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The impact of saltwater intrusion on coastal forests and farmland is typically understood as sea-level-driven inundation of a static terrestrial landscape, where ecosystems neither adapt to nor influence saltwater intrusion. Yet recent observations of tree mortality and reduced crop yields have inspired new process-based research into the hydrologic, geomorphic, biotic, and anthropogenic mechanisms involved. We review several negative feedbacks that help stabilize ecosystems in the early stages of salinity stress (e.g., reduced water use and resource competition in surviving trees, soil accretion, and farmland management). However, processes that reduce salinity are often accompanied by increases in hypoxia and other changes that may amplify saltwater intrusion and vegetation shifts after a threshold is exceeded (e.g., subsidence following tree root mortality). This conceptual framework helps explain observed rates of vegetation change that are less than predicted for a static landscape while recognizing the inevitability of large-scale change.

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Fertilized temperate croplands export large amounts of reactive nitrogen (N), which degrades water and air quality and contributes to climate change. Fertilizer use is poised to increase in the tropics, where widespread food insecurity persists and increased agricultural productivity will be needed, but much less is known about the potential consequences of increased tropical N fertilizer application. We conducted a meta-analysis of tropical field studies of nitrate leaching, nitrous oxide emissions, nitric oxide emissions, and ammonia volatilization totaling more than 1,000 observations. We found that the relationship between N inputs and losses differed little between temperate and tropical croplands, although total nitric oxide losses were higher in the tropics. Among the potential drivers we studied, the N input rate controlled all N losses, but soil texture and water inputs also controlled hydrological N losses. Irrigated systems had significantly higher losses of ammonia, and pasture agroecosystems had higher nitric oxide losses. Tripling of fertilizer N inputs to tropical croplands from 50 to 150 kg N ha-1  year-1 would have substantial environmental implications and would lead to increases in nitrate leaching (+30%), nitrous oxide emissions (+30%), nitric oxide (+66%) emissions, and ammonia volatilization (+74%), bringing tropical agricultural nitrate, nitrous oxide, and ammonia losses in line with temperate losses and raising nitric oxide losses above them.

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Cover crops are well recognized as a tool to reduce NO leaching from agroecosystems. However, their effectiveness varies from site to site and year to year depending on soil, cash and cover crop management, and climate. We conducted a meta-analysis using 238 observations from 28 studies (i) to assess the overall effect of cover crops on NO leaching and subsequent crop yields, and (ii) to examine how soil, cash and cover crop management, and climate impact the effect of non-leguminous cover crops on NO leaching. There is a clear indication that nonleguminous cover crops can substantially reduce NO leaching into freshwater systems, on average by 56%. Nonlegume-legume cover crop mixtures reduced NO leaching as effectively as nonlegumes, but significantly more than legumes. The lack of variance information in most published literature prevents greater insight into the degree to which cover crops can improve water quality. Among the factors investigated, we identified cover crop planting dates, shoot biomass, and precipitation relative to long-term mean precipitation as potential drivers for the observed variability in nonleguminous cover crop effectiveness in reducing NO leaching. We found evidence indicating greater reduction in NO leaching with nonleguminous cover crops on coarse-textured soils and during years of low precipitation (<90% of the long-term normal). Earlier fall planting and greater nonleguminous shoot biomass further reduced NO leaching. Overall, this meta-analysis confirms many prior studies showing that nonleguminous cover crops are an effective way to reduce NO leaching and should be integrated into cropping systems to improve water quality.

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Livestock keeping is ubiquitous in tropical Africa. Urine and dung from livestock release greenhouse gases (GHGs), such as nitrous oxide (NO) and methane (CH), to the atmosphere. However, the extent of GHG's impact is uncertain due to the lack of in situ measurements in the region. Here we measured NO and CH emissions from cow urine and dung depositions in two Kenyan pastures that received different amounts of rainfall using static chambers across wet and dry seasons. Cumulative NO emissions were greater under dung+urine and urine-only patches ( 0.0001), more than three times higher in the wet compared with the dry season ( 0.0001), and higher in the farm receiving higher rainfall overall ( 0.0001). Cumulative CH emissions differed across treatments ( = 0.012), driven primarily by soil CH uptake from the urine-only treatment. Cumulative NO emissions were positively related to N input rate in excreta. However, the relationship was linear during the dry season ( 0.99; 0.001) and exponential during the wet season ( 0.99; < 0.0001). Nitrous oxide emission factors were 0.05% (dry season) and 0.18% (wet season) of N in urine and dung+urine, which is less than 10% of the IPCC Default Tier 1 emission factor of 2%. We predict that emissions from cattle urine in Kenya are approximately 1.7 Gg NO-N yr (FAO estimates 11.9 Gg NO-N yr). Our findings suggest that current estimates may overestimate the contribution of excreta to national GHG emissions and that emission factors from urine and dung need to account for agroecosystems with distinct wet and dry seasons.

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Crop yields in sub-Saharan Africa remain stagnant at 1 ton ha-1 , and 260 million people lack access to adequate food resources. Order-of-magnitude increases in fertilizer use are seen as a critical step in attaining food security. This increase represents an unprecedented input of nitrogen (N) to African ecosystems and will likely be accompanied by increased soil emissions of nitric oxide (NO). NO is a precursor to tropospheric ozone, an air pollutant and greenhouse gas. Emissions of NO from soils occur primarily during denitrification and nitrification, and N input rates are a key determinant of emission rates. We established experimental maize plots in western Kenya to allow us to quantify the response function relating NO flux to N input rate during the main 2011 and 2012 growing seasons. NO emissions followed a sigmoid response to fertilizer inputs and have emission factors under 1% for the roughly two-month measurement period in each year, although linear and step relationships could not be excluded in 2011. At fertilization rates above 100 kg N ha-1 , NO emissions increased without a concomitant increase in yields. We used the geos-chem chemical transport model to evaluate local impacts of increased NO emissions on tropospheric ozone concentrations. Mean 4-hour afternoon tropospheric ozone concentrations in Western Kenya increased by up to roughly 2.63 ppbv under fertilization rates of 150 kg N ha-1 or higher. Using AOT40, a metric for assessing crop damage from ozone, we find that the increased ozone concentrations result in an increase in AOT40 exposure of approximately 110 ppbh for inputs of 150 kg N ha-1 during the March-April-May crop growing season, compared with unfertilized simulations, with negligible impacts on crop productivity. Our results suggest that it may be possible to manage Kenyan agricultural systems for high yields while avoiding substantial impacts on air quality.

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Fertilizer applications are poised to increase across sub-Saharan Africa (SSA), but the fate of added nitrogen (N) is largely unknown. We measured vertical distributions and temporal variations of soil inorganic N following fertilizer application in two maize (Zea mays L.)-growing regions of contrasting soil type. Fertilizer trials were established on a clayey soil in Yala, Kenya, and on a sandy soil in Tumbi, Tanzania, with application rates of 0-200 kg N/ha/yr. Soil profiles were collected (0-400 cm) annually (for three years in Yala and two years in Tumbi) to examine changes in inorganic N pools. Topsoils (0-15 cm) were collected every 3-6 weeks to determine how precipitation and fertilizer management influenced plant-available soil N. Fertilizer management altered soil inorganic N, and there were large differences between sites that were consistent with differences in soil texture. Initial soil N pools were larger in Yala than Tumbi (240 vs. 79 kg/ha). Inorganic N pools did not change in Yala (277 kg/ha), but increased fourfold after cultivation and fertilization in Tumbi (371 kg/ha). Intra-annual variability in NO-3 -N concentrations (3-33 µg/g) in Tumbi topsoils strongly suggested that the sandier soils were prone to high leaching losses. Information on soil inorganic N pools and movement through soil profiles can h vulnerability of SSA croplands to N losses and determine best fertilizer management practices as N application rates increase. A better understanding of the vertical and temporal patterns of soil N pools improves our ability to predict the potential environmental effects of a dramatic increase in fertilizer application rates that will accompany the intensification of African croplands.

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Tropical smallholder agriculture is undergoing rapid transformation in nutrient cycling pathways as international development efforts strongly promote greater use of mineral fertilizers to increase crop yields. These changes in nutrient availability may alter the composition of microbial communities with consequences for rates of biogeochemical processes that control nutrient losses to the environment. Ecological theory suggests that altered microbial diversity will strongly influence processes performed by relatively few microbial taxa, such as denitrification and hence nitrogen losses as nitrous oxide, a powerful greenhouse gas. Whether this theory helps predict nutrient losses from agriculture depends on the relative effects of microbial community change and increased nutrient availability on ecosystem processes. We find that mineral and organic nutrient addition to smallholder farms in Kenya alters the taxonomic and functional diversity of soil microbes. However, we find that the direct effects of farm management on both denitrification and carbon mineralization are greater than indirect effects through changes in the taxonomic and functional diversity of microbial communities. Changes in functional diversity are strongly coupled to changes in specific functional genes involved in denitrification, suggesting that it is the expression, rather than abundance, of key functional genes that can serve as an indicator of ecosystem process rates. Our results thus suggest that widely used broad summary statistics of microbial diversity based on DNA may be inappropriate for linking microbial communities to ecosystem processes in certain applied settings. Our results also raise doubts about the relative control of microbial composition compared to direct effects of management on nutrient losses in applied settings such as tropical agriculture.

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In a coffee agroforest, the crop is cultivated under the shade of fruit-bearing and nitrogen (N)-fixing trees. These trees are periodically pruned to promote flowering and fruiting as well as to make nutrients stored in tree biomass available to plants. We investigated the effect of canopy composition and substrate quality on decomposition rates and patterns of nutrient release from pruning residues in a coffee agroforest located in Costa Rica's Central Valley. Initial phosphorus (P) release was enhanced under a canopy composed solely of N-fixing, Erythrina poeppigiana compared to a mixed canopy of Erythrina and Musa acuminata (banana). Both initial and final N release were similar under the two canopy types. However, after five months of decomposition, a higher proportion of initial N had been released under the single canopy. Although patterns of decomposition and nutrient release were not predicted by initial substrate quality, mass loss in leaf mixtures rates were well predicted by mean mass loss of their component species. This study identifies specific pruning regimes that may regulate N and P release during crucial growth periods, and it suggests that strategic pruning can enhance nutrient availability. For example, during the onset of rapid fruit growth, a two-species mixture may release more P than a three-species mixture. However, by the time of the harvest, the two- and three-species mixtures have released roughly the same amount of N and P. These nutrients do not always follow the same pattern, as N release can be maximized in single-species substrates, while P release is often facilitated in species mixtures. Our study indicates the importance of management practices in mediating patterns of nutrient release. Future research should investigate how canopy composition and farm management can also mediate on-farm nutrient losses.

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