The influence of drought and heat stress on long-term carbon fluxes of bioenergy crops grown in the Midwestern USA

Genome-wide profiling of histone (H3) lysine 4 (K4) tri-methylation (me3) under drought, heat, and combined stresses in switchgrass

BACKGROUND

Switchgrass (Panicum virgatum L.) is a warm-season perennial (C4) grass identified as an important biofuel crop in the United States. It is well adapted to the marginal environment where heat and moisture stresses predominantly affect crop growth. However, the underlying molecular mechanisms associated with heat and drought stress tolerance still need to be fully understood in switchgrass. The methylation of H3K4 is often associated with transcriptional activation of genes, including stress-responsive. Therefore, this study aimed to analyze genome-wide histone H3K4-tri-methylation in switchgrass under heat, drought, and combined stress.

RESULTS

In total, ~ 1.3 million H3K4me3 peaks were identified in this study using SICER. Among them, 7,342; 6,510; and 8,536 peaks responded under drought (DT), drought and heat (DTHT), and heat (HT) stresses, respectively. Most DT and DTHT peaks spanned 0 to + 2000 bases from the transcription start site [TSS]. By comparing differentially marked peaks with RNA-Seq data, we identified peaks associated with genes: 155 DT-responsive peaks with 118 DT-responsive genes, 121 DTHT-responsive peaks with 110 DTHT-responsive genes, and 175 HT-responsive peaks with 136 HT-responsive genes. We have identified various transcription factors involved in DT, DTHT, and HT stresses. Gene Ontology analysis using the AgriGO revealed that most genes belonged to biological processes. Most annotated peaks belonged to metabolite interconversion, RNA metabolism, transporter, protein modifying, defense/immunity, membrane traffic protein, transmembrane signal receptor, and transcriptional regulator protein families. Further, we identified significant peaks associated with TFs, hormones, signaling, fatty acid and carbohydrate metabolism, and secondary metabolites. qRT-PCR analysis revealed the relative expressions of six abiotic stress-responsive genes (transketolase, chromatin remodeling factor-CDH3, fatty-acid desaturase A, transmembrane protein 14C, beta-amylase 1, and integrase-type DNA binding protein genes) that were significantly (P < 0.05) marked during drought, heat, and combined stresses by comparing stress-induced against un-stressed and input controls.

CONCLUSION

Our study provides a comprehensive and reproducible epigenomic analysis of drought, heat, and combined stress responses in switchgrass. Significant enrichment of H3K4me3 peaks downstream of the TSS of protein-coding genes was observed. In addition, the cost-effective experimental design, modified ChIP-Seq approach, and analyses presented here can serve as a prototype for other non-model plant species for conducting stress studies.

Improved net carbon budgets in the US Midwest through direct measured impacts of enhanced weathering

Terrestrial enhanced weathering (EW) through the application of Mg- or Ca-rich rock dust to soil is a negative emission technology with the potential to address impacts of climate change. The effectiveness of EW was tested over 4 years by spreading ground basalt (50 t ha-1  year-1 ) on maize/soybean and miscanthus cropping systems in the Midwest US. The major elements of the carbon budget were quantified through measurements of eddy covariance, soil carbon flux, and biomass. The movement of Mg and Ca to deep soil, released by weathering, balanced by a corresponding alkalinity flux, was used to measure the drawdown of CO2 , where the release of cations from basalt was measured as the ratio of rare earth elements to base cations in the applied rock dust and in the surface soil. Basalt application stimulated peak biomass and net primary production in both cropping systems and caused a small but significant stimulation of soil respiration. Net ecosystem carbon balance (NECB) was strongly negative for maize/soybean (-199 to -453 g C m-2  year-1 ) indicating this system was losing carbon to the atmosphere. Average EW (102 g C m-2  year-1 ) offset carbon loss in the maize/soybean by 23%-42%. NECB of miscanthus was positive (63-129 g C m-2  year-1 ), indicating carbon gain in the system, and EW greatly increased inorganic carbon storage by an additional 234 g C m-2  year-1 . Our analysis indicates a co-deployment of a perennial biofuel crop (miscanthus) with EW leads to major wins-increased harvested yields of 29%-42% with additional carbon dioxide removal (CDR) of 8.6 t CO2  ha-1  year-1 . EW applied to maize/soybean drives a CDR of 3.7 t CO2  ha-1  year-1 , which partially offsets well-established carbon losses from soil from this crop rotation. EW applied in the US Midwest creates measurable improvements to the carbon budgets perennial bioenergy crops and conventional row crops.

CO2 flux in a wheat-soybean succession in subtropical Brazil: A carbon sink

The subtropical region of Brazil is home to 33% of the soybean [Glycine max (L.) Merr.] growing area and 90% of the wheat (Tritucum aestivum L.) growing area of this country. A soybean-wheat succession with fallow between crops is used in about 11% of the cultivated area. No study has quantified CO2 fluxes in annual soybean-wheat succession in this region. Hence, this study analyzed the seasonality of CO2 exchange (net ecosystem exchange [NEE]) in a 2015/2016 wheat-soybean succession in a commercial farm located in Carazinho, Rio Grande do Sul State, Brazil. The eddy covariance method was used to estimate the annual C balance of this system. The NEE was partitioned between gross primary productivity and ecosystem respiration to understand the dynamics of these fluxes during a year of wheat-soybean succession. Considering the net ecosystem balance between photosynthesis and respiration during the growing season, both soybean and wheat absorbed CO2 from the atmosphere (NEE wheat: -347 ± 4 g C m-2 ; NEE soybean: -242 ± 3 g C m-2 ). The fallow periods between growing seasons, however, acted as a source of 156 ± 2 g C m-2 , reducing the C absorbed by the crops by 27%. For 1 yr, the net biome productivity was -50 g C m-2  yr-1 . The results obtained here demonstrate that the wheat-soybean succession was a net C sink under these specific climatic conditions and field management practices and that the long fallow period between crops limited the agroecosystem from becoming a more efficient CO2 sink.

Comparing Evapotranspiration Products of Different Temporal and Spatial Scales in Native and Managed Prairie Pastures

Grasslands in the Southern Great Plains of the United States have major ecological and economic importance, with strong climate and water cycle connections. The historic native prairie grassland has been managed differently for enhancing productivity, while consequently altering water vapor fluxes. However, little is known about the impacts of different management activities on evapotranspiration (ET) at different spatio-temporal scales. In this study, we quantified and compared ET between co-located introduced managed pasture (MP) and native prairie (NP) pasture. Additionally, we compared the Moderate Resolution Imaging Spectroradiometer (MODIS)-derived ET at four different spatial scales: 30 m (ETMOD30), 200 m (ETMOD200), 500 m (ETMOD500), and 1000 m (ETMOD1000) with eddy covariance-measured ET (ETEC). Large differences in ETEC were observed between two pastures from half-hourly to seasonal scales, with variations mainly controlled by the amount of rainfall and management activities. The results demonstrated differential responses of MP and NP in a pluvial year. The ETMOD30 showed a better agreement with ETEC than did the ETMOD200, ETMOD500, and ETMOD1000. The ETMOD200, ETMOD500, and ETMOD1000 largely underestimated ETEC, most likely due to their inability to capture the spatial heterogeneity of vegetation growth impacted by various management activities. Our results facilitate understanding of the difference in ET of MP and NP due to differences in vegetation resulting from different management activities and their differential responses to precipitation.

Drought Characterization and Trend Detection Using the Reconnaissance Drought Index for Setsoto Municipality of the Free State Province of South Africa and the Impact on Maize Yield

The reconnaissance drought index (RDI) for the Setsoto municipality of the Free State province in South Africa was calculated for the period between 1985 and 2019 at 3 month (October–December), 6 month (October–March), and 12 month (October–September) intervals. Rainfall and minimum and maximum temperature data from four weather stations (Clocolan, Ficksburg, Marquard, and Senekal) were used for this study to characterize drought using “DrinC” software together with the Mann Kendall test with Sen’s slope to detect drought trends and the rate of change. Extreme, severe, and moderate droughts were recorded for all the stations, with RDIs ranging from −3.6 to −1.0 at different temporal scales. The years 1991, 1994, 2006, 2011, and 2015 were highlighted using the RDI 3, 6, and 12 month calculations. Results showed that the yield decreased either in the year of the drought or in the subsequent year, due to the exact timing of the low-rainfall events in the season and soil moisture storage. Yields were low, on average 2.5 tons ha−1 year−1, with high variability. Optimal growing conditions are essential in the early part of the season, October–December, for maximizing yield; if droughts are experienced at this time then the yield is more greatly impacted than if the droughts occur later in the season. Spatial analysis shows a large variability of drought patterns across the Municipality, over the years, with the 3 month RDI values giving a more detailed picture of this variability than the 6 and 12 month RDI values.

Spatiotemporal Derivation of Intermittent Ponding in a Maize–Soybean Landscape from Planet Labs CubeSat Images

Climate change is increasing the frequency and intensity of heavy precipitation in the US Midwest, overwhelming existing tile drainage, and resulting in temporary soil ponding across the landscape. However, lack of direct observations of the dynamics of temporal soil ponding limits our understanding of its impacts on crop growth and biogeochemical cycling. Satellite remote sensing offers a unique opportunity to observe and analyze this dynamic phenomenon at the landscape scale. Here we analyzed a series of red–green–blue (RGB) and near infrared (NIR) remote sensing images from the Planet Labs CubeSat constellation following a period of heavy precipitation in May 2017 to determine the spatiotemporal characteristics of ponding events in the maize–soybean cropland of Champaign County, Illinois USA. We trained Random Forest algorithms for near-daily images to create binary classifications of surface water versus none, which achieved kappa values around 0.9. We then analyzed the morphology of classification results for connected pixels across space and time and found that 2.5% (5180 ha) of this cropland was classified as water surface at some point during this period. The frequency distribution of areal ponding extent exhibited a log–log relationship; the mean and median areas of ponds were 1231 m2 and 126 m2, respectively, with 26.1% of identified ponds being at the minimum threshold area of 45 m2, and 2.5% of the ponds having an area greater than 104 m2 (1 ha). Ponds lasted for a mean duration of 2.4 ± 1.7 days, and 2.3% of ponds lasted for more than a week. Our results suggest that transient ponding may be significant at the landscape scale and ought to be considered in assessments of crop risk, soil and water conservation, biogeochemistry, and sustainability.

Carbon and water relations in perennial Kernza (Thinopyrum intermedium): An overview

Perennial crops have been proposed as a more sustainable alternative to annual crops, because they have extended growing seasons, continuous ground cover, reduced nutrient leakage, and sequester more carbon in the soils than annual crops. One example is intermediate wheatgrass (Thinopyrum intermedium), a perennial crop that has been used as a cool-season forage throughout the USA and Canada and also across its native range in Eurasia. Since the 1980's, intermediate wheatgrass has been under domestication to improve seed fertility and grain yield. Commercial products are being sold under the trade name Kernza, owned by The Land Institute, located in Salina, Kansas, USA. This review provides a comprehensive framework about the physical and biological aspects involving the water and carbon cycles in Kernza plants. The main aspects we highlight here are based on previous findings regarding Kernza: i) the ability of maintaining a relatively high water-use efficiency throughout the whole growing season, which is beneficial to mitigate water stress, representing an important physiological mean to acclimate under severe, unfavorable weather conditions, and ii) its higher evapotranspiration (ET) and net carbon uptake rates, particularly when compared to annual counterparts. Only a thorough multifaceted assessment of the repercussion for carbon and water fluxes of a shift from annual crops to Kernza will allow assessing the perspectives of such novel perennial crop to support food security and a number of ecosystem services, particularly under future climates.

Soil CO2 emission in response to organic amendments, temperature, and rainfall

Vegetated land surfaces play an important role in determining the fate of carbon in the global carbon cycle. However, our understanding of the terrestrial biosphere on a global scale is subject to considerable uncertainty, especially concerning the impacts of climatic variables on the carbon cycle. Soil is a source and also a sink of CO₂ exchange and helps in carbon sequestration. Agricultural management practices influence soil water dynamics, as well as carbon cycling by changing soil CO₂ emission and uptake rates. The rate of soil CO₂ emission varies for different crops and different organic amendments. The major goal of this study was to assess the impacts of the type and rate of organic amendment on soil CO₂ emission in a collard greens crop grown in the southeast Texas environment. Thirty-six plots were developed to grow collard greens on Prairie View A&M University’s Research Farm. Three types of organic amendments (Chicken manure, Dairy manure, and Milorganite), at four levels of application (0, 168, 336, and 672 kg N/ha) were used and replicated three times. Each organic amendment type was applied to nine randomly selected plots. Three random plots were used as a control in each row. We measured daily soil CO₂ emission for the first two weeks and every other day in a week during the experiment. We evaluated the effects of organic amendments and the application rates on soil CO₂ emission for collard greens during two growing seasons. The results showed higher the application rates for each organic amendment, higher the CO₂ emissions from the soil. The results also showed higher cumulative CO₂ emissions for the soils amended with chicken manure and milorganite, but lowest for the soils amended with dairy manure. This field experiment and analyses help better understand the temporal and spatial variations of soil CO₂ emission, and also help to develop best management practices to maximize carbon sequestration and to minimize soil CO₂ emissions during the growth periods of collard greens under changing temperatures using different organic amendments, and application rates.

Evaluation of miscanthus productivity and water use efficiency in southeastern United States

Second generation biofuels, such as perennial grasses, have potential to provide biofuel feedstock while growing on degraded land with minimal inputs. Perennial grasses have been reported to sequester large amounts of soil organic carbon (SOC) in the Midwestern United States (USA). However, there has been little work on biofuel and carbon sequestration potential of perennial grasses in the Southeastern US. Biofuel productivity for dryland Miscanthus × gigantus and irrigated maize in Georgia, USA were quantified using eddy covariance observations of evapotranspiration (ET) and net ecosystem exchange (NEE) of carbon. Miscanthus biomass yield was 15.54 Mg ha^-1 in 2015 and 11.80 Mg ha^-1 in 2016, while maize produced 30.20 Mg ha^-1 of biomass in 2016. Carbon budgets indicated that both miscanthus and maize fields lost carbon over the experiment. The miscanthus field lost 5 Mg C ha^-1 in both 2015 and 2016 while the maize field lost 1.37 Mg C ha^-1 for the single year of study. Eddy covariance measurement indicated that for 2016 the miscanthus crop evapotranspired 598 mm and harvest water use efficiencies ranged from 6.95 to 13.84 kg C ha^-1 mm^-1. Maize evapotranspired 659 mm with a harvest water use efficiency of 19.12 kg C ha^-1 mm^-1. While biomass yields and gross primary production were relatively high, high ecosystem respiration rates resulted in a loss of ecosystem carbon. Relatively low biomass production, low water use efficiency and high respiration for Miscanthus × gigantus in this experiment suggest that this strain of miscanthus may not be well-suited for dryland production under the environmental conditions found in South Georgia USA.

Cultivation of C4 perennial energy grasses on heavy metal contaminated arable land: Impact on soil, biomass, and photosynthetic traits

The objective of this study was to evaluate the potential of three C4 perennial grasses (Miscanthus x giganteus, Panicum virgatum and Spartina pectinata) for biomass production on arable land unsuitable for food crop cultivation due to Pb, Cd and Zn contamination. We assessed soil properties, biomass yield, metal concentrations, and the photosynthetic performance of each species. Physico-chemical and elemental analyses were performed on soil samples before plantation establishment (2014) and after three years of cultivation (2016), when leaf area index, plant height, yield and heavy metal content of biomass were also determined. Physiological measurements (gas exchange, pigment content, chlorophyll a fluorescence) were recorded monthly between June and September on mature plants in 2016. Cultivation of investigated plants resulted in increased pH, nitrogen, and organic matter (OM) content in soil, although OM increase (13%) was significant only for S. pectinata plots. During the most productive months, maximal quantum yield values of primary photochemistry (F_v/F_m) and gas exchange parameter values reflected literature data of those plants grown on uncontaminated sites. Biomass yields of M. x giganteus (15.0 ± 0.4 t d.m. ha^-1) and S. pectinata (12.6 ± 1.2 t d.m. ha^-1) were also equivalent to data published from uncontaminated land. P. virgatum performed poorly (4.1 ± 0.4 t d.m. ha^-1), probably due to unfavourable climatic conditions, although metal uptake in this species was the highest (3.6 times that of M. x giganteus for Pb). Yield and physiological measurements indicated that M. x giganteus and S. pectinata were unaffected by the levels of contamination and therefore offer alternatives for areas where food production is prohibited. The broad cultivatable latitudinal range of these species suggests these results are widely relevant for development of the bioeconomy. We recommend multi-location trials under diverse contaminant and environmental regimes to determine the full potential of these species.

Net ecosystem carbon and greenhouse gas budgets in fiber and cereal cropping systems

To assess the contributions of fiber and cereal production on climate change, the net ecosystem exchange of carbon dioxide (CO₂), main exchanges of non-CO₂ carbon, and methane (CH₄) and nitrous oxide (N₂O) fluxes were continuously monitored throughout two year-round crop cycles (Y1 and Y2: 1^st and 2^nd year-round crop cycles, respectively) using eddy covariance, biometric observation, and static chamber methods in typical cotton and wheat-maize rotational cropping systems in China. The evaluation of net ecosystem carbon budgets (NECBs: considering net ecosystem CO₂ exchange and non-CO₂ carbon exchanges by fertilization, seeding, and harvest) and greenhouse gas budgets (GHGBs: adding CH₄ and N₂O fluxes to the NECBs based on CO₂ equivalents) showed that the cotton cropping system persistently functioned as an intensive carbon (-1527 and -974 kg C ha^-1 yr^-1) and greenhouse gas (GHG) source (5618 and 3591 kg CO₂-eq ha^-1 yr^-1) because of the large CO₂ emissions during the long fallow periods (5748 and 5160 kg CO₂ ha^-1 in Y1 and Y2, respectively). The wheat-maize cropping system had high net ecosystem production (NEP) and low harvest index and therefore, served as a notable carbon sink (1461 kg C ha^-1 yr^-1 in Y2). Although high irrigation water and chemical fertilizer inputs stimulated N₂O emissions, the wheat-maize cropping system still behaved as an important GHG sink (-4257 kg CO₂-eq ha^-1 yr^-1 in Y2) because of the tremendous net carbon sequestration. However, in Y1 incidental wind damage lowered the NEP and turned the wheat-maize cropping system into a GHG source (2144 kg CO₂-eq ha^-1 yr^-1). The NEP, NECBs, and GHGBs of the double cropping system generally exceeded those of the single cropping system. The traditional rotation between double and single cropping systems should be restored to maintain soil carbon storage and alleviate the radiative forcing effects of cotton production.

Carbon dioxide and water vapor fluxes in winter wheat and tallgrass prairie in central Oklahoma

Winter wheat (Triticum aestivum L.) and tallgrass prairie are common land cover types in the Southern Plains of the United States. During the last century, agricultural expansion into native grasslands was extensive, particularly managed pasture or winter wheat. In this study, we measured carbon dioxide (CO₂) and water vapor (H₂O) fluxes from winter wheat and tallgrass prairie sites in Central Oklahoma using the eddy covariance in 2015 and 2016. The objective of this study was to contrast CO₂ and H₂O fluxes between these two ecosystems to provide insights on the impacts of conversion of tallgrass prairie to winter wheat on carbon and water budgets. Daily net ecosystem CO₂ exchange (NEE) reached seasonal peaks of -9.4 and -8.8 g C m^-2 in 2015 and -6.2 and -7.5 g C m^-2 in 2016 at winter wheat and tall grass prairie sites, respectively. Both sites were net sink of carbon during their growing seasons. At the annual scale, the winter wheat site was a net source of carbon (56 ± 13 and 33 ± 9 g C m^-2 year^-1 in 2015 and 2016, respectively). In contrast, the tallgrass prairie site was a net sink of carbon (-128 ± 69 and -119 ± 53 g C m^-2 year^-1 in 2015 and 2016, respectively). Daily ET reached seasonal maximums of 6.0 and 5.3 mm day^-1 in 2015, and 7.2 and 8.2 mm day^-1 in 2016 at the winter wheat and tallgrass prairie sites, respectively. Although ecosystem water use efficiency (EWUE) was higher in winter wheat than in tallgrass prairie at the seasonal scale, summer fallow contributed higher water loss from the wheat site per unit of carbon fixed, resulting into lower EWUE at the annual scale. Results indicate that the differences in magnitudes and patterns of fluxes between the two ecosystems can influence carbon and water budgets.

Gut microbiomes of mobile predators vary with landscape context and species identity

Landscape context affects predator–prey interactions and predator diet composition, yet little is known about landscape effects on insect gut microbiomes, a determinant of physiology and condition. Here, we combine laboratory and field experiments to examine the effects of landscape context on the gut bacterial community and body condition of predatory insects. Under laboratory conditions, we found that prey diversity increased bacterial richness in insect guts. In the field, we studied the performance and gut microbiota of six predatory insect species along a landscape complexity gradient in two local habitat types (soybean fields vs. prairie). Insects from soy fields had richer gut bacteria and lower fat content than those from prairies, suggesting better feeding conditions in prairies. Species origin mediated landscape context effects, suggesting differences in foraging of exotic and native predators on a landscape scale. Overall, our study highlights complex interactions among gut microbiota, predator identity, and landscape context.