J.N. “Ding” Darling National Wildlife Refuge (DDNWR) is located on Sanibel Island along the southwestern coast of Florida, USA. There, eutrophication attributed to agricultural discharge along the Caloosahatchee River has affected the area’s aquatic habitat. In anticipation of additional nutrient loading, we experimentally fertilized mangrove forests with nitrogen (+N; NH4) and phosphorus (+P; P2O5) for 3 years, and monitored soil and pneumatophore CO2 fluxes and tree sap flow from two mangrove species. Furthermore, we modeled individual tree and stand water use, from which we developed carbon (C) budgets for +N and + P vs. control simulations based on a novel application of water use efficiency conversion. Many of the measured response variables provided hints of subtle changes in response to +P rather than +N, which were enhanced when scaled. From this, we found that additional P loading is expected to reduce both gross and net primary productivity as well as CO2 uptake via net ecosystem exchange of C, likely pressing the system beyond metabolic capacity and leading to a 48–62% decrease in projected lateral C export. Greater eutrophication will likely compound vulnerabilities to sea-level rise submergence, especially where P concentrations are high and already reducing soil surface elevations.

Nitrogen (N) is a major plant nutrient, and its supply is very often limiting growth. The main forms of inorganic N in soil supplying plants are ammonium and nitrate ions. Although the soil availability of N can vary greatly, the cytoplasmic nutrient ion activities in a typical plant cell are maintained at set points that are independent of changes in supply. By contrast, the storage of N as protein and vacuolar nitrate depends on the external supply. Measurements of cellular homeostasis of ammonium and nitrate are limited by methodology. The upper limits for cytoplasmic set points are likely to depend on toxicity, and for ammonium this is well known but less clear for nitrate. An intracellular set point for N must be maintained by membrane transport systems and assimilation processes. Crop N use efficiency has uptake and assimilation components, and understanding homeostasis is fundamentally important for improving this important trait.

In Australia, Sorghum bicolor is frequently produced under dryland cropping systems, making these crops particularly susceptible to stress. Sorghum also contains the cyanogenic glucoside dhurrin, a toxic metabolite which is a major concern where sorghum is grown as livestock forage. The wild Australian relatives of S. bicolor, including species within the Chaetosorghum and Stiposorghum subgenera, contain minimal concentrations of dhurrin compared to domesticated sorghum. As the core biosynthetic enzymes are conserved, they provide a valuable comparative system to explore differences in the regulation of dhurrin biosynthesis. This study examined the transcriptional and metabolic response of Sorghum macrospermum to nitrogen resupply following nitrogen-limiting growth. Over a 48-hour time-course, changes in nitrate and dhurrin accumulation, and expression of key genes involved in nitrogen metabolism, dhurrin biosynthesis, and candidate transcriptional regulators were measured. In S. macrospermum, dhurrin accumulation and upregulation of the biosynthetic gene SmCYP79A1 occurred in root tissues from 12 to 48 hours post-resupply. Very low dhurrin levels and negligible SmCYP79A1 expression were observed in leaves and stems. Notably, nitrate levels remained stable over time, suggesting distinct nitrogen management strategies. Candidate regulators previously implicated in dhurrin biosynthesis in S. bicolor were not detected in the roots of S. macrospermum, indicating that different regulatory mechanisms drive the root-specific response. These findings highlight the evolutionary divergence in nitrogen and dhurrin regulation between domesticated and wild sorghum species. They further highlight S. macrospermum as a potential genetic resource for developing low-cyanide and nitrogen-use efficient sorghum with improved resilience to suit dryland cropping systems.

Tropical urban estuaries are understudied, where ecosystem health is often considered through a temperate lens. Here, we use stable isotopes and other biogeochemical parameters to begin to address the hypothesis that the biogeochemical drivers of water column chemistry in tropical urban estuaries are qualitatively different from those in temperate systems. We measured salinity, dissolved oxygen, temperature, turbidity, dissolved nutrients, enterococcus concentrations, and suspended particulate stable isotope and nitrogen (N) and carbon concentrations every two weeks for three years in the San Juan Bay Estuary, Puerto Rico. Enterococcus concentrations exceeded acceptable limits (35 CFU 100 ml-1) in all but three water samples measured in a densely populated channel within the estuary that receives urban runoff and untreated sewage (n = 207). The δ15N values were lowest in this channel, highest in the portion of the estuary with open exchange with the sea, and negatively correlated with dissolved inorganic nitrogen concentrations. This observation, is contrary to current paradigms that were developed in temperate estuaries. The source of the low δ15N values is unknown, but consistent with observations in the sediment and consistent with high rates of N fixation. In addition to the need for a basic understanding of the biogeochemical and ecological processes involved, these data serve as a baseline to compare the effects of restoration efforts and climate change.

The inclusion of legumes in crop rotations can provide numerous benefits to crop productivity and environmental sustainability. However, these benefits have primarily been documented in systems that involve regular fertilisation, limiting our understanding of legume effects under low-input or long-term unfertilised conditions. Though soybean (Glycine max L.) is one of the globally most important cultivated legumes, data on its effect on subsequent common wheat (Triticum aestivum L.) crop in low-input European systems are scarce. This study builds on long-term historically consistent trails of two rotation systems: maize-winter wheat (M-W) and maize-soybean-winter wheat (M-S-W) under rainfed conditions on a Chernozem in Serbia, maintained without fertilisation for over 70 years. The aim of our work was to evaluate the effect of soybean as pre-crop on wheat yield and yield components and accumulation of Fe, Zn, Cu and Mn in grain. Over five growing seasons, the soybean pre-crop effect resulted in a grain yield increase ranging from 43% to 301%. Results showed that threefold higher soil mineral N promoted productive tillering, spike development and grain setting in M-S-W. Two-year data on micronutrient concentrations in grain revealed significantly higher levels of Zn and Cu in M-S-W, as well as grain protein content. However, the yield dilution effect in the M-S-W rotation led to reduced levels for both Fe and Mn in one growing season. This long-term field experiment underscores the agronomic and environmental significance of soybean-based rotations, enhancing soil N fertility and carbon sequestration and offering a sustainable solution for winter wheat production.

Reducing crude protein in amino acid-adequate diets for broiler chickens is effective in reducing nitrogenous emissions and competition for resources between the food and feed sectors. This review provides a comprehensive analysis of the literature on the relevance of nonessential amino acids in low protein diets for broiler chickens. Glycine and serine, owing to their interconvertibility summarised as glycine equivalents (Glyequi), limit growth when dietary crude protein is reduced below 19% in up to 3-week-old birds. Considering essential amino acids and the variable Glyequi requirements enables the reduction of dietary crude protein to ∼16% without compromising growth. Variation in Glyequi requirements likely occurs predominantly from the varying amounts of uric acid formed. Other influences seem to exert lower impacts on dietary Glyequi requirements. Asparagine or glutamine is probably the growth-limiting amino acid when crude protein is reduced below 16%. Alternatively, nonspecific amino-nitrogen may be lacking in such diets. The current potential to reduce dietary crude protein when using free essential and nonessential amino acids enables to increase the efficiency of nitrogen utilisation to a value above 80%. This coincides with reduced uric acid synthesis and energy expenditure for nitrogen excretion. The lower nitrogen excretion via the urine results in a lower energy expenditure. Hence, dietary energy may prospectively be reduced once the energy-sparing effect is quantified, thereby further reducing the competition for resources between food and feed.

Scientific progress relies on reproducibility, replicability, and robustness of research outcomes. After briefly discussing these terms and their significance for reliable scientific discovery, we argue for the importance of investigating robustness of outcomes to experimental protocol variations. We highlight challenges in achieving robust, replicable results in multi-step plant science experiments, using split-root assays in Arabidopsis thaliana as a case study. These experiments are important for unraveling the contributions of local, systemic and long-distance signalling in plant responses and play a central role in nutrient foraging research. The complexity of these experiments allows for extensive variation in protocols. We investigate what variations do or do not result in similar outcomes and provide concrete recommendations for enhancing the replicability and robustness of these and other complex experiments by extending the level of detail in research protocols.

Protein fermentation in the human gut is often associated with adverse health effects. Hence, understanding the fermentation characteristics of dietary undigested proteins is important for a comprehensive nutritional value of foods. This study investigated the protein fermentation kinetics of diet-derived proteins from thirty-one different foods using an in vitro model and human faecal inoculum. The undigested diet-derived protein substrate originated from porcine ileal digesta obtained from assessment of the digestible indispensable amino acid score (DIAAS) of the foods. Significant variations in fermentation kinetic parameters, particularly in maximum gas production rate (Rmax) and time to reach cumulative gas production (GP) from the substrate (TGPs), were observed. The Rmax ranged from 15·5 (se 0·7) ml/h for wheat bran-derived to 24·5 (se 0·9) ml/h for oatmeal-derived proteins. Egg-derived proteins had the shortest TGPs (14·7 (se 0·7) h), while mushroom-derived proteins had the longest (27·6 (se 7·1) h). When foods were categorised into five groups (‘animal protein’, ‘grains’, ‘legumes’, ‘fungi, algae and microorganisms’ and ‘others’), no significant differences were found in fermentation kinetics parameters. Samples were additionally incubated with porcine inoculum to assess potential donor-species effects. Human inoculum showed significantly lower Rmax, cumulative GP and microbiota turnover than porcine inoculum, indicating reduced fermentative activity. Linear regression analysis revealed correlations between human and porcine-derived inoculum only for Rmax (R2 = 0·78, P < 0·01) and TGPs (R² = 0·17, P < 0·05). These findings underscore the importance of using human inoculum in in vitro studies to better predict health implications of foods with DIAAS values.

Rapid advances in species distribution modelling have been facilitated by open availability of ‘big data’ and powerful statistical methods. A key consideration remains the time window over which field recorded occurrence data are sampled to develop a baseline species distribution. Too narrow, and distributions are incomplete and affected by sampling bias, too broad and distributions may fail to meet an assumption of equilibrium, having been affected by dynamic change across a range of different predictors. Lichens are a case in point; being diverse, functionally important and the subject of bioclimatic modelling for conservation assessment, they are nevertheless a specialist taxonomic group that is comparatively less well recorded compared to birds, mammals or vascular plants, for example. In this study, we examined the distribution of the ‘hair-lichen’ Bryoria fuscescens, based on UK record data. We partitioned records into sub-decadal periods (1970s, 1990s, 2010s), and accounting for recording effort, we compared these distributions to three predictors: an historical reconstruction of two different pollutants (sulphur dioxide and nitrogen deposition), and the climate (minimum mean temperature). We asked whether the strength of evidence for the effect of environmental predictors on Bryoria fuscescens distribution varied among the different decades, while also considering a potential for lag-effects. We show that a Bryoria fuscescens distribution that appears static, is dynamic when referenced against patterns of field recording effort. Climate was consistently important in explaining Bryoria fuscescens distribution, which was also affected by the changing pattern of pollution over time. This included a lag-effect of peak sulphur dioxide in the 1970s, and accrued effects of nitrogen deposition that strengthen over time. Overall, we conclude that Bryoria fuscescens has undergone a long-term decline in extent over the last six decades, caused by complex multivariate effects of air pollution, probably combined with climate warming. The ability to resolve these trends for assessment against future conservation targets depends critically on maintaining field identification skills and a sufficiently robust recording effort.

In order to recognize the best nutrient supply options for profitable and sustainable production systems, observations were recorded from 2001 to 2020 (20 years) in a long-term fertilizer experiment initiated in 1995–96 with soybean–wheat cropping systems (SWCSs) under irrigated conditions. The experiment comprised of seven treatments including control, organic, inorganic and their combinations. A combined use of 10 Mg farmyard manure (FYM)/ha (M) along with 120 kg N/ha provided statistically (P < 0.05) similar yield and economic benefits to the M + NPK and also provided a positive yield trend (30.0 and 16.2 kg/ha/year) and net return (14.7 and 5.81 US$/ha/year) over the year in both wheat and soybean, respectively. The combined use of organic and chemical fertilizers, provided 32–41% higher production efficiency than their individual use. In contrast, long-term chemical fertilization provided a negative yield trend in both the crops with the highest reduction in sole N-fertilized plots ranged from −39 to −42 kg/ha/year. Water-use efficiency ranged from 3.20 to 12.3 kg/ha/mm in soybean–wheat rotation and increased almost 1.74–3.15 times in wheat and 1.30–1.80 times in soybean due to fertilizer application. A similar trend was observed for water-expense efficiency and remain closely associated with fertilization practice. Long-term chemical fertilizers declined the yield potential of the studied crops while their conjoint application with FYM in the winter season considered as an input efficient approach to sustain the overall productivity and profitability of SWCSs.

Samples of the bones of 47 individuals from 46 Czech and Moravian ossuaries were dated by the 14C method and analyzed for the collagen isotopic composition of carbon (δ13C) and nitrogen (δ15N). Most of the data for the ages of the remains corresponded to the cooler and damper periods described over the past 1000 years. Of the studied samples, the greatest number of remains corresponded to the Spörer (1400–1570), Dalton (1790–1830) and Wolf minima (1280–1350). One sample studied falls within the Maunder minimum (1645–1715). It can be assumed that these minima are connected with a reduced production of food and fodder, that may have initiated famines, epidemics and armed conflicts. Individual climatic minima showed positive correlations between δ13C and δ15N values, indicating that the individuals studied consumed complementary plant or animal diets to different degrees. The elevated δ15N values in our studied samples compared to the skeletal compositions of the population of the La Tène period (380 – 150 BC) and Germanic inhabitants in the territory of Bohemia (5th–6th centuries AD) and Great Moravia (9th–early 10th centuries AD) might reflect the effect of greater consumption of animal proteins or the proteins of omnivorous animals and fish, which compensated for the lack of plant foodstuffs during the colder periods.

The isotopic composition of carbon and nitrogen of the bone collagen for the Spörer and Dalton minima differs from the Wolf minimum. The younger minima show higher δ15N values for a given δ13C value.

The use of silvopastoral systems with tree legumes is a viable alternative to recover and develop pastures, as they add N to the system influencing pasture growth. This study hypothesized that the herbage and litter of signalgrass (Urochloa decumbens Stapf) is affected by legume trees in the pasture. Treatments were composed of (1) signalgrass + Mimosa caesalpiniifolia Benth.; (2) signalgrass + Gliricidia sepium Jacq.; and (3) signalgrass monoculture. The 3-year experiment followed a randomized complete block design with three replications. Tree legumes were planted in double rows (15 × 1 × 0.5 m), in 1 ha paddocks. Litter samples were taken in five distance points (0, 1.8, 3.7, 5.6 and 7.5 m) perpendicular to tree legume rows. Signalgrass was taller at longer distances from the trees (P < 0.05). Signalgrass height differed between treatments, with taller signalgrass found in pastures mixed with G. sepium (15.6 cm) compared to M. caesalpiniifolia (9 cm) (P < 0.05). Herbage N content decreased with increasing distance from tree rows (P < 0.05). Litter N content followed a similar pattern, ranging from 23 g/kg under the trees to 12 g/kg at 7.5 m away from tree rows. Signalgrass did not grow under the tree crown (0–1.8 m), especially when intercropped with M. caesalpiniifolia. The findings of this study suggest that the type of legume trees used in the silvopastoral system has the potential to modify the pattern of grass growth and content of N in pasture litter.

Reactions of smectite with phenols were investigated to understand the role of clay minerals in abating transport of these organic pollutants to ground water. Sorption of o-methylphenol, o-chlorophenol, and m-methylphenol by the clay with different exchange cations was accomplished by passing phenol vapors in a slow stream of air or nitrogen through the samples. The resulting products, extracted with methanol and analyzed by using mass spectrometry, included monomers, dimers, trimers, and tetramers of the parent phenol and of the corresponding quinones, the oxidation product of the phenols. In extracts from the Fe-clay-phenol complexes formed in air, traces of the phenolic pentamers were also detected. Both sorption and polymerization were much higher in air than in nitrogen. The greatly reduced polymerization in nitrogen suggests that anaerobic environment of the landfill sites may facilitate phenol transport to ground water. The degree of polymerization and its magnitude was in the order Fe- > Al- > Ca- > Na-clay.

Naturally occurring ammonium illites have been discovered in black shales surrounding a stratiform base metal deposit in the DeLong Mountains, northern Alaska. Infrared spectra of the samples exhibit pronounced absorption at 1430 cm−1, the resonant-banding frequency for NH4+ coordinated in the illite interlayer. X-ray powder diffraction characteristics of the ammonium illites include an expanded d(001) spacing, with values as large as 10.16 Å, and ratios for I001/I003 and I002/I005 of about 2. Infrared analyses of physical mixtures of NH4Cl with a standard illite, and comparisons with synthetic ammonium micas indicate significant substitution (>50%) of NH4+ for K+ in the illite interlayer position. Nitrogen determinations on two ammonium illites after removal of carbonaceous matter gave values of 1.48 wt. % NH4+ and 1.44 wt. % NH4+. A survey of more than 150 different shale horizons indicates that the NH4+ content of the illites increases in proximity to the stratiform base metal mineralization.

Soil fertility and disturbance can potentially modify weed dynamics in a corn–soybean rotation. Knowing how added mineral fertilizers and tillage influence weed populations in the long term can provide insight into weed community shifts, which may affect future weed management requirements. The first objective of this study was to evaluate the effect of 24 to 25 years of nitrogen and phosphorus fertilization treatments and tillage (moldboard vs. no-till) on weeds (density, biomass, and composition) before and after herbicide applications in 2016/corn and 2017/soybean. The second objective was to evaluate the effect of the same treatments 6 yr after no postemergence weed management in 2022/corn. Since the last evaluation performed in 2004, weed density, richness, and diversity increased, and more annual grasses were observed under both tillage regimes. No fertilization effect was observed on any weed variables, including composition, except for increased biomass when left to grow all season after crop planting. In managed plots, the density and biomass of annuals and perennials were generally higher in no-till, and discrepancies were highest for annual grass densities before herbicide application. Weed species richness and diversity based on counts were equivalent between tillage regimes, but total biomass was distributed between more species in no-till. Higher weed densities and concurrent weed biomass, observed in no-till, reduced crop yields in 2016/soybean only. The combination of low crop diversity and low use of residual herbicides during the trial potentially led to the observed species shifts and increased weed density.

A siliceous sinter collected from Octopus Spring in Yellowstone National Park, USA contains an occluded volcanic rock fragment that has undergone alteration. The sinter piece beyond the fragment is mostly dominated by opal-A with trace amounts of bacterial cells, calcite and detrital quartz. Within the altered rock region, the mineral assemblage is dominated by dioctahedral smectite and quartz with trace amounts of pseudobrookite, ilmenite, rutile and hematite. Onset of opal-CT formation was only found in the outer spicular region of the sinter, which is unexpected given that this outer part represents newest growth. A reaction mechanism is proposed whereby the alteration of feldspar to smectitic clay locally produces excess silica, and alkali metal, and raises pH. As the clay mineral forms, it sequesters ions from pore fluids thereby inhibiting the opal-A phase change to more ordered opal-CT. Ions such as Mg are known to promote the opal-A to opal-CT reaction. Smectite formation therefore may assist microbial-texture preservation processes as excess silica produced increases the rate at which primary opal-A is formed. The altered zone also retains the greatest amount of fixed C and fixed N (operationally defined as C and N retained upon combustion at 450°C). The fixed N probably represents ammonium trapped in the exchangeable interlayer site of the smectite. This fixed N may serve as a potential biological signature of microbial activity in ancient rocks formed in similar environments.

Crabgrass (Digitaria spp.) is an annual summer grass capable of self-reseeding and can provide forage with high nutritive value. However, knowledge is still limited about crabgrass management. Our objective was to compare the forage accumulation (FA) and nutritive value of two crabgrass varieties (Mojo and Quick-N-Big) for 2 years under combinations of nitrogen rates and harvesting management. The experimental design was in randomized complete blocks with five treatments and three replications for each crabgrass variety, totalling 15 experimental units for Mojo and 15 for Quick-N-Big, in adjacent fields. Treatments were combinations of nitrogen rates (0, 112, and 224 kg N/ha) and harvest management (harvesting once or twice during the growing season). Nitrogen fertilization increased FA in Mojo and Quick-N-Big. The combination of two harvests and 224 kg N/ha (H2N224) resulted in a total forage accumulation (TFA) of 7840 kg DM/ha/yr for Mojo in 2020 and 8550 kg DM/ha/yr for Quick-N-Big in 2021. The H2N224 management also resulted in the highest crude protein (CP) accumulation. Nitrogen fertilization accelerates plant maturity, which can increase neutral detergent fibre (NDF). In this case, harvesting twice stimulates new tissue production, limits NDF and increases CP and total digestible nutrients (TDN). Therefore, increasing harvesting frequency (twice during the growing season) as N is input increases TFA, CP and TDN, and also enhances N recovery, which may contribute to reducing animal supplementation costs and improve the economic return of forage-based livestock systems.

The growing need for agricultural products and the challenges posed by environmental and economic factors have created a demand for enhanced agricultural systems management. Machine learning has increasingly been leveraged to tackle agricultural optimization problems, and in particular, reinforcement learning (RL), a subfield of machine learning, seems a promising tool for data-driven discovery of future farm management policies. In this work, we present the development of CropGym, a Gymnasium environment, where a reinforcement learning agent can learn crop management policies using a variety of process-based crop growth models. As a use case, we report on the discovery of strategies for nitrogen application in winter wheat. An RL agent is trained to decide weekly on applying a discrete amount of nitrogen fertilizer, with the aim of achieving a balance between maximizing yield and minimizing environmental impact. Results show that close to optimal strategies are learned, competitive with standard practices set by domain experts. In addition, we evaluate, as an out-of-distribution test, whether the obtained policies are resilient against a change in climate conditions. We find that, when rainfall is sufficient, the RL agent remains close to the optimal policy. With CropGym, we aim to facilitate collaboration between the RL and agronomy communities to address the challenges of future agricultural decision-making.