Cropping Systems Research Laboratory

Rice, a staple food for more than half of the world's population, is grown in >100 countries with 90% of the total global production from Asia. Although there are more than 110,000 cultivated varieties of rice that vary in quality and nutritional content, after post-harvest processing, rice can be categorized as either white or brown. Regional and cultural preferences as well as need for stability during storage and transport are the final determinants of market availability and final consumption. In addition to calories, rice is a good source of magnesium, phosphorus, manganese, selenium, iron, folic acid, thiamin and niacin; but it is low in fiber and fat. Although brown rice is promoted as being "healthier" because of bioactive compounds, including minerals and vitamins not present in white rice after polishing, white rice is more widely consumed than brown. This is for several reasons, including cooking ease, palatability, and shelf life. Polished rice has a higher glycemic load and may impact glucose homeostasis but when combined with other foods, it can be considered part of a "healthy" plate. With the projected increase in the global population, rice will remain a staple. However, it will be important to encourage intake of the whole grain (brown rice) and to identify ways to harness the phytonutrients that are lost during milling. Furthermore, as the world faces environmental challenges, changing demographics and consumer demands, farmers, healthcare providers, food manufacturers and nutritionists must work collaboratively to assure adequate supply, nutritional integrity and sustainability of rice production systems globally.

BACKGROUND: Diabetic extremity ulcers are associated with chronic infections. Such ulcer infections are too often followed by amputation because there is little or no understanding of the ecology of such infections or how to control or eliminate this type of chronic infection. A primary impediment to the healing of chronic wounds is biofilm phenotype infections. Diabetic foot ulcers are the most common, disabling, and costly complications of diabetes. Here we seek to derive a better understanding of the polymicrobial nature of chronic diabetic extremity ulcer infections. METHODS AND FINDINGS: Using a new bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP) approach we have evaluated the bacterial diversity of 40 chronic diabetic foot ulcers from different patients. The most prevalent bacterial genus associated with diabetic chronic wounds was Corynebacterium spp. Findings also show that obligate anaerobes including Bacteroides, Peptoniphilus, Fingoldia, Anaerococcus, and Peptostreptococcus spp. are ubiquitous in diabetic ulcers, comprising a significant portion of the wound biofilm communities. Other major components of the bacterial communities included commonly cultured genera such as Streptococcus, Serratia, Staphylococcus and Enterococcus spp. CONCLUSIONS: In this article, we highlight the patterns of population diversity observed in the samples and introduce preliminary evidence to support the concept of functional equivalent pathogroups (FEP). Here we introduce FEP as consortia of genotypically distinct bacteria that symbiotically produce a pathogenic community. According to this hypothesis, individual members of these communities when they occur alone may not cause disease but when they coaggregate or consort together into a FEP the synergistic effect provides the functional equivalence of well-known pathogens, such as Staphylococcus aureus, giving the biofilm community the factors necessary to maintain chronic biofilm infections. Further work is definitely warranted and needed in order to prove whether the FEPs concept is a viable hypothesis. The findings here also suggest that traditional culturing methods may be extremely biased as a diagnostic tool as they select for easily cultured organisms such as Staphylococcus aureus and against difficult to culture bacteria such as anaerobes. While PCR methods also have bias, further work is now needed in comparing traditional culture results to high-resolution molecular diagnostic methods such as bTEFAP.

Overexpression of a tobacco glutathione S-transferase with glutathione peroxidase activity (GST/GPX) in transgenic tobacco (Nicotiana tabacum L.) enhanced seedling growth under a variety of stressful conditions. In addition to increased GST and GPX activity, transgenic GST/GPXexpressing (GST+) seedlings had elevated levels of monodehydroascorbate reductase activity. GST+ seedlings also contained higher levels of glutathione and ascorbate than wildtype seedlings and the glutathione pools were more oxidized. Thermal or salt-stress treatments that inhibited the growth of wild-type seedlings also caused increased levels of lipid peroxidation. These treatments had less effect on the growth of GST+ seedling growth and did not lead to increased lipid peroxidation. Stress-induced damage resulted in reduced metabolic activity in wild-type seedlings while GST+ seedlings maintained metabolic activity levels comparable to seedlings grown under control conditions. These results indicate that overexpression of GST/GPX in transgenic tobacco seedlings provides increased glutathione-dependent peroxide scavenging and alterations in glutathione and ascorbate metabolism that lead to reduced oxidative damage. We conclude that this protective effect is primarily responsible for the ability of GST+ seedlings to maintain growth under stressful conditions.

-induced deficits of protein, minerals, and vitamins in rice were correlated to the lowest overall gross domestic product per capita for the highest rice-consuming countries, suggesting potential consequences for a global population of approximately 600 million.

Our objective is to provide an optimistic strategy for reversing soil degradation by increasing public and private research efforts to understand the role of soil biology, particularly microbiology, on the health of our world’s soils. We begin by defining soil quality/soil health (which we consider to be interchangeable terms), characterizing healthy soil resources, and relating the significance of soil health to agroecosystems and their functions. We examine how soil biology influences soil health and how biological properties and processes contribute to sustainability of agriculture and ecosystem services. We continue by examining what can be done to manipulate soil biology to: (i) increase nutrient availability for production of high yielding, high quality crops; (ii) protect crops from pests, pathogens, weeds; and (iii) manage other factors limiting production, provision of ecosystem services, and resilience to stresses like droughts. Next we look to the future by asking what needs to be known about soil biology that is not currently recognized or fully understood and how these needs could be addressed using emerging research tools. We conclude, based on our perceptions of how new knowledge regarding soil biology will help make agriculture more sustainable and productive, by recommending research emphases that should receive first priority through enhanced public and private research in order to reverse the trajectory toward global soil degradation.

The extent to which microorganisms impair wound healing is an ongoing controversy in the management of chronic wounds. Because the high diversity and extreme variability of the microbiota between individual chronic wounds lead to inconsistent findings in small cohort studies, evaluation of a large number of chronic wounds using identical sequencing and bioinformatics methods is necessary for clinicians to be able to select appropriate empiric therapies. In this study, we utilized 16S rDNA pyrosequencing to analyze the composition of the bacterial communities present in samples obtained from patients with chronic diabetic foot ulcers (N = 910), venous leg ulcers (N = 916), decubitus ulcers (N = 767), and nonhealing surgical wounds (N = 370). The wound samples contained a high proportion of Staphylococcus and Pseudomonas species in 63 and 25% of all wounds, respectively; however, a high prevalence of anaerobic bacteria and bacteria traditionally considered commensalistic was also observed. Our results suggest that neither patient demographics nor wound type influenced the bacterial composition of the chronic wound microbiome. Collectively, these findings indicate that empiric antibiotic selection need not be based on nor altered for wound type. Furthermore, the results provide a much clearer understanding of chronic wound microbiota in general; clinical application of this new knowledge over time may help in its translation to improved wound healing outcomes.

Association mapping is a powerful strategy for identifying genes underlying quantitative traits in plants. We have assembled and characterized genetic and phenotypic diversity of a sorghum [ Sorghum bicolor (L.) Moench] panel suitable for association mapping, comprised of 377 accessions representing all major cultivated races (tropical lines from diverse geographic and climatic regions), and important U.S. breeding lines and their progenitors. Accessions were phenotyped for eight traits, and levels of population structure and familial relatedness were assessed with 47 simple sequence repeat (SSR) loci. The panel exhibited substantial morphological variation and little genotypic differentiation was observed between the converted tropical and breeding lines. The phenotypic and genotypic data were used to evaluate the performance of several association models in controlling for spurious associations. Our analysis indicated that association models that accounted for both population structure and kinship performed better than those that did not. In addition, we found that the optimal number of subpopulations used to correct for population structure was trait dependent. Although augmentation of the genotypic data with additional SSR loci may be necessary, the association models, genotypic data, and germplasm panel described here provide a starting point for sorghum researchers to begin association studies of traits and markers or candidate genes of interest.

Bryophytes are a non-monophyletic group of three major lineages (liverworts, hornworts, and mosses) that descend from the earliest branching events in the phylogeny of land plants. We postulate that desiccation tolerance is a primitive trait, thus mechanisms by which the first land plants achieved tolerance may be reflected in how extant desiccation-tolerant bryophytes survive drying. Evidence is consistent with extant bryophytes employing a tolerance strategy of constitutive cellular protection coupled with induction of a recovery/repair mechanism upon rehydration. Cellular structures appear intact in the desiccated state but are disrupted by rapid uptake of water upon rehydration, but cellular integrity is rapidly regained. The photosynthetic machinery appears to be protected such that photosynthetic activity recovers quickly. Gene expression responds following rehydration and not during drying. Gene expression is translationally controlled and results in the synthesis of a number of proteins, collectively called rehydrins. Some prominent rehydrins are similar to Late Embryogenesis Abundant (LEA) proteins, classically ascribed a protection function during desiccation. The role of LEA proteins in a rehydrating system is unknown but data indicates a function in stabilization and reconstitution of membranes. Phylogenetic studies using a Tortula ruralis LEA-like rehydrin led to a re-examination of the evolution of desiccation tolerance. A new phylogenetic analysis suggests that: (i) the basic mechanisms of tolerance seen in modern day bryophytes have changed little from the earliest manifestations of desiccation tolerance in land plants, and (ii) vegetative desiccation tolerance in the early land plants may have evolved from a mechanism present first in spores.

The Arabidopsis gene AVP1 encodes a vacuolar pyrophosphatase that functions as a proton pump on the vacuolar membrane. Overexpression of AVP1 in Arabidopsis, tomato and rice enhances plant performance under salt and drought stress conditions, because up-regulation of the type I H+-PPase from Arabidopsis may result in a higher proton electrochemical gradient, which facilitates enhanced sequestering of ions and sugars into the vacuole, reducing water potential and resulting in increased drought- and salt tolerance when compared to wild-type plants. Furthermore, overexpression of AVP1 stimulates auxin transport in the root system and leads to larger root systems, which helps transgenic plants absorb water more efficiently under drought conditions. Using the same approach, AVP1-expressing cotton plants were created and tested for their performance under high-salt and reduced irrigation conditions. The AVP1-expressing cotton plants showed more vigorous growth than wild-type plants in the presence of 200 mM NaCl under hydroponic growth conditions. The soil-grown AVP1-expressing cotton plants also displayed significantly improved tolerance to both drought and salt stresses in greenhouse conditions. Furthermore, the fibre yield of AVP1-expressing cotton plants is at least 20% higher than that of wild-type plants under dry-land conditions in the field. This research indicates that AVP1 has the potential to be used for improving crop's drought- and salt tolerance in areas where water and salinity are limiting factors for agricultural productivity.

Abstract. Simulations of the dust cycle and its interactions with the changing Earth system are hindered by the empirical nature of dust emission parameterizations in weather and climate models. Here we take a step towards improving dust cycle simulations by using a combination of theory and numerical simulations to derive a physically based dust emission parameterization. Our parameterization is straightforward to implement into large-scale models, as it depends only on the wind friction velocity and the soil's threshold friction velocity. Moreover, it accounts for two processes missing from most existing parameterizations: a soil's increased ability to produce dust under saltation bombardment as it becomes more erodible, and the increased scaling of the dust flux with wind speed as a soil becomes less erodible. Our treatment of both these processes is supported by a compilation of quality-controlled vertical dust flux measurements. Furthermore, our scheme reproduces this measurement compilation with substantially less error than the existing dust flux parameterizations we were able to compare against. A critical insight from both our theory and the measurement compilation is that dust fluxes are substantially more sensitive to the soil's threshold friction velocity than most current schemes account for.

We consider the appropriateness of institutionalizing soil quality\nas a defined parameter in soil science. The soil management research\nof land grant universities and the Agricultural Research Service (ARS)\nand the mission and goals of state, federal, and private conservation\nagencies stand to be significantly affected. We feel that a non-advocative\nexamination of this concept could provide a positive contribution.\nThe definition of soil quality has proven elusive and value laden.\nThere is concern by some that the concept has developed arbitrary\npolicy overtones. Our reservations stem from concerns regarding premature\nacceptance and institutionalization of an incompletely formulated\nand largely untested paradigm, potential unintended negative\noutcomes, promotion of a narrowly defined environmental policy in a\ncontext normally associated with value-neutral science, and taxonomic\nand/or regional bias in establishing the paradigm. To date, soil quality\nassessments have drawn from a relatively narrow crop production and\necological perspective to positively or negatively weight soil quality\nassessment factors. Although the soil quality paradigm acknowledges\nmulti-defined soil functions, it has yet to operationally recognize and\nintegrate the simultaneity of diverse and often conflicting functions\nand soil property requirements. Thus, we are attempting to articulate\nthe concerns of many of our colleagues who are reluctant to endorse\nredefining the soil science paradigm away from the value-neutral\ntradition of edaphology and specific problem solving to a paradigm\nbased on variable, and often subjective societal perceptions of environmental\nholism. Traditionally, it has been the soil science profession's\nrole to perform the science to enable resource management policy\nand problem solving, not to establish relational-based value systems\nwithin the science. We suggest emphasizing quality soil management\nrather than soil quality management as a professional and scientific\ngoal.

Choline (Cho) is an essential nutrient for humans as well as the precursor of glycine betaine (GlyBet), an important compatible solute in eukaryotes that protects cells from osmotic stress caused by dehydrating conditions. The key enzyme for plant Cho synthesis is phosphoethanolamine N-methyltransferase (PEAMT), which catalyzes all three methylation steps, including the rate-limiting N-methylation of phosphoethanolamine. Herein, we report that the beneficial soil bacterium Bacillus subtilis (strain GB03) enhances Arabidopsis Cho and GlyBet synthesis associated with enhanced plant tolerance to osmotic stress. When stressed with 100 mM exogenous mannitol, GB03-exposed plants exhibit increased transcript level of PEAMT compared with stressed plants without bacterial exposure. Endogenous Cho and GlyBet metabolite pools were elevated by more than two- and fivefold, respectively, by GB03 treatment, consistent with increased stress tolerance. Moreover, in the xipotl mutant line with reduced Cho production, a loss of GB03-induced drought tolerance is observed. Osmotic-stressed plants with or without GB03 exposure show similar levels of abscsisic acid (ABA) accumulation in both shoots and roots, suggesting that GB03-induced osmoprotection is ABA independent. GB03 treatment also improves drought tolerance in soil-grown plants as characterized by phenotypic comparisons, supported by an elevated accumulation of osmoprotectants. These results provide a biological strategy to enhance Cho biosynthesis in plants and, in turn, increase plant tolerance to osmotic stress by elevating osmoprotectant accumulation.

Gene expression profiling holds tremendous promise for dissecting the regulatory mechanisms and transcriptional networks that underlie biological processes. Here we provide details of approaches used by others and ourselves for gene expression profiling in plants with emphasis on cDNA microarrays and discussion of both experimental design and downstream analysis. We focus on methods and techniques emphasizing fabrication of cDNA microarrays, fluorescent labeling, cDNA hybridization, experimental design, and data processing. We include specific examples that demonstrate how this technology can be used to further our understanding of plant physiology and development (specifically fruit development and ripening) and for comparative genomics by comparing transcriptome activity in tomato and pepper fruit.

Isopentenyltransferase (IPT) is a critical enzyme in the cytokinin biosynthetic pathway. The expression of IPT under the control of a maturation- and stress-induced promoter was shown to delay stress-induced plant senescence that resulted in an enhanced drought tolerance in both monocot and dicot plants. This report extends the earlier findings in tobacco and rice to peanut (Arachis hypogaea L.), an important oil crop and protein source. Regulated expression of IPT in peanut significantly improved drought tolerance in both laboratory and field conditions. Transgenic peanut plants maintained higher photosynthetic rates, higher stomatal conductance and higher transpiration than wild-type control plants under reduced irrigation conditions. More importantly, transgenic peanut plants produced significantly higher yields than wild-type control plants in the field, indicating a great potential for the development of crops with improved performance and yield in water-limited areas of the world.

Sharp debridement is the most clinically and cost-effective way of physically removing and suppressing a biofilm. Continued debridement, as part of a multifaceted treatment strategy, will keep the biofilm in a weakened state.

Continuous monoculture systems can reduce soil organic matter because of low organic inputs and disturbance from tillage practices. Integrated cotton ( Gossypium hirsutum ) cropping and livestock production systems in West Texas may provide more sustainable alternatives to the traditional continuous cotton system and improve soil quality. Our study was conducted on a Pullman soil (Fine, mixed, thermic Torrertic Paleustolls) after 5 yr as a complete randomized block design (three replications) that compared continuous cotton and an integrated livestock‐crop system with a perennial warm‐season grass pasture ( Bothriochloa bladhii ) paddock and two paddocks (two stages) of a rotation (wheat [ Triticum aestivum ]‐fallow‐rye [ Secale cereale ]‐cotton). Total N (average: 1.0 g kg −1 soil) remained similar among systems and soil pH was >8.1. Organic C was higher (13.5 g kg −1 soil) in perennial pasture compared with continuous cotton (9.0 g kg −1 soil) at 0 to 5 cm. A similar trend was found for the soil aggregate stability. Soil microbial biomass C (C mic ) was greater in perennial pasture (193 mg kg −1 soil) and the rotation under rye and cotton (237 mg kg −1 soil) compared with continuous cotton (124 mg kg −1 soil) at 0 to 5 cm, and in perennial pasture at 5 to 10 and 10 to 15 cm. Soil microbial biomass N (N mic ) showed similar trends. Soil enzyme activities were greater in perennial pasture and the rotation (under rye and cotton) than under continuous cotton at 0 to 5 cm. The integrated crop‐livestock system had higher protozoa (20:4ω6c = 1.98%) and fungi (18:3ω9c = 1.30%) than continuous cotton (20:4ω6c = 1.09%; 18:3ω9c = 0.76%). These findings suggest positive differences in soil function and sustainability of the integrated crop–livestock system compared with continuous cotton.

Knowledge of temperature effects on whole canopy photosynthesis, growth, and development of potato ( Solanum tuberosum L.) is important for crop model development and evaluation. The objective of this study was to quantify the effects of temperature on canopy photosynthesis, development, growth, and partitioning of potato cv. Atlantic under elevated atmospheric CO 2 concentration (700 μL L −1 CO 2 ). Potato plants were grown in day‐lit plant growth chambers at six constant day/night temperatures, (12, 16, 20, 24, 28, and 32°C) during a 52‐d experimental period in 1999 in Beltsville, MD. Main stem length and main stem expanded leaf number were measured nondestructively at 4 d intervals while leaf, stem, root, and tuber weights were obtained by destructive harvesting at biweekly time intervals. Canopy level net photosynthesis ( P N ) was obtained from gas exchange measurements. The optimum temperature for canopy photosynthesis was 24°C early in the growth period and shifted to lower temperatures as the plants aged. Total end‐of‐season biomass was highest in the 20°C treatment. End‐of‐season tuber mass and the ratio of tuber to total biomass decreased with increasing temperature above 24°C. Accumulated biomass was a linear function of total C gain with a common slope for all treatments. However, the proportion of C allocated to tubers decreased with increasing temperatures. High respiration losses decreased total C gain at higher temperatures. When simulating photosynthesis and C assimilation in crop models, source–sink relationships with temperature and photosynthesis need to be accounted for.

Drought and high temperature are two major environmental factors that severely limit plant productivity in the United States and worldwide, often causing extensive economic loss to agriculture. As global climate change progresses, agricultural production worldwide faces serious threats from frequent extreme weather conditions. Integrated approaches that improve the efficiency of agricultural water use and development of plant varieties that can alleviate the negative impacts of environmental stresses to maintain yield stability are essential to sustain and increase agriculture production. Maize (<i>Zea mays</i> L.) is a major crop in the United States and worldwide. Its production and yield stability are greatly affected by drought and high temperature stresses. Improving drought and heat tolerance in maize has become one of the top priorities for maize breeding programs in both private and public sectors. Identification of maize germplasm with superior drought and/or heat tolerance is essential and prerequisite for such propose. In this report, we evaluated a selection of maize inbred lines for drought and heat stress tolerance under field conditions in 2009 and 2010 and identified several inbred lines that showed high tolerance to drought. Tolerant inbred lines (Tx205, C2A554-4, and B76) were able to maintain relatively high leaf relative water content when subjected to drought stress, while sensitive lines (B73 and C273A) showed a rapid reduction in leaf relative water content at very early stage of drought. The tolerant lines also showed significantly greater ability to maintain vegetative growth and alleviate damage to reproductive tissues under drought conditions compared to the sensitive lines. Maize inbred lines and hybrids were also evaluated for tolerance to high temperature under well-watered conditions through field observations following the occurrence of major heat events. Maize inbred lines of distinct heat tolerance phenotype were identified. Furthermore, genetic and phenotypic analysis showed that maize hybrids made from inbred lines with superior heat tolerance inherited an enhanced tolerance to elevated temperatures. The tolerant germplasm accessions, like those identified in this study, are essential materials for breeding drought- and/or heat-tolerant maize hybrids. Study for the potential use of such materials to produce maize hybrids that are able to alleviate the negative impacts of drought and heat stress on the growth and development of maize plants is underway.

The thanatomicrobiome (thanatos, Greek for death) is a relatively new term and is the study of the microbes colonizing the internal organs and orifices after death. Recent scientific breakthroughs in an initial study of the thanatomicrobiome have revealed that a majority of the microbes within the human body are the obligate anaerobes, Clostridium spp., in the internal postmortem microbial communities. We hypothesized that time-dependent changes in the thanatomicrobiome within internal organs can estimate the time of death as a human body decays. Here we report a cross-sectional study of the sampling of 27 human corpses from criminal cases with postmortem intervals between 3.5-240 hours. The impetus for examining microbial communities in different internal organs is to address the paucity of empirical data on thanatomicrobiomic succession caused by the limited access to these organs prior to death and a dearth of knowledge regarding the movement of microbes within remains. Our sequencing results of 16S rRNA gene amplicons of 27 postmortem samples from cadavers demonstrated statistically significant time-, organ-, and sex-dependent changes. These results suggest that comprehensive knowledge of the number and abundance of each organ's signature microorganisms could be useful to forensic microbiologists as a new source of data for estimating postmortem interval.

BACKGROUND: The cellular response of plants to water-deficits has both economic and evolutionary importance directly affecting plant productivity in agriculture and plant survival in the natural environment. Genes induced by water-deficit stress have been successfully enumerated in plants that are relatively sensitive to cellular dehydration, however we have little knowledge as to the adaptive role of these genes in establishing tolerance to water loss at the cellular level. Our approach to address this problem has been to investigate the genetic responses of plants that are capable of tolerating extremes of dehydration, in particular the desiccation-tolerant bryophyte, Tortula ruralis. To establish a sound basis for characterizing the Tortula genome in regards to desiccation tolerance, we analyzed 10,368 expressed sequence tags (ESTs) from rehydrated rapid-dried Tortula gametophytes, a stage previously determined to exhibit the maximum stress induced change in gene expression. RESULTS: The 10, 368 ESTs formed 5,563 EST clusters (contig groups representing individual genes) of which 3,321 (59.7%) exhibited similarity to genes present in the public databases and 2,242 were categorized as unknowns based on protein homology scores. The 3,321 clusters were classified by function using the Gene Ontology (GO) hierarchy and the KEGG database. The results indicate that the transcriptome contains a diverse population of transcripts that reflects, as expected, a period of metabolic upheaval in the gametophyte cells. Much of the emphasis within the transcriptome is centered on the protein synthetic machinery, ion and metabolite transport, and membrane biosynthesis and repair. Rehydrating gametophytes also have an abundance of transcripts that code for enzymes involved in oxidative stress metabolism and phosphorylating activities. The functional classifications reflect a remarkable consistency with what we have previously established with regards to the metabolic activities that are important in the recovery of the gametophytes from desiccation. A comparison of the GO distribution of Tortula clusters with an identical analysis of 9,981 clusters from the desiccation sensitive bryophyte species Physcomitrella patens, revealed, and accentuated, the differences between stressed and unstressed transcriptomes. Cross species sequence comparisons indicated that on the whole the Tortula clusters were more closely related to those from Physcomitrella than Arabidopsis (complete genome BLASTx comparison) although because of the differences in the databases there were more high scoring matches to the Arabidopsis sequences. The most abundant transcripts contained within the Tortula ESTs encode Late Embryogenesis Abundant (LEA) proteins that are normally associated with drying plant tissues. This suggests that LEAs may also play a role in recovery from desiccation when water is reintroduced into a dried tissue. CONCLUSION: The establishment of a rehydration EST collection for Tortula ruralis, an important plant model for plant stress responses and vegetative desiccation tolerance, is an important step in understanding the genome level response to cellular dehydration. The type of transcript analysis performed here has laid the foundation for more detailed functional and genome level analyses of the genes involved in desiccation tolerance in plants.