Transcripts of plant organelle genes are modified by cytidine-to-uridine (C-to-U) RNA editing, often changing the encoded amino acid predicted from the DNA sequence. Members of the PLS subclass of the pentatricopeptide repeat (PPR) motif-containing family are site-specific recognition factors for either chloroplast or mitochondrial C targets of editing. However, other than PPR proteins and the cis -elements on the organelle transcripts, no other components of the editing machinery in either organelle have previously been identified. The Arabidopsis chloroplast PPR protein Required for AccD RNA Editing 1 (RARE1) specifies editing of a C in the accD transcript. RARE1 was detected in a complex of >200 kDa. We immunoprecipitated epitope-tagged RARE1, and tandem MS/MS analysis identified a protein of unknown function lacking PPR motifs; we named it RNA-editing factor interacting protein 1 (RIP1). Yeast two-hybrid analysis confirmed RIP1 interaction with RARE1, and RIP1-GFP fusions were found in both chloroplasts and mitochondria. Editing assays for all 34 known Arabidopsis chloroplast targets in a rip1 mutant revealed altered efficiency of 14 editing events. In mitochondria, 266 editing events were found to have reduced efficiency, with major loss of editing at 108 C targets. Virus-induced gene silencing of RIP1 confirmed the altered editing efficiency. Transient introduction of a WT RIP1 allele into rip1 improved the defective RNA editing. The presence of RIP1 in a protein complex along with chloroplast editing factor RARE1 indicates that RIP1 is an important component of the RNA editing apparatus that acts on many chloroplast and mitochondrial C targets.

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Pathogenic invasions are a major source of change in both agricultural and natural ecosystems. In forests, fungal pathogens can kill habitat-generating plant species such as canopy trees, but methods for remote detection, mapping and monitoring of such outbreaks are poorly developed. Two novel species of the fungal genus Ceratocystis have spread rapidly across humid and mesic forests of Hawaiʻi Island, causing widespread mortality of the keystone endemic canopy tree species, Metrosideros polymorpha (common name: ʻōhiʻa). The process, known as Rapid Ohia Death (ROD), causes browning of canopy leaves in weeks to months following infection by the pathogen. An operational mapping approach is needed to track the spread of the disease. We combined field studies of leaf spectroscopy with laboratory chemical studies and airborne remote sensing to develop a spectral signature for ROD. We found that close to 80% of ROD-infected plants undergo marked decreases in foliar concentrations of chlorophyll, water and non-structural carbohydrates, which collectively result in strong consistent changes in leaf spectral reflectance in the visible (400–700 nm) and shortwave-infrared (1300–2500 nm) wavelength regions. Leaf-level results were replicated at the canopy level using airborne laser-guided imaging spectroscopy, with quantitative spectral separability of normal green-leaf canopies from suspected ROD-infected brown-leaf canopies in the visible and shortwave-infrared spectrum. Our results provide the spectral–chemical basis for detection, mapping and monitoring of the spread of ROD in native Hawaiian forests.

Ceratocystis lukuohia and C. huliohia are recently described fungal species that cause rapid ‘ōhi‘a death (ROD) of Metrosideros polymorpha, Hawaii’s most abundant and ecologically important native species. Although the pathogens are now widespread on Hawaiʻi Island, a major effort is underway to study and manage affected forests, and particularly to prevent the disease from spreading to other islands in the State or throughout the Pacific. Rapid and accurate detection is critical. Molecular diagnostic real-time PCR protocols were developed to detect and distinguish the two pathogens, suitable for detection of fungal DNA from extracts of wood, soil, and insect frass. The assays detect as few as 2 to 4 or 16 spores of C. huliohia or C. lukuohia, respectively. These assays are valuable tools for monitoring disease spread and offer a significant advantage over culture-based methods for diagnostics, requiring <1 day to arrive at definitive results.

The nutrient concentration of fruits and vegetables in the U.S.A. has declined in the past 50–70 years. Crop management practices utilizing on-farm inputs are thought to increase crop nutritional quality, but few studies have evaluated this under long-term side-by-side trials. An experiment was conducted from 2004 to 2005 at Rodale Institute’s long-term Farming Systems Trial to investigate the nutritional quality of vegetables under organic manure (MNR) and conventional (CNV) farming systems, with or without arbuscular mycorrhizal fungi (AMF) treatment. AMF reduced the vitamin C content in carrots in both systems in 2004, but the reduction was 87% in CNV and 28% in MNR. AMF also reduced antioxidants in carrots in both CNV and MNR. This trend was likely due to the suppression of native AMF colonization by the non-native AMF inoculum used. Between 2004 and 2005, MNR increased the vitamin C in green peppers by 50% while CNV decreased the vitamin C in red peppers by 48%. Tomatoes under MNR had a 40% greater vitamin C content compared to CNV in 2005. The vegetable yield declined between 2004 and 2005, except for tomato, where the yield increased by 51% and 44% under CNV and MNR, respectively. In general, MNR tended to increase the nutrient concentration of vegetables compared with CNV, while the AMF effects were inconclusive.