To determine if damage to foliage by biotic agents, including arthropods, fungi, bacteria and viral pathogens, universally downregulates the expression of genes involved in photosynthesis, we compared transcriptome data from microarray experiments after twenty two different forms of biotic damage on eight different plant species. Transcript levels of photosynthesis light reaction, carbon reduction cycle and pigment synthesis genes decreased regardless of the type of biotic attack. The corresponding upregulation of genes coding for the synthesis of jasmonic acid and those involved in the responses to salicylic acid and ethylene suggest that the downregulation of photosynthesis‐related genes was part of a defence response. Analysis of the sub‐cellular targeting of co‐expressed gene clusters revealed that the transcript levels of 84% of the genes that carry a chloroplast targeting peptide sequence decreased. The majority of these downregulated genes shared common regulatory elements, such as G‐box (CACGTG), T‐box (ACTTTG) and SORLIP (GCCAC) motifs. Strong convergence in the response of transcription suggests that the universal downregulation of photosynthesis‐related gene expression is an adaptive response to biotic attack. We hypothesize that slow turnover of many photosynthetic proteins allows plants to invest resources in immediate defence needs without debilitating near term losses in photosynthetic capacity.

One potentially significant impact of growing biofuel crops will be the sequestration or release of carbon (C) in soil. Soil organic carbon (SOC) represents an important C sink in the lifecycle C balances of biofuels and strongly influences soil quality. We assembled and analyzed published estimates of SOC change following conversion of natural or agricultural land to biofuel crops of corn with residue harvest, sugarcane, Miscanthus x giganteus, switchgrass, or restored prairie. We estimated SOC losses associated with land conversion and rates of change in SOC over time by regressing net change in SOC relative to a control against age since establishment year. Conversion of uncultivated land to biofuel agriculture resulted in significant SOC losses – an effect that was most pronounced when native land was converted to sugarcane agriculture. Corn residue harvest (at 25–100% removal) consistently resulted in SOC losses averaging 3–8 Mg ha⁻¹ in the top 30 cm, whereas SOC accumulated under all four perennial grasses, with SOC accumulation rates averaging <1 Mg ha⁻¹ yr⁻¹ in the top 30 cm. More intensive harvests led to decreased C gains or increased C losses – an effect that was particularly clear for residue harvest in corn. Direct or indirect conversion of previously uncultivated land for biofuel agriculture will result in SOC losses that counteract the benefits of fossil fuel displacement. Additionally, SOC losses under corn residue harvest imply that its potential to offset C emissions may be overestimated, whereas SOC sequestration under perennial grasses represents an additional benefit that has rarely been accounted for in life cycle analyses of biofuels.