Foreign Agricultural Service

Flowering time is a complex trait that controls adaptation of plants to their local environment in the outcrossing species Zea mays (maize). We dissected variation for flowering time with a set of 5000 recombinant inbred lines (maize Nested Association Mapping population, NAM). Nearly a million plants were assayed in eight environments but showed no evidence for any single large-effect quantitative trait loci (QTLs). Instead, we identified evidence for numerous small-effect QTLs shared among families; however, allelic effects differ across founder lines. We identified no individual QTLs at which allelic effects are determined by geographic origin or large effects for epistasis or environmental interactions. Thus, a simple additive model accurately predicts flowering time for maize, in contrast to the genetic architecture observed in the selfing plant species rice and Arabidopsis.

Maize genetic diversity has been used to understand the molecular basis of phenotypic variation and to improve agricultural efficiency and sustainability. We crossed 25 diverse inbred maize lines to the B73 reference line, capturing a total of 136,000 recombination events. Variation for recombination frequencies was observed among families, influenced by local (cis) genetic variation. We identified evidence for numerous minor single-locus effects but little two-locus linkage disequilibrium or segregation distortion, which indicated a limited role for genes with large effects and epistatic interactions on fitness. We observed excess residual heterozygosity in pericentromeric regions, which suggested that selection in inbred lines has been less efficient in these regions because of reduced recombination frequency. This implies that pericentromeric regions may contribute disproportionally to heterosis.

A-Maize-ing Maize is one of our oldest and most important crops, having been domesticated approximately 9000 years ago in central Mexico. Schnable et al. (p. 1112 ; see the cover) present the results of sequencing the B73 inbred maize line. The findings elucidate how maize became diploid after an ancestral doubling of its chromosomes and reveals transposable element movement and activity and recombination. Vielle-Calzada et al. (p. 1078 ) have sequenced the Palomero Toluqueño ( Palomero ) landrace, a highland popcorn from Mexico, which, when compared to the B73 line, reveals multiple loci impacted by domestication. Swanson-Wagner et al. (p. 1118 ) exploit possession of the genome to analyze expression differences occurring between lines. The identification of single nucleotide polymorphisms and copy number variations among lines was used by Gore et al. (p. 1115 ) to generate a Haplotype map of maize. While chromosomal diversity in maize is high, it is likely that recombination is the major force affecting the levels of heterozygosity in maize. The availability of the maize genome will help to guide future agricultural and biofuel applications (see the Perspective by Feuillet and Eversole ).

We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in three sub-clades, which was reinforced by high levels of synteny, size of core genomes, and relatedness of orthologous genes between strains within a sub-clade. The heterogeneity of the P. fluorescens group was reflected in the large size of its pan-genome, which makes up approximately 54% of the pan-genome of the genus as a whole, and a core genome representing only 45-52% of the genome of any individual strain. We discovered genes for traits that were not known previously in the strains, including genes for the biosynthesis of the siderophores achromobactin and pseudomonine and the antibiotic 2-hexyl-5-propyl-alkylresorcinol; novel bacteriocins; type II, III, and VI secretion systems; and insect toxins. Certain gene clusters, such as those for two type III secretion systems, are present only in specific sub-clades, suggesting vertical inheritance. Almost all of the genes associated with multitrophic interactions map to genomic regions present in only a subset of the strains or unique to a specific strain. To explore the evolutionary origin of these genes, we mapped their distributions relative to the locations of mobile genetic elements and repetitive extragenic palindromic (REP) elements in each genome. The mobile genetic elements and many strain-specific genes fall into regions devoid of REP elements (i.e., REP deserts) and regions displaying atypical tri-nucleotide composition, possibly indicating relatively recent acquisition of these loci. Collectively, the results of this study highlight the enormous heterogeneity of the P. fluorescens group and the importance of the variable genome in tailoring individual strains to their specific lifestyles and functional repertoire.

Abstract Pearl millet [ Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D 2 B 1 -P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop.

Abstract Three thousand forty‐five surface soil samples from 307 different soil series were analyzed for Pb, Cd, Zn, Cu, Ni, cation exchange capacity (CEC), organic C, and pH in the course of a study of trace element uptake by major agricultural crops. The soil data from this study are summarized here statistically and in map form to show their interactions and generalized geographic distribution patterns. Amounts of all five metal elements are generally low in the Southeast. A regional high of about 15 mg/kg Pb covers the Mississipi, Ohio, and Missouri River valleys. Higher values for other elements are generally concentrated in the West and in the lower Mississippi River Valley. Maximum Cd levels were found in soils of the coast ranges of central and southern California. Copper levels are noticeably higher in organic soil areas of Florida, Oregon, and the Great Lakes. Nickel and Cu concentrations are high in serpentine soil areas of California. Nickel levels are also somewhat higher in the glaciated areas of the northern great plains and in northern Maine. For the entire dataset, the values of the minimum‐maximum, 5th, 50th, and 95th percentiles are as follows: (mg/kg dry soil) Cd, <0.005 to 2.0, 0.036, 0.20, 0.78; Pb, 0.5 to 135, 4.0, 11, 23; Zn, 1.5 to 264, 8.0, 53, 126; Cu, 0.3 to 495, 3.8, 18.5, 95; Ni, 0.7 to 269, 4.1, 18.2, 57; pH (pH units) 3.9–8.9, 4.7, 6.1, 8.1; CEC (cmol/kg) 0.6 to 204, 2.4, 14.0, 135; and organic C % 0.09 to 63, 0.36, 1.05, 33.3. Metal levels generally increased with increasing clay concentration.

Nonpoint sources of P leaving the agricultural landscape can cause eutrophication of surface water and the associated growth of undesirable aquatic plants. USDA is developing an indexing procedure for identifying soils, landforms, and management practices that could have unfavorable impacts on water bodies because of P movement. This indexing procedure uses the characteristic of the field site, including soil erosion rates, runoff, available P soil test levels, and fertilizer and organic P application rates and methods to assess the degree of vulnerability of P movement from the site. A weighting procedure has been developed to include the various contributions each site characteristic may have: A summation of the products of the weighted site characteristic yields a site vulnerability rating. An assessment tool using the Phosphorus Index will assist field staff working with landusers to identify sensitive areas and recommend management alternatives to reduce risk of P losses. Problem The movement of P from the agricultural landscape is a concern because of the potential problem of surface water eutrophication and subsequent growth of undesirable aquatic plants. Landowners, producers, and field staffs striving for natural resource management must assess the soil, hydrology, and management of individual fields in order to identify those areas that have a greater‐than‐desired impact on the movement of P. By targeting these areas, landusers and resource planners can develop the necessary management practices that could reduce the potential for P movement. A field‐level P index is needed to make this assessment and assist in the development of management practices to lessen the potential for P movement. Background Models and equations have been used to assess a number of natural resource concerns, such as soil erosion by water and wind, nitrate leaching, and pesticide movement. A few simulation programs have attempted to calculate the potential delivery of P to the edge of the field. No assessment model, however, provides the user with a simple tool to measure the relative potential of P movement from the site based on readily available field parameter values. Project Description A two dimensional matrix has been developed that relates field site characteristics to values of categories based on the severity of the P movement problem (Table ). The site characteristics have been assigned a weighting factor based on the potential for that characteristic to affect P movement. There are eight site characteristics in version 1.0 of the Phosphorus Index. The eight characteristics with their weighting factor are: soil erosion (1.5) irrigation erosion (13) runoff (0.5) soil P test (1.0) P fertilizer application rate (0.75) P fertilizer application method (0.5) organic P source application rate (1.0) organic P source application method (1.0) Value categories are defined as measured levels of each site characteristic. The higher the value the greater is the potential for phosphorus to leave the site. The five value categories are: None Low Medium High Very high Applied Questions How does the Phosphorus Index work? To make an assessment using the Phosphorus Index, select a rating value for each site characteristic in the field based on available field data. Use the rating categories None, Low, Medium, High, and Very high. Multiply the site weight factor by the rating value to get the weighted value for that site characteristic. Proceed to rate and multiply each characteristic of the index. Sum the weighted values for all eight characteristics and compare the total with a site vulnerability chart (Table ). The vulnerability is a relative rating of the potential for P to move from the field site. How can the Phosphorus Index be used in planning management practices to reduce the potential for phosphorus movement.? Upon completion of the Phosphorus Index assessment, the matrix can be analyzed for each individual site characteristic. Those site characteristics that rate High or Very high should be examined closely in order to develop management strategies that can lower the rating; that is, move the rating to the left on the matrix to a Low or Medium. Such analysis of the matrix for each site characteristic will formulate a management plan for that particular site. Each site will require its own analysis based on its particular site characteristics. Phosphorus Index, version 1.0, with the site characteristics and weighting factor in the left column and the values of the categories in each row. Summation of the weighted rating value is used to determine the site vulnerability. Phosphorus loss rating (Value) Site characteristic (weight) None (0) Low (1) Medium (21 High (4) Very high (8) Soil erosion (1.5) Not applicable &lt;5 tons/acre 5–10 tons/acre 10–15 tons/acre &gt;15 tons/acre Irrigation erosion (1.5) Not applicable Tailwater recovery or QS QS &gt; 10 for erosion QS &gt; 10 for erodible QS &gt; 6 for very &lt; 6 for very erodible resistant soils soils erodible sols soils or QS 5 10 for other soils Runoff class (0.5) Negligible Very low or Low Medium High Very high Soil P test (1.0) Not applicable Low Medium High Excessive P fertilizer application rate None applied 1–30 P 2 O 5 lb/acre 31–90 P 2 O 5 lb/acre 91–150 P 2 O 5 lb/acre &gt;150 Po 5 lb/acre (0.75) P fertilizer application method None applied Placed with planter deeper Incorporated immediately Incorporated &gt;3 months Surface applied (0.5) than 2 in. before crop before crop or surface &gt;3 months before applied &lt; 3 months before crop crop Organic P source application None applied 1–30 P 2 O 5 lb/acre 31–60 P 2 O 5 lb/acre 61–90 P 2 O 5 lb/acre &gt;90 P 2 O 5 lb/acre rate (1.0) Organic P source application None Injected deeper than 2 in. Incorporated immediately Incorporated &gt; 3 months Surface applied to method (1.0) before crop before crop or surface pasture, or &gt;3 applied &lt; 3 months before months before crop crop <jats:tit

Brown marmorated stink bug, &lt;it&gt;Halyomorpha halys&lt;/it&gt; Stål, is an invasive, herbivorous insect species that was accidentally introduced to the United States from Asia. First discovered in Allentown, PA, in 1996, &lt;it&gt;H. halys&lt;/it&gt; has now been reported from at least 40 states in the United States. Additional invasions have been detected in Canada, Switzerland, France, Germany, Italy, and Lichtenstein, suggesting this invasive species could emerge as a cosmopolitan pest species. In its native range, &lt;it&gt;H. halys&lt;/it&gt; is classified as an outbreak pest; however, in North America, &lt;it&gt;H. halys&lt;/it&gt; has become a major agricultural pest across a wide range of commodities. &lt;it&gt;H. halys&lt;/it&gt; is a generalist herbivore, capable of consuming &gt;100 different species of host plants, often resulting in substantial economic damage; its feeding damage resulted in US$37 million of losses in apple in 2010, but this stink bug species also attacks other fruit, vegetable, field crop, and ornamental plant species. &lt;it&gt;H. halys&lt;/it&gt; has disrupted integrated pest management programs for multiple cropping systems. Pesticide applications, including broad-spectrum insecticides, have increased in response to &lt;it&gt;H. halys&lt;/it&gt; infestations, potentially negatively influencing populations of beneficial arthropods and increasing secondary pest outbreaks. &lt;it&gt;H. halys&lt;/it&gt; is also challenging because it affects homeowners as a nuisance pest; the bug tends to overwinter in homes and outbuildings. Although more research is required to better understand the ecology and biology of &lt;it&gt;H. halys&lt;/it&gt;, we present its life history, host plant damage, and the management options available for this invasive pest species.

Hristov, A. N., Hanigan, M., Cole, A., Todd, R., McAllister T. A., Ndegwa, P. and Rotz, A. 2011. Review: Ammonia emissions from dairy farms and beef feedlots. Can. J. Anim. Sci. 91: 1–35. Ammonia emitted from animal feeding operations is an environmental and human health hazard, contributing to eutrophication of surface waters and nitrate contamination of ground waters, soil acidity, and fine particulate matter formation. It may also contribute to global warming through nitrous oxide formation. Along with these societal concerns, ammonia emission is a net loss of manure fertilizer value to the producer. A significant portion of cattle manure nitrogen, primarily from urinary urea, is converted to ammonium and eventually lost to the atmosphere as ammonia. Determining ammonia emissions from cattle operations is complicated by the multifaceted nature of the factors regulating ammonia volatilization, such as manure management, ambient temperature, wind speed, and manure composition and pH. Approaches to quantify ammonia emissions include micrometeorological methods, mass balance accounting and enclosures. Each method has its advantages, disadvantages and appropriate application. It is also of interest to determine the ammonia emitting potential of manure (AEP) independent of environmental factors. The ratio of nitrogen to non-volatile minerals (phosphorus, potassium, ash) or nitrogen isotopes ratio in manure has been suggested as a useful indicator of AEP. Existing data on ammonia emission factors and flux rates are extremely variable. For dairy farms, emission factors from 0.82 to 250 g ammonia per cow per day have been reported, with an average of 59 g per cow per day (n=31). Ammonia flux rates for dairy farms averaged 1.03 g m −2 h −1 (n=24). Ammonia losses are significantly greater from beef feedlots, where emission factors average 119 g per animal per day (n=9) with values as high as 280 g per animal per day. Ammonia flux rate for beef feedlots averaged 0.174 g m −2 h −1 (n=12). Using nitrogen mass balance approaches, daily ammonia nitrogen losses of 25 to 50% of the nitrogen excreted in manure have been estimated for dairy cows and feedlot cattle. Practices to mitigate ammonia emissions include reducing excreted N (particularly urinary N), acidifying ammonia sources, or binding ammonium to a substrate. Reducing crude protein concentration in cattle diets and ruminal protein degradability are powerful tools for reducing N excretion, AEP, and whole-farm ammonia emissions. Reducing dietary protein can also benefit the producer by reducing feed cost. These interventions, however, have to be balanced with the risk of lost production. Manure treatment techniques that reduce volatile N species (e.g., urease inhibition, pH reduction, nitrification-denitrification) are also effective for mitigating ammonia emissions. Another option for reducing ammonia emissions is capture and treatment of released ammonia. Examples in the latter category include biofilters, permeable and impermeable covers, and manure incorporation into the soil for crop or pasture production. Process-level simulation of ammonia formation and emission provides a useful tool for estimating emissions over a wide range of production practices and evaluating the potential benefits of mitigation strategies. Reducing ammonia emissions from dairy and beef cattle operations is critical to achieving environmentally sustainable animal production that will benefit producers and society at large.

The evolutionary significance of hybridization and subsequent introgression has long been appreciated, but evaluation of the genome-wide effects of these phenomena has only recently become possible. Crop-wild study systems represent ideal opportunities to examine evolution through hybridization. For example, maize and the conspecific wild teosinte Zea mays ssp. mexicana (hereafter, mexicana) are known to hybridize in the fields of highland Mexico. Despite widespread evidence of gene flow, maize and mexicana maintain distinct morphologies and have done so in sympatry for thousands of years. Neither the genomic extent nor the evolutionary importance of introgression between these taxa is understood. In this study we assessed patterns of genome-wide introgression based on 39,029 single nucleotide polymorphisms genotyped in 189 individuals from nine sympatric maize-mexicana populations and reference allopatric populations. While portions of the maize and mexicana genomes appeared resistant to introgression (notably near known cross-incompatibility and domestication loci), we detected widespread evidence for introgression in both directions of gene flow. Through further characterization of these genomic regions and preliminary growth chamber experiments, we found evidence suggestive of the incorporation of adaptive mexicana alleles into maize during its expansion to the highlands of central Mexico. In contrast, very little evidence was found for adaptive introgression from maize to mexicana. The methods we have applied here can be replicated widely, and such analyses have the potential to greatly inform our understanding of evolution through introgressive hybridization. Crop species, due to their exceptional genomic resources and frequent histories of spread into sympatry with relatives, should be particularly influential in these studies.

Soil moisture is a fundamental data source used by the United States Department of Agriculture (USDA) International Production Assessment Division (IPAD) to monitor crop growth stage and condition and subsequently, globally forecast agricultural yields. Currently, the USDA IPAD estimates surface and root-zone soil moisture using a two-layer modified Palmer soil moisture model forced by global precipitation and temperature measurements. However, this approach suffers from well-known errors arising from uncertainty in model forcing data and highly simplified model physics. Here, we attempt to correct for these errors by designing and applying an Ensemble Kalman filter (EnKF) data assimilation system to integrate surface soil moisture retrievals from the NASA Advanced Microwave Scanning Radiometer (AMSR-E) into the USDA modified Palmer soil moisture model. An assessment of soil moisture analysis products produced from this assimilation has been completed for a five-year (2002 to 2007) period over the North American continent between 23° N-50° N and 128° W-65° W. In particular, a data denial experimental approach is utilized to isolate the added utility of integrating remotely sensed soil moisture by comparing EnKF soil moisture results obtained using (relatively) low-quality precipitation products obtained from real-time satellite imagery to baseline Palmer model runs forced with higher quality rainfall. An analysis of root-zone anomalies for each model simulation suggests that the assimilation of AMSR-E surface soil moisture retrievals can add significant value to USDA root-zone predictions derived from real-time satellite precipitation products.

To effectively meet growing food demands, the global agronomic community will require a better understanding of factors that are currently limiting crop yields and where production can be viably expanded with minimal environmental consequences. Remote sensing can inform these analyses, providing valuable spatiotemporal information about yield-limiting moisture conditions and crop response under current climate conditions. In this paper we study correlations for the period 2003–2013 between yield estimates for major crops grown in Brazil and the Evaporative Stress Index (ESI) – an indicator of agricultural drought that describes anomalies in the actual/reference evapotranspiration (ET) ratio, retrieved using remotely sensed inputs of land surface temperature (LST) and leaf area index (LAI). The strength and timing of peak ESI-yield correlations are compared with results using remotely sensed anomalies in water supply (rainfall from the Tropical Rainfall Mapping Mission; TRMM) and biomass accumulation (LAI from the Moderate Resolution Imaging Spectroradiometer; MODIS). Correlation patterns were generally similar between all indices, both spatially and temporally, with the strongest correlations found in the south and northeast where severe flash droughts have occurred over the past decade, and where yield variability was the highest. Peak correlations tended to occur during sensitive crop growth stages. At the state scale, the ESI provided higher yield correlations for most crops and regions in comparison with TRMM and LAI anomalies. Using finer scale yield estimates reported at the municipality level, ESI correlations with soybean yields peaked higher and earlier by 10 to 25 days in comparison to TRMM and LAI, respectively. In most states, TRMM peak correlations were marginally higher on average with municipality-level annual corn yield estimates, although these estimates do not distinguish between primary and late season harvests. A notable exception occurred in the northeastern state of Bahia, where the ESI better captured effects of rapid cycling of moisture conditions on corn yields during a series of flash drought events. The results demonstrate that for monitoring agricultural drought in Brazil, value is added by combining LAI with LST indicators within a physically based model of crop water use.

Global and regional scale agricultural monitoring systems aim to provide up-to-date information regarding food production to different actors and decision makers in support of global and national food security. To help reduce price volatility of the kind experienced between 2007 and 2011, a global system of agricultural monitoring systems is needed to ensure the coordinated flow of information in a timely manner for early warning purposes. A number of systems now exist that fill this role. This paper provides an overview of the eight main global and regional scale agricultural monitoring systems currently in operation and compares them based on the input data and models used, the outputs produced and other characteristics such as the role of the analyst, their interaction with other systems and the geographical scale at which they operate. Despite improvements in access to high resolution satellite imagery over the last decade and the use of numerous remote-sensing based products by the different systems, there are still fundamental gaps. Based on a questionnaire, discussions with the system experts and the literature, we present the main gaps in the data and in the methods. Finally, we propose some recommendations for addressing these gaps through ongoing improvements in remote sensing, harnessing new and innovative data streams and the continued sharing of more and more data.

In recent years there has been a dramatic increase in the demand for timely, comprehensive global agricultural intelligence. Timely information on global crop production is indispensable for combating the growing stress on the world’s crop production and for securing both short-term and long-term stable and reliable supply of food. Global agriculture monitoring systems are critical to providing this kind of intelligence and global earth observations are an essential component of an effective global agricultural monitoring system as they offer timely, objective, global information on croplands distribution, crop development and conditions as the growing season progresses. The Global Agriculture Monitoring Project (GLAM), a joint NASA, USDA, UMD and SDSU initiative, has built a global agricultural monitoring system that provides the USDA Foreign Agricultural Service (FAS) with timely, easily accessible, scientifically-validated remotely-sensed data and derived products as well as data analysis tools, for crop-condition monitoring and production assessment. This system is an integral component of the USDA’s FAS Decision Support System (DSS) for agriculture. It has significantly improved the FAS crop analysts’ ability to monitor crop conditions, and to quantitatively forecast crop yields through the provision of timely, high-quality global earth observations data in a format customized for FAS alongside a suite of data analysis tools. FAS crop analysts use these satellite data in a ‘convergence of evidence’ approach with meteorological data, field reports, crop models, attaché reports and local reports. The USDA FAS is currently the only operational provider of timely, objective crop production forecasts at the global scale. These forecasts are routinely used by the other US Federal government agencies as well as by commodity trading companies, farmers, relief agencies and foreign governments. This paper discusses the operational components and new developments of the GLAM monitoring system as well as the future role of earth observations in global agricultural monitoring.

Ingestion of vertebrate blood is essential for egg maturation and transmission of disease-causing parasites by female mosquitoes. Prior studies with the yellow fever mosquito, Aedes aegypti, indicated blood feeding stimulates egg production by triggering the release of hormones from medial neurosecretory cells in the mosquito brain. The ability of bovine insulin to stimulate a similar response further suggested this trigger is an endogenous insulin-like peptide (ILP). A. aegypti encodes eight predicted ILPs. Here, we report that synthetic ILP3 dose-dependently stimulated yolk uptake by oocytes and ecdysteroid production by the ovaries at lower concentrations than bovine insulin. ILP3 also exhibited metabolic activity by elevating carbohydrate and lipid storage. Binding studies using ovary membranes indicated that ILP3 had an IC(50) value of 5.9 nM that was poorly competed by bovine insulin. Autoradiography and immunoblotting studies suggested that ILP3 binds the mosquito insulin receptor (MIR), whereas loss-of-function experiments showed that ILP3 activity requires MIR expression. Overall, our results identify ILP3 as a critical regulator of egg production by A. aegypti.

Summary 1. Despite recent interest in linkages between above‐ and below‐ground communities and their consequences for ecosystem processes, much remains unknown about their responses to long‐term ecosystem change. We synthesize multiple lines of evidence from a long‐term ‘natural experiment’ to illustrate how ecosystem retrogression (the decline in ecosystem process rates due to long‐term absence of major disturbance) drives vegetation change, and thus above‐ground and below‐ground carbon (C) sequestration, and communities of consumer biota. 2. Our study system involves 30 islands in Swedish boreal forest that form a 5000‐year, fire‐driven retrogressive chronosequence. Here, retrogression leads to lower plant productivity and slower decomposition and a community shift from plants with traits associated with resource acquisition to those linked with resource conservation. 3. We present consistent evidence that above‐ground ecosystem C sequestration declines, while below‐ground and total C storage increases linearly for at least 5000 years following fire absence. This increase is driven primarily by changes in vegetation characteristics, impairment of decomposer organisms and absence of humus combustion. 4. Data from contrasting trophic groups show that during retrogression, biomass or abundance of plants and decomposer biota decreases, while that of above‐ground invertebrates and birds increases, due to different organisms accessing resources via distinct energy channels. Meanwhile, diversity measures of vascular plants and above‐ground (but not below‐ground) consumers respond positively to retrogression. 5. We show that taxonomic richness of plants and above‐ground consumers are positively correlated with total ecosystem C storage, suggesting that conserving old‐growth forests simultaneously maximizes biodiversity and C sequestration. However, we find little observational or experimental evidence that plant diversity is a major driver of ecosystem C storage on the islands relative to other biotic and abiotic factors. 6. Synthesis. Our study reveals that across contrasting islands differing in exposure to a key extrinsic driver (historical disturbance regime and resulting retrogression), there are coordinated responses of soil fertility, vegetation, consumer communities and ecosystem C sequestration, which all feed back to one another. It also highlights the value of well‐replicated natural experiments for tackling questions about above‐ground–below‐ground linkages over temporal and spatial scales that are otherwise unachievable.

Salicylic acid (SA), an essential regulator of plant defense, is derived from chorismate via either the phenylalanine ammonia lyase (PAL) or the isochorismate synthase (ICS) catalyzed steps. The ICS pathway is thought to be the primary contributor of defense-related SA, at least in Arabidopsis. We investigated the relative contributions of PAL and ICS to defense-related SA accumulation in soybean (Glycine max). Soybean plants silenced for five PAL isoforms or two ICS isoforms were analyzed for SA concentrations and SA-derived defense responses to the hemibiotrophic pathogens Pseudomonas syringae and Phytophthora sojae. We show that, unlike in Arabidopsis, PAL and ICS pathways are equally important for pathogen-induced SA biosynthesis in soybean. Knock-down of either pathway shuts down SA biosynthesis and abrogates pathogen resistance. Moreover, unlike in Arabidopsis, pathogen infection is associated with the suppression of ICS gene expression. Pathogen-induced biosynthesis of SA via the PAL pathway correlates inversely with phenylalanine concentrations. Although infections with either virulent or avirulent strains of the pathogens increase SA concentrations, resistance protein-mediated response to avirulent P. sojae strains may function in an SA-independent manner. These results show that PAL- and ICS-catalyzed reactions function cooperatively in soybean defense and highlight the importance of PAL in pathogen-induced SA biosynthesis.

The human pathogen Vibrio cholerae is a highly motile organism by virtue of a polar flagellum. Flagellar transcriptional regulatory factors have been demonstrated to contribute to V. cholerae virulence, but the role these factors play in the transcription hierarchy controlling flagellar synthesis has been unclear. The flagellar genes revealed by the V. cholerae genome sequence are located in three large clusters, with the exception of the motor genes, which are found in three additional locations. It had previously been demonstrated that the alternative sigma factor sigma54 and the sigma54-dependent activators FlrA and FlrC are necessary for flagellar synthesis. The V. cholerae genome sequence revealed the presence of a fliA gene, which is predicted to encode the alternative flagellar sigma factor sigma28. A V. cholerae DeltafliA mutant strain is non-motile, and synthesizes a truncated flagellum. Vibrio cholerae FliA complements both V. cholerae and Salmonella typhimurium fliA mutants for motility, consistent with its function as an alternative flagellar sigma factor. Analysis of lacZ transcriptional fusions of the V. cholerae flagellar promoters in both V. cholerae and S. typhimurium identified sigma28-, sigma54-, FlrA- and FlrC-dependent promoters, as well as promoters that were independent of all these factors. Our results support a model of V. cholerae flagellar gene transcription as a novel hierarchy composed of four classes of genes. Class I is composed solely of the gene encoding the sigma54-dependent activator FlrA, which along with the sigma54-holoenzyme form of RNA polymerase activates expression of Class II genes. These genes include structural components of the MS ring, switch and export apparatus, as well as the genes encoding both FliA and FlrC. FlrC, along with sigma54-holoenzyme, activates expression of Class III genes, which include basal body, hook and filament genes. Finally, sigma28-holoenzyme activates expression of Class IV genes, which include additional filament genes as well as motor genes. Thus, this novel V. cholerae flagellar hierarchy has incorporated elements from both the sigma54-dependent Caulobacter crescentus polar flagellar hierarchy and the sigma28-dependent S. typhimurium peritrichous flagellar hierarchy.

Mannans are hemicellulosic polysaccharides that have previously been implicated as structural constituents of cell walls and as storage reserves but which may serve other functions during plant growth and development. Several members of the Arabidopsis cellulose synthase-like A (CSLA) family have previously been shown to synthesise mannan polysaccharides in vitro when heterologously expressed. It has also been found that CSLA7 is essential for embryogenesis, suggesting a role for the CSLA7 product in development. To determine whether the CSLA proteins are responsible for glucomannan synthesis in vivo, we characterised insertion mutants in each of the nine Arabidopsis CSLA genes and several double and triple mutant combinations. csla9 mutants showed substantially reduced glucomannan, and triple csla2csla3csla9 mutants lacked detectable glucomannan in stems. Nevertheless, these mutants showed no alteration in stem development or strength. Overexpression of CSLA2, CSLA7 and CSLA9 increased the glucomannan content in stems. Increased glucomannan synthesis also caused defective embryogenesis, leading to delayed development and occasional embryo death. The embryo lethality of csla7 was complemented by overexpression of CSLA9, suggesting that the glucomannan products are similar. We conclude that CSLA2, CSLA3 and CSLA9 are responsible for the synthesis of all detectable glucomannan in Arabidopsis stems, and that CSLA7 synthesises glucomannan in embryos. These results are inconsistent with a substantial role for glucomannan in wall strength in Arabidopsis stems, but indicate that glucomannan levels affect embryogenesis. Together with earlier heterologous expression studies, the glucomannan deficiency observed in csla mutant plants demonstrates that the CSLA family encodes glucomannan synthases.

Episodes of population loss and cultural change, including the famous Classic Collapse, punctuated the long course of Maya civilization. In many cases, these downturns in the fortunes of individual sites and entire regions included significant environmental components such as droughts or anthropogenic environmental degradation. Some afflicted areas remained depopulated for long periods, whereas others recovered more quickly. We examine the dynamics of growth and decline in several areas in the Maya Lowlands in terms of both environmental and cultural resilience and with a focus on downturns that occurred in the Terminal Preclassic (second century Common Era) and Terminal Classic (9th and 10th centuries CE) periods. This examination of available data indicates that the elevated interior areas of the Yucatán Peninsula were more susceptible to system collapse and less suitable for resilient recovery than adjacent lower-lying areas.