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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Multiseriate cortical sclerenchyma enhance root penetration in compacted soils

Mechanical impedance limits soil exploration and resource capture by plant roots. We examine the role of root anatomy in regulating plant adaptation to mechanical impedance and identify a root anatomical phene in maize (Zea mays) and wheat (Triticum aestivum) associated with penetration of hard soil: Multiseriate cortical sclerenchyma (MCS). We characterize this trait and evaluate the utility of MCS for root penetration in compacted soils. Roots with MCS had a greater cell wall-to-lumen ratio and a distinct UV emission spectrum in outer cortical cells. Genome-wide association mapping revealed that MCS is heritable and genetically controlled. We identified a candidate gene associated with MCS. Across all root classes and nodal positions, maize genotypes with MCS had 13% greater root lignin concentration compared to genotypes without MCS. Genotypes without MCS formed MCS upon exogenous ethylene exposure. Genotypes with MCS had greater lignin concentration and bending strength at the root tip. In controlled environments, MCS in maize and wheat was associated improved root tensile strength and increased penetration ability in compacted soils. Maize genotypes with MCS had root systems with 22% greater depth and 49% greater shoot biomass in compacted soils in the field compared to lines without MCS. Of the lines we assessed, MCS was present in 30 to 50% of modern maize, wheat, and barley cultivars but was absent in teosinte and wild and landrace accessions of wheat and barley. MCS merits investigation as a trait for improving plant performance in maize, wheat, and other grasses under edaphic stress.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

An outbreak of Septoria canker caused by Sphaerulina musiva on Populus trichocarpa in eastern Oregon

Branch and stem cankers were observed in a Populus trichocarpa L. plantation in late summer of 2018 near Boardman, Oregon USA. Stem cankers were flat faced with swollen margins and the bark in the center of the cankers was black and depressed (Figure 1). 254 out of 1054 trees (25%) observed had cankers. Symptomatic stems and branches from several trees were brought to Oregon State University for identification. Cankers were surface-disinfested in a 5% NaOCl for 2 min and rinsed twice in deionized H 2 O for 2 min. Bark was removed from cankers and pieces of wood at the margin between healthy and necrotic tissue were plated on KV8 medium amended with streptomycin sulfate at 100 mg liter–1 and chloramphenicol (Amresco) at 240 mg liter–1 (Dunnell and LeBoldus 2017). Eight sporulating colonies typical of Sphaerulina musiva (Peck) Quaedvlieg, Verkley, and Crous (Syn. = Septoria musiva Peck) developed within 7 days of plating. S. musiva was identified by morphological characteristics (conidium size = 28–54 × 3.5–4 µm) and confirmed by comparing the sequence of the ITS region (accession numbers: MN275180-MN275187) to JX901814 with 99% identity. We tested 13 additional cankers collected from the plantation using S. musiva specific primers (Abraham et al. 2018). Eight of the 13 samples were positive for S. musiva DNA. Dormant cuttings from three genotypes of P. trichocarpa (BESC-184; BESC-259; BESC-388) were collected in a field planting near Oregon State University (OSU). These were planted in cone-tainers in the greenhouse at OSU and grown to approximately 30 cm in height. Four replicates of each of the three genotypes were inoculated in the greenhouse with one Oregon isolate using a suspension of 1x10 6 conidia ml-1. The entire tree was sprayed until runoff using a spray bottle (LeBoldus et al. 2010). The experimental design was a completely randomized design with four replicates of each genotype. Sterile deionized H 2 O was sprayed on one control tree of each genotype. The mean number of resulting cankers were BESC-184 = 11, BESC-259 = 1, and BESC-388 = 13.75. The controls did not develop any cankers. The pathogen was successfully reisolated from one canker from each genotype. Sphaerulina musiva can cause severely damaging leaf spot and stem canker diseases in the eastern and central USA and Canada (Bier 1939; Herath et al. 2016). Susceptible Populus species and hybrids develop cankers which can girdle and weaken stems, leading to breakage or tree death (Bier 1939). A previous survey of the region did not detect S. musiva (Newcombe et al. 1995). This outbreak of Septoria canker underscores the potential threat of this pathogen to P. trichocarpa in the Pacific Northwest where it is a keystone species in riparian ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Signatures of local nitrogen adaptation in the Brachypodium distachyon root microbiome

Plants associate with diverse microbiomes that impact their fitness, yet the contribution of the microbiome to plant adaptation is uncertain. As plant recruitment of its microbiome can be both highly variable and genetically determined, we hypothesized this recruitment process may be the result of adaptive evolution, and contributing to plant local adaptation. We investigated the evolution and adaptive benefit of plant–microbiome recruitment by characterizing the rhizosphere communities across a genotypic panel of Brachypodium distachyon in a common garden experiment. By linking microbial communities to their host genotype's historic environment, we identified signatures of selection on plant–microbiome recruitment. Plant–microbiome composition was significantly correlated with the host genotype's historic environment, with enrichment of microbial traits aligned to local resource conditions. For example, genotypes from low-nitrogen environments recruited communities enriched in nitrogen acquisition traits. In a complementary experiment evaluating plant nitrogen response, these same genotypes were well-adapted to low-nitrogen environments, contingent on the presence of key nitrogen-cycling microbes. These results suggest that local adaptation in plants may partially be mediated by recruitment of beneficial microbiomes. This perspective suggests that plant adaptation may be an emergent property of host–microbe interactions, where evolutionary responses favor traits that promote recruitment of locally beneficial microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Recent aspects on epidemiology, clinical disease, and genetic diversity of Toxoplasma gondii infections in Australasian marsupials

Toxoplasma gondii infections are common in humans and animals worldwide. Among all intermediate hosts of T. gondii, captive marsupials from Australia and New Zealand are highly susceptible to clinical toxoplasmosis. However, most free-range marsupials establish chronic T. gondii infection. Infected marsupial meat may serve as a source of T. gondii infection for humans. Differences in mortality patterns in different species of kangaroos and other marsupials are not fully understood. Lifestyle, habitat, and the genotype of T. gondii are predicted to be risk factors. For example, koalas are rarely exposed to T. gondii because they live on treetops whereas wallabies on land are frequently exposed to infection. The present review summarizes worldwide information on the prevalence of clinical and subclinical infections, epidemiology, and genetic diversity of T. gondii infecting Australasian marsupials in their native habitat and among exported animals over the past decade. The role of genetic types of T. gondii and clinical disease is discussed. Fatal toxoplasmosis has been diagnosed in captive Australasian marsupials in Argentina, Chile, China, Germany, Hungary, Japan, Spain, Turkey, and the USA. Most deaths occurred because of disseminated toxoplasmosis. Genetic characterization of T. gondii strains isolated from fatal marsupial infections identified Type III as well as atypical, nonclonal genotypes. Fatal toxoplasmosis was also diagnosed in free-ranging wombats (Vombatus ursinus) in Australia. Genetic characterization of DNA amplified directly from host tissues of subclinical culled kangaroos at slaughter identified many mixed-strain infections with both atypical and recombinant genotypes of T. gondii. Most Australasian marsupials in their native land, Australia and New Zealand, have high prevalence of T. gondii, and kangaroo meat can be a source of infection for humans if consumed uncooked/undercooked. The genotypes prevalent in kangaroos in Australia and New Zealand were genetically distinct from those isolated or genotyped from most macropods in the USA and other countries. Thus, clinical toxoplasmosis in marsupials imported from Australia is most likely to occur from infections acquired after importation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Data from Managing Flowering Time in Miscanthus and Sugarcane to Facilitate Intra- and Intergeneric Crosses

Miscanthus is a close relative of saccharum and a potentially valuable genetic resource for improving sugarcane. Differences in flowering time within and between miscanthus and saccharum hinders intra- and interspecific hybridizations. A series of greenhouse experiments were conducted over three years to determine how to synchronize flowering time of saccharum and miscanthus genotypes. We found that day length was an important factor influencing when miscanthus and saccharum flowered. Sugarcane could be induced to flower in a central Illinois greenhouse using supplemental lighting to reduce the rate at which days shortened during the autumn and winter to 1 min d-1, which allowed us to synchronize the flowering of some sugarcane genotypes with Miscanthus genotypes primarily from low latitudes. In a complementary growth chamber experiment, we evaluated 33 miscanthus genotypes, including 28 M. sinensis , 2 M. floridulus , and 3 M. ×giganteus collected from 20.9° S to 44.9° N for response to three day lengths (10 h, 12.5 h, and 15 h). High latitude-adapted M. sinensis flowered mainly under 15 h days, but unexpectedly, short days resulted in short, stocky plants that did not flower; in some cases, flag leaves developed under short days but heading did not occur. In contrast, for M. sinensis and M. floridulus from low latitudes, shorter day lengths typically resulted in earlier flowering, and for some low latitude genotypes, 15 h days resulted in no flowering. However, the highest ratio of reproductive shoots to total number of culms was typically observed for 12.5 h or 15 h days. Latitude of origin was significantly associated with culm length, and the shorter the days, the stronger the relationship. Nearly all entries achieved maximal culm length under the 15 h treatment, but the nearer to the equator an accession originated, the less of a difference in culm length between the short-day treatments and the 15 h day treatment. Under short days, short culms for high-latitude accessions was achieved by different physiological mechanisms for M. sinensis genetic groups from the mainland in comparison to those from Japan; for mainland accessions, the mechanism was reduced internode length, whereas for Japanese accessions the phyllochron under short days was greater than under long days. Thus, for M. sinensis , short days typically hastened floral induction, consistent with the expectations for a facultative short-day plant. However, for high latitude accessions of M. sinensis , days less than 12.5 h also signaled that plants should prepare for winter by producing many short culms with limited elongation and development; moreover, this response was also epistatic to flowering. Thus, to flower M. sinensis that originates from high latitudes synchronously with sugarcane, the former needs day lengths >12.5 h (perhaps as high as 15 h), whereas that the latter needs day lengths <12.5 h.

Feedstock Production↗
DOE OSTI2021

Managing flowering time in Miscanthus and sugarcane to facilitate intra- and intergeneric crosses

Miscanthus is a close relative of Saccharum and a potentially valuable genetic resource for improving sugarcane. Differences in flowering time within and between Miscanthus and Saccharum hinders intra- and interspecific hybridizations. A series of greenhouse experiments were conducted over three years to determine how to synchronize flowering time of Saccharum and Miscanthus genotypes. We found that day length was an important factor influencing when Miscanthus and Saccharum flowered. Sugarcane could be induced to flower in a central Illinois greenhouse using supplemental lighting to reduce the rate at which days shortened during the autumn and winter to 1 min d -1 , which allowed us to synchronize the flowering of some sugarcane genotypes with Miscanthus genotypes primarily from low latitudes. In a complementary growth chamber experiment, we evaluated 33 Miscanthus genotypes, including 28 M . sinensis , 2 M . floridulus , and 3 M . ×giganteus collected from 20.9° S to 44.9° N for response to three day lengths (10 h, 12.5 h, and 15 h). High latitude-adapted M . sinensis flowered mainly under 15 h days, but unexpectedly, short days resulted in short, stocky plants that did not flower; in some cases, flag leaves developed under short days but heading did not occur. In contrast, for M . sinensis and M . floridulus from low latitudes, shorter day lengths typically resulted in earlier flowering, and for some low latitude genotypes, 15 h days resulted in no flowering. However, the highest ratio of reproductive shoots to total number of culms was typically observed for 12.5 h or 15 h days. Latitude of origin was significantly associated with culm length, and the shorter the days, the stronger the relationship. Nearly all entries achieved maximal culm length under the 15 h treatment, but the nearer to the equator an accession originated, the less of a difference in culm length between the short-day treatments and the 15 h day treatment. Under short days, short culms for high-latitude accessions was achieved by different physiological mechanisms for M . sinensis genetic groups from the mainland in comparison to those from Japan; for mainland accessions, the mechanism was reduced internode length, whereas for Japanese accessions the phyllochron under short days was greater than under long days. Thus, for M . sinensis , short days typically hastened floral induction, consistent with the expectations for a facultative short-day plant. However, for high latitude accessions of M . sinensis , days less than 12.5 h also signaled that plants should prepare for winter by producing many short culms with limited elongation and development; moreover, this response was also epistatic to flowering. Thus, to flower M . sinensis that originates from high latitudes synchronously with sugarcane, the former needs day lengths >12.5 h (perhaps as high as 15 h), whereas that the latter needs day lengths <12.5 h.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Elemental profiling and genomewide association studies reveal genomic variants modulating ionomic composition in Populus trichocarpa leaves

Samples were collected from a population of 1,089 black cottonwood genotypes (P. trichocarpa) assembled from native stands to encompass the central portion of the natural range of the species, stretching from 38.8° to 54.3° N Q13 latitude from California, USA, to British Columbia, Canada. Establishment of the common garden, growth conditions, and site maintenance have been described by Muchero et al (2015). In this study, leaf samples for ionomic profiling were collected from 4-year-old trees, during the growing season, in July 2012, from a field located in Clatskanie, Oregon, USA (46°6′11″N 123°12′13″W). The field site was located in a protected alluvial floodplain containing a uniform Wauna-Locoda silt loam soil area characterized by an acidic pH, in Columbia County, Oregon. A subset of 584 out of the 1,089 P. trichocarpa genotypes were represented in this sampling. These genotypes were randomly selected to represent the geographical distribution of the population. A single fully mature (LPI 7-9) leaf on the south side of the tree exposed to full sunlight conditions was removed from the tree within a 6-hour window centering on solar noon and immediately frozen under dry ice before processing. Leaf samples of 584 P. trichocarpa genotypes were finely ground to 40 mm particle size using a mortar and pestle, and ionomic composition was analyzed using ICP-MS. In total, 20 elements were profiled, including aluminum (Al27), arsenic (As75), boron (B11), cadmium (Cd111), calcium (Ca43), cobalt (Co), copper (Cu), iron (Fe57), magnesium (Mg25), manganese (Mn55), molybdenum (Mo), nickel (Ni60), phosphorus (P31), potassium (K39), rubidium (Rb85), selenium (Se82), sodium (Na23), strontium (Sr88), sulfur (S34), and zinc (Zn66), following a protocol established by Ziegler et al. (2013). For each sample, 75mg of powder was digested overnight in 2.5 mL HNO3 containing 20 parts per billion (ppb) indium as an internal standard, following the protocol described in Ziegler et al. (2013). Following a dilution, concentration of the 20 elements was measured using an Elan 6000 DRC-e mass spectrometer (Perkin-Elmer SCIEX) connected to a PFA microflow nebulizer (Elemental Scientific) and Apex HF desolvator (Elemental Scientific). One measurement per sample per genotype was done. For subsequent analyses, the quantifications were converted to total element concentration.

CBI ionomics, GWAS, plasma-mass spectrometry, neut↗
DOE OSTI2021

Impact of Harvest on Switchgrass Leaf Microbial Communities

Switchgrass is a promising feedstock for biofuel production, with potential for leveraging its native microbial community to increase productivity and resilience to environmental stress. Here, we characterized the bacterial, archaeal and fungal diversity of the leaf microbial community associated with four switchgrass (Panicum virgatum) genotypes, subjected to two harvest treatments (annual harvest and unharvested control), and two fertilization levels (fertilized and unfertilized control), based on 16S rRNA gene and internal transcribed spacer (ITS) region amplicon sequencing. Leaf surface and leaf endosphere bacterial communities were significantly different with Alphaproteobacteria enriched in the leaf surface and Gammaproteobacteria and Bacilli enriched in the leaf endosphere. Harvest treatment significantly shifted presence/absence and abundances of bacterial and fungal leaf surface community members: Gammaproteobacteria were significantly enriched in harvested and Alphaproteobacteria were significantly enriched in unharvested leaf surface communities. These shifts were most prominent in the upland genotype DAC where the leaf surface showed the highest enrichment of Gammaproteobacteria, including taxa with 100% identity to those previously shown to have phytopathogenic function. Fertilization did not have any significant impact on bacterial or fungal communities. We also identified bacterial and fungal taxa present in both the leaf surface and leaf endosphere across all genotypes and treatments. These core taxa were dominated by Methylobacterium, Enterobacteriaceae, and Curtobacterium, in addition to Aureobasidium, Cladosporium, Alternaria and Dothideales. Local core leaf bacterial and fungal taxa represent promising targets for plant microbe engineering and manipulation across various genotypes and harvest treatments. Our study showcases, for the first time, the significant impact that harvest treatment can have on bacterial and fungal taxa inhabiting switchgrass leaves and the need to include this factor in future plant microbial community studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Metabolomic, photoprotective, and photosynthetic acclimatory responses to post‐flowering drought in sorghum

Abstract Climate change is globally affecting rainfall patterns, necessitating the improvement of drought tolerance in crops. Sorghum bicolor is a relatively drought‐tolerant cereal. Functional stay‐green sorghum genotypes can maintain green leaf area and efficient grain filling during terminal post‐flowering water deprivation, a period of ~10 weeks. To obtain molecular insights into these characteristics, two drought‐tolerant genotypes, BTx642 and RTx430, were grown in replicated control and terminal post‐flowering drought field plots in California's Central Valley. Photosynthetic, photoprotective, and water dynamics traits were quantified and correlated with metabolomic data collected from leaves, stems, and roots at multiple timepoints during control and drought conditions. Physiological and metabolomic data were then compared to longitudinal RNA sequencing data collected from these two genotypes. The unique metabolic and transcriptomic response to post‐flowering drought in sorghum supports a role for the metabolite galactinol in controlling photosynthetic activity through regulating stomatal closure in post‐flowering drought. Additionally, in the functional stay‐green genotype BTx642, photoprotective responses were specifically induced in post‐flowering drought, supporting a role for photoprotection in the molecular response associated with the functional stay‐green trait. From these insights, new pathways are identified that can be targeted to maximize yields under growth conditions with limited water.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

The rhizosphere and cropping system, but not arbuscular mycorrhizae, affect ammonia oxidizing archaea and bacteria abundances in two agricultural soils

Arbuscular mycorrhizal fungi (AMF) form symbioses with roots that can enhance plant nutrition. While AMF have been shown to have a role in soil nitrogen (N) cycling, it is unclear whether AMF affect N cycling microbes such as ammonia-oxidizing bacteria (AOB) and archaea (AOA), which convert ammonium into nitrite in the first step of nitrification. In this study, we examined the effects of AMF on AOA and AOB abundances within the corn rhizosphere and bulk soil of conventional (corn-soybean rotation with inorganic fertilizer) and diversified (cornsoybean- oats/alfalfa-oats rotation with composted manure) systems. We hypothesized that AMF would decrease AOA and AOB abundances in a cropping-system dependent manner, possibly due to competition for ammonium. We grew corn deficient or proficient in AMF symbiosis in microcosms for 10 weeks. At the end of the experiment, both soils planted with the AMF-proficient corn genotype had higher ammonium and lower nitrate pool sizes compared to the same soils planted with the AMF-deficient corn genotype. Likewise, total plant N was higher in the AMF-proficient genotype compared to the AMF-deficient genotype. Despite changes in soil inorganic N pool sizes, AOA and AOB abundances were unaffected by plant AMF-proficiency. Instead, AOA abundance was greater in the rhizosphere than in the bulk soil regardless of cropping system, and AOB abundance was greater in the conventional than the diversified cropping system soil regardless of proximity to the root. These data indicate that 1) AMF did not affect AOA or AOB abundance in these N-rich soils but other factors such as root proximity and inorganic fertilization did and 2) AOA and AOB have differing ecological niches within rhizosphere and bulk soil that should be considered when managing for nitrogen losses.

Wattenburger, Cassandra↗
DOE OSTI2022

Evaluation of UAV-derived multimodal remote sensing data for biomass prediction and drought tolerance assessment in bioenergy sorghum

Screening for drought tolerance is critical to ensure high biomass production of bioenergy sorghum in arid or semi-arid environments. The bottleneck in drought tolerance selection is the challenge of accurately predicting biomass for a large number of genotypes. Although biomass prediction by low-altitude remote sensing has been widely investigated on various crops, the performance of the predictions are not consistent, especially when applied in a breeding context with hundreds of genotypes. In some cases, biomass prediction of a large group of genotypes benefited from multimodal remote sensing data; while in other cases, the benefits were not obvious. In this study, we evaluated the performance of single and multimodal data (thermal, RGB, and multispectral) derived from an unmanned aerial vehicle (UAV) for biomass prediction for drought tolerance assessments within a context of bioenergy sorghum breeding. The biomass of 360 sorghum genotypes grown under well-watered and water-stressed regimes was predicted with a series of UAV-derived canopy features, including canopy structure, spectral reflectance, and thermal radiation features. Biomass predictions using canopy features derived from the multimodal data showed comparable performance with the best results obtained with the single modal data with coefficients of determination (R 2 ) ranging from 0.40 to 0.53 under water-stressed environment and 0.11 to 0.35 under well-watered environment. The significance in biomass prediction was highest with multispectral followed by RGB and lowest with the thermal sensor. Finally, two well-recognized yield-based drought tolerance indices were calculated from ground truth biomass data and UAV predicted biomass, respectively. Results showed that the geometric mean productivity index outperformed the yield stability index in terms of the potential for reliable predictions by the remotely sensed data. Collectively, this study demonstrated a promising strategy for the use of different UAV-based imaging sensors to quantify yield-based drought tolerance.

09 BIOMASS FUELS↗
DOE OSTI2025

Migrating Populus with climate change: Phenology, coppice management, cold spell susceptibility, leaf dynamics, and biomass production

Understanding the phenology and productivity of Populus species is crucial for effective management and conservation strategies amid climate change. We investigated leaf budbreak timing, susceptibility to cold damage, leaf dynamics, and biomass production of 168 Populus genotypes with diverse provenances in the southeastern United States. Our study revealed significant variation in budbreak timing across different taxa and years, with genotypes inheriting traits adapted to their parents’ local climates. Temperature emerged as a key factor triggering budbreak, while leaf development depended on other environmental cues such as photoperiod. Notably, budbreak occurred approximately 20 days earlier in 2023 compared to 2022 due to higher accumulated degree days (ADDs). Short-rotation-coppice (SRC) management delayed budbreak by five to ten days. Cold damage was significant in 2023, particularly for genotypes from northern provenances and those with P. maximowiczii parentage. Severe damage was also observed in eastern cottonwood ( Populus deltoides ​× ​ Populus deltoides (D ​× ​D)) genotypes, despite most having southeastern US parentages. Leaf dynamics, including leaf duration and leaf area index (LAI), varied across taxa and sites, with earlier budbreak correlating with extended growing seasons and increased LAI. Biomass production was intricately linked to phenological events, with earlier budbreak leading to increased biomass production and greater susceptibility to cold damage. Our findings highlight the importance of genetics, environment, and coppicing management in understanding and managing Populus phenology and biomass production. These insights provide valuable guidance for developing effective breeding, conservation, and management strategies for Populus species in the context of climate change.

Accumulated degree days (ADDs)↗
DOE OSTI2023

A genomic data archive from the Network for Pancreatic Organ donors with Diabetes

The Network for Pancreatic Organ donors with Diabetes (nPOD) is the largest biorepository of human pancreata and associated immune organs from donors with type 1 diabetes (T1D), maturity-onset diabetes of the young (MODY), cystic fibrosis-related diabetes (CFRD), type 2 diabetes (T2D), gestational diabetes, islet autoantibody positivity (AAb+), and without diabetes. nPOD recovers, processes, analyzes, and distributes high-quality biospecimens, collected using optimized standard operating procedures, and associated de-identified data/metadata to researchers around the world. Herein describes the release of high-parameter genotyping data from this collection. 372 donors were genotyped using a custom precision medicine single nucleotide polymorphism (SNP) microarray. Data were technically validated using published algorithms to evaluate donor relatedness, ancestry, imputed HLA, and T1D genetic risk score. Additionally, 207 donors were assessed for rare known and novel coding region variants via whole exome sequencing (WES). These data are publicly-available to enable genotype-specific sample requests and the study of novel genotype:phenotype associations, aiding in the mission of nPOD to enhance understanding of diabetes pathogenesis to promote the development of novel therapies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Xylem-dwelling pathogen unaffected by local xylem vessel network properties in grapevines ( Vitis spp.)

Abstract Background and aims Xylella fastidiosa (Xf) is the xylem-dwelling bacterium associated with Pierce’s disease (PD), which causes mortality in agriculturally important species, such as grapevine (Vitis vinifera). The development of PD symptoms in grapevines depends on the ability of Xf to produce cell-wall-degrading enzymes to break up intervessel pit membranes and systematically spread through the xylem vessel network. Our objective here was to investigate whether PD resistance could be mechanistically linked to xylem vessel network local connectivity. Methods We used high-resolution X-ray micro-computed tomography (microCT) imaging to identify and describe the type, area and spatial distribution of intervessel connections for six different grapevine genotypes from three genetic backgrounds, with varying resistance to PD (four PD resistant and two PD susceptible). Key results Our results suggest that PD resistance is unlikely to derive from local xylem network connectivity. The intervessel pit area (Ai) varied from 0.07 ± 0.01 mm2 mm−3 in Lenoir to 0.17 ± 0.03 mm2 mm−3 in Blanc do Bois, both PD resistant. Intervessel contact fraction (Cp) was not statically significant, but the two PD-susceptible genotypes, Syrah (0.056 ± 0.015) and Chardonnay (0.041 ± 0.013), were among the most highly connected vessel networks. Neither Ai nor Cp explained differences in PD resistance among the six genotypes. Bayesian re-analysis of our data shows moderate evidence against the effects of the traits analysed: Ai (BF01 = 4.88), mean vessel density (4.86), relay diameter (4.30), relay density (3.31) and solitary vessel proportion (3.19). Conclusions Our results show that radial and tangential xylem network connectivity is highly conserved within the six different Vitis genotypes we sampled. The way that Xf traverses the vessel network may limit the importance of local network properties to its spread and may confer greater importance on host biochemical responses.

Plant Sciences↗
DOE OSTI2023

Occurrence and molecular characterization of Enterocytozoon bieneusi in wild and domestic animal species in Portugal

Abstract The phylum Microsporidia encompasses a diverse group of obligate, intracellular, and spore-forming organisms able to infect a wide range of animal hosts. Among them, Enterocytozoon bieneusi is the most frequently reported species in humans and animals. Little is known about the presence and epidemiology of E. bieneusi in wildlife. We investigated E. bieneusi occurrence and genetic diversity in wild and domestic mammals, through molecular-detection methods, from different regions across Portugal. A total of 756 samples were collected from 288, 242, and 226 wild carnivores, wild ungulates, and domestic animals, respectively. Overall, eight specimens were E. bieneusi-positive (1.1%, 8/756) obtained from five wild (Iberian lynx, Iberian wolf, red fox, stone marten, and wild boar) and one domestic (sheep) host. Nucleotide sequence analysis identified four genotypes of E. bieneusi, Type IV, Wildboar3, BEB6, and PtEbIX. Three of those genotypes belong to Groups 1 (Type IV and Wildboar3) and 2 (BEB6), which are known to contain genotypes capable of infecting a variety of hosts, including humans, highlighting their public health importance. PtEbIX belongs to the dog-specific Group 11. This study represents the first, largest, and most comprehensive molecular-based epidemiology survey carried out in Portugal in wild and domestic animals to date and the first worldwide identification of E. bieneusi in wolf species. Our study showed that wild carnivores and ungulates may act as reservoirs of zoonotic genotypes of E. bieneusi, establishing their role in maintaining the sylvatic cycle of this parasite while representing a potential source of infection for humans and domestic animals.

Figueiredo, Ana M. (ORCID:0000000226236340)↗
DOE OSTI2022

Uncoupling differential water usage from drought resistance in a dwarf Arabidopsis mutant

Abstract Understanding the molecular and physiological mechanisms of how plants respond to drought is paramount to breeding more drought-resistant crops. Certain mutations or allelic variations result in plants with altered water-use requirements. To correctly identify genetic differences which confer a drought phenotype, plants with different genotypes must be subjected to equal levels of drought stress. Many reports of advantageous mutations conferring drought resistance do not control for soil water content (SWC) variations across genotypes and may therefore need to be re-examined. Here, we reassessed the drought phenotype of the Arabidopsis (Arabidopsis thaliana) dwarf mutant, chiquita1-1 (chiq1-1, also called constitutively stressed 1 (cost1)), by growing mutant seedlings together with the wild-type to ensure uniform soil water availability across genotypes. Our results demonstrate that the dwarf phenotype conferred by loss of CHIQ1 function results in constitutively lower water usage per plant, but not increased drought resistance. Our study provides an easily reproducible, low-cost method to measure and control for SWC and to compare drought-resistant genotypes more accurately.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Quantitative genetic-by-soil microbiome interactions in a perennial grass affect functional traits

Plants interact with diverse microbiomes that can impact plant growth and performance. Recent studies highlight the potential beneficial aspects of plant microbiomes, including the possibility that microbes facilitate the process of local adaptation in their host plants. Microbially mediated local adaptation in plants occurs when local host genotypes have higher fitness than foreign genotypes because of their affiliation with locally beneficial microbes. Here, plant adaptation results from genetic interactions of the host with locally beneficial microbes (e.g. host genotype-by-microbiome interactions). We used a recombinant inbred line (RIL) mapping population derived from upland and lowland ecotypes of the diploid C4 perennial bunch grass Panicum hallii to explore quantitative genetic responses to soil microbiomes focusing on functional root and shoot traits involved in ecotypic divergence. We show that the growth and development of ecotypes and their trait divergence depends on soil microbiomes. Moreover, we find that the genetic architecture is modified by soil microbiomes, revealing important plant genotype-by-microbiome interactions for quantitative traits. We detected a number of quantitative trait loci (QTL) that interact with the soil microbiome. Our results highlight the importance of microbial interactions in ecotypic divergence and trait genetic architecture in C4 perennial grasses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Assembly of the Populus Microbiome Is Temporally Dynamic and Determined by Selective and Stochastic Factors

Recent work shows that the plant microbiome, particularly the initial assembly of this microbiome, influences plant health, survival, and fitness. Here, we characterize the initial assembly of the Populus microbiome across ten genotypes belonging to two poplar species in a common garden using 16S rRNA gene and ITS2 region amplicon sequencing of the leaf endosphere, leaf surface, root endosphere, and rhizosphere. We sampled these microbiomes three times throughout the first growing season and found that the composition of the microbiome changed dramatically over time across all plant-associated habitats and host genotypes. For archaea and bacteria, these changes were dominated by strong homogenizing selection (accounting for 29 to 62% of pairwise comparisons). However, fungal assembly was generally characterized by multiple ecological assembly processes (i.e., a mix of weak selective and dispersal processes). Interestingly, genotype, while a significant moderator of microbiome composition, generally explained less variation than sample date across plant-associated habitats. We defined a set of core genera that accounted for, on average, 36% of the microbiome. The relative abundance of this core community was consistent over time. Additionally, using source tracking modeling, we determined that new microbial taxa colonize from both aboveground and belowground sources, and combined with our ecological assembly null models, we found that both selective and dispersal processes explained the differences between exo- (i.e., leaf surface and rhizosphere) and endospheric microbiomes. Taken together, our results suggest that the initial assembly of the Populus microbiome is time-, genotype-, and habitat-dependent and is moderated by both selective and stochastic factors.

16S rRNA↗