In the search for renewable fuel alternatives, biofuels have gained strong political momentum. In the last decade, extensive mandates, policies, and subsidies have been adopted to foster the development of a biofuels industry in the United States. The Biofuels Initiative in the Mississippi Delta resulted in a 47-percent decrease in cotton acreage with a concurrent 288-percent increase in corn acreage in 2007. Because corn uses 80 percent more water for irrigation than cotton, and more nitrogen fertilizer is recommended for corn cultivation than for cotton, this widespread shift in crop type has implications for water quantity and water quality in the Delta. Increased water use for corn is accelerating water-level declines in the Mississippi River Valley alluvial aquifer at a time when conservation is being encouraged because of concerns about sustainability of the groundwater resource. Results from a mathematical model calibrated to existing conditions in the Delta indicate that increased fertilizer application on corn also likely will increase the extent of nitrate-nitrogen movement into the alluvial aquifer. Preliminary estimates based on surface-water modeling results indicate that higher application rates of nitrogen increase the nitrogen exported from the Yazoo River Basin to the Mississippi River by about 7 percent. Thus, the shift from cotton to corn may further contribute to hypoxic (low dissolved oxygen) conditions in the Gulf of Mexico.

Agriculture is the most dominant land use globally and is projected to increase in the future to support a growing human population but also threatens ecosystem structure and services. Bacteria mediate numerous biogeochemical pathways within ecosystems. Therefore, identifying linkages between stressors associated with agricultural land use and responses of bacterial diversity is an important step in understanding and improving resource management. Here, we use the Mississippi Alluvial Plain (MAP) ecoregion, a highly modified agroecosystem, as a case study to better understand agriculturally associated drivers of stream bacterial diversity and assembly mechanisms. In the MAP, we found that planktonic bacterial communities were strongly influenced by salinity. Tolerant taxa increased with increasing ion concentrations, likely driving homogenous selection which accounted for ~90% of assembly processes. Sediment bacterial phylogenetic diversity increased with increasing agricultural land use and was influenced by sediment particle size, with assembly mechanisms shifting from homogenous to variable selection as differences in median particle size increased. Within individual streams, sediment heterogeneity was correlated with bacterial diversity and a subsidy‐stress relationship along the particle size gradient was observed. Planktonic and sediment communities within the same stream also diverged as sediment particle size decreased. Nutrients including carbon, nitrogen, and phosphorus, which tend to be elevated in agroecosystems, were also associated with detectable shifts in bacterial community structure. Collectively, our results establish that two understudied variables, salinity and sediment texture, are the primary drivers of bacterial diversity within the studied agroecosystem, whereas nutrients are secondary drivers. Although numerous macrobiological communities respond negatively, we observed increasing bacterial diversity in response to agricultural stressors including salinization and sedimentation. Elevated taxonomic and phylogenetic bacterial diversity likely increases the probability of detecting community responses to stressors. Thus, bacteria community responses may be more reliable for establishing water quality goals within highly modified agroecosystems that have experienced shifting baselines.

Subsidy–stress gradients offer a useful framework for understanding ecological responses to perturbation and may help inform ecological metrics in highly modified systems. Historic, region‐wide shifts from bottomland hardwood forest to row crop agriculture can cause positively skewed impact gradients in alluvial plain ecoregions, resulting in tolerant organisms that typically exhibit a subsidy response (increased abundance in response to environmental stressors) shifting to a stress response (declining abundance at higher concentrations). As a result, observed biological tolerance in modified ecosystems may differ from less modified regions, creating significant challenges for detecting biological responses to restoration efforts. Using the agriculturally dominated Mississippi Alluvial Plain (MAP) ecoregion in Mississippi, USA, as a case study, we tested the hypothesis that macroinvertebrate taxa that typically display a subsidy response to nutrient enrichment in less modified ecoregions (i.e., nutrient‐tolerance) shift to a stress response to increasing nutrients in highly modified watersheds with elevated baseline nutrient conditions (i.e., nutrient intolerance). The abundance and diversity of MAP‐specific intolerant taxa identified with threshold indicator taxa analysis were either unresponsive or exhibited a subsidy response to increasing nutrients in less modified ecoregions in Mississippi with less land alteration and lower nutrient concentrations, but declined at higher concentrations, providing evidence for a stress response to elevated nutrients in the MAP. Additionally, MAP‐specific tolerant and intolerant taxa richness responded to increased nutrients predictably and consistently across space and time within the MAP. However, in MAP streams, elevated specific conductance was predicted to dampen the response of tolerant and intolerant taxa richness to increasing nutrient concentrations, highlighting the importance of considering multistressor interactions when interpreting biological data. Lastly, we demonstrate the efficacy of this approach with sediment bacterial communities characterized with amplicon sequencing, which lack sufficient life history characteristics necessary for the development of multimetric indices. Both macroinvertebrate and bacterial communities responded similarly to increasing nutrient concentrations, suggesting DNA‐based approaches may provide an efficient biological assessment tool for monitoring water quality improvements in highly modified watersheds.

In large, alluvial floodplains dominated by agriculture, small streams have the potential to experience nutrient enrichment affecting algal assemblage structure and metabolism. Nutrient enrichment is largely driven by application of nutrients and altered hydrologic regimes. To inform stressor–response‐based nutrient reduction goals for agricultural alluvial plain streams, diatom assemblages were sampled from 25 streams located within the Mississippi Alluvial Plain (MAP) with various land management practices and associated P and N inputs. From August through September 2015, epidendric diatom assemblage samples were collected from instream woody debris. Field nutrient gradients were skewed toward higher concentrations, and ranges of previously reported diatom assemblage response thresholds indicative of oligotrophic conditions were not well represented. Ordination analysis identified a gradient in species composition associated with increasing P and decreasing dissolved oxygen. A significant shift in diatom assemblage structure occurred when total P concentrations in the MAP streams exceeded 0.12 mg L−¹. Phosphorus‐enriched systems were represented by a distinct set of indicator species, lower abundances of ubiquitous species, greater abundances of highly tolerant species, and greater abundances of high‐P indicator species. No relationships were observed among diatom assemblage measures or traits with increasing N. Current results do not address potential criteria for identifying high‐quality, oligotrophic streams. However, measures of diatom assemblage structure have potential for helping set benchmarks to reduce nutrient impacts and monitor effects of agricultural best management practices on MAP streams.Core Ideas: Identifying stream nutrient indicators is difficult in agricultural landscapes. Diatoms found in Mississippi Alluvial Plain streams are sensitive to changes in P concentrations. Diatom assemblages shifted when stream total P concentrations exceeded ∼0.12 mg L⁻¹. Diatom measures can help set nutrient reduction goals for agricultural streams. Stream diatom indicators may improve monitoring success of nutrient best management practices.

To assess the status and trends of conditions of surface waters throughout Mississippi, the U.S. Geological Survey, in cooperation with the Mississippi Department of Environmental Quality (MDEQ), summarized concentrations and estimated loads, yields, trends, and spatial and temporal patterns of total nitrogen (TN) and total phosphorus (TP) at 20 stream sites in MDEQ’s ambient water-quality monitoring network and 2 stream sites in the U.S. Geological Survey’s National Water-Quality Assessment Project’s monitoring network.Comparison of streamflow at the time of water-quality sample collection to flow-duration curves for each site showed that samples were relatively evenly spread over a wide range of flows, indicating that load estimations were representative of a wide range of flows. Relation of streamflow to concentrations of TN and TP varied among sites and land use. Sites with high agriculture land use in the drainage basin tended to have a positive correlation between streamflow and concentration, suggesting influence of event-driven nonpoint-source runoff. Sites near urban (developed) areas tended to have a negative correlation between streamflow and concentration, suggesting chronic point-source influences during low-flow conditions. Sites with high forest land use and lower agriculture and urban (developed) land use showed little to no association between streamflow and concentration.Seasonal distributions of concentrations of TN and TP also corresponded closely with variations in land use. Sites near urban (developed) land had the highest concentrations in late summer and fall, sites with a high percentage of agricultural land had the highest concentrations in the spring, and sites that were primarily forested or with little developed land did not exhibit substantial changes in concentration across seasons.Eight sites had statistical likelihoods for upward trends of TN loads, and seven sites had statistical likelihoods for downward trends. Trends in TN loads at six sites were considered “about as likely as not,” meaning that a site has an equal chance of having an upward or downward trend. Trend results of mean annual flow-normalized loads of TP for the period of analysis (2008–18) showed that 16 sites had upward trends, 3 sites had downward trends, and 2 sites were considered “about as likely as not.”Results from our study were compared to results from existing regional models to assess accuracy of predictions at a local scale. Comparisons of yields predicted from 2012 regional-scale SPAtially Referenced Regressions on Watershed attributes (SPARROW) to results from this study showed the 2012 SPARROW-predicted estimates varied in consistency with results from this study. The 2012 SPARROW-prediction model underestimated TN yields, more often and by a slightly larger degree, more than it overestimated TN yields. The 2012 SPARROW-predicted model tended to underestimate yields at study sites with higher yields. All four sites in the predominantly agricultural area of northwest Mississippi, locally known as the Mississippi Delta, were underestimated by 2012 SPARROW. For TP, yield comparisons at sites with lower yields were consistent, yields at sites with midrange yields tended to be overestimated by SPARROW, and yields at sites with high yields tended to be underestimated by SPARROW. TP yields at four sites in the Mississippi Delta were underestimated by the 2012 SPARROW-predicted model.Results of select sites from our study were also compared to other published load estimates from an earlier time period to evaluate possible trends. Comparison of TN yields at four sites and TP yields at three sites from the study-derived estimates to estimates made from data spanning 1993–2004 showed decreasing TN yields at all four sites and decreasing TP yields at two of three sites, with increasing yields of TP at the Yazoo River lower site. Also, a third comparison of the TN and TP yields of the Yazoo River lower site of this study to estimates made from data spanning 1996–97 showed decreasing TN yields but similar TP yields. This suggests that TN yields may have decreased over the last 20–30 years, but TP yields remain constant or are increasing.