integrifolium</i> (henceforth referred to as
 <i>Silphium </i>or S), <i>Medicago sativa</i>
 (henceforth referred to as alfalfa or A) and <i>Thinopyrum
 intermedium</i> (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 <i>Silphium
 </i>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.
 <i>Silphium </i>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. <i>Water availability
 </i> 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). <i>Data collection</i>
 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.
description: 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)