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Salt marshes are hot spots for nitrogen (N) cycling due to complex and dynamic redox gradients. Soils of salt marshes contain a wide diversity of microbes capable of carrying out steps in the N cycle. Recent discoveries demonstrate that chemolithotrophic (e.g., sulfide oxidation coupled with N 2 fixation), as well as heterotrophic metabolisms, are important for N cycling in salt marshes. N removal via denitrification is an important ecosystem service provided by salt marshes. N fixation and N retention due to dissimilatory nitrate reduction to ammonium (DNRA) are more important than previously thought and may contribute to salt marsh productivity. Salt marshes sit at the terrestrial–aquatic interface of oceans around the world. Unique features of salt marshes that differentiate them from their upland or offshore counterparts include high rates of primary production from vascular plants and saturated saline soils that lead to sharp redox gradients and a diversity of electron acceptors and donors. Moreover, the dynamic nature of root oxygen loss and tidal forcing leads to unique biogeochemical conditions that promote nitrogen cycling. Here, we highlight recent advances in our understanding of key nitrogen cycling processes in salt marshes and discuss areas where additional research is needed to better predict how salt marsh N cycling will respond to future environmental change. [ABSTRACT FROM AUTHOR]

Roots of salt marsh grasses contribute to soil building but also affect decomposition by releasing bioavailable carbon exudates and oxygen. Disentangling exudate and oxygen effects on decomposition is difficult in the field but essential for marsh carbon models and predicting the impacts of global change disturbances. We tested how pulsed, simulated exudates affect soil metabolism under oxic and anoxic conditions, and whether carbon and oxygen availability facilitate mineralization of existing organic matter (i.e., priming). We conducted a laboratory experiment in flow-through reactors, adding carbon pulses weekly for 84 days and then following starvation under low carbon conditions. Oxygen consumption and sulfide production were inhibited under anoxic and oxic conditions and slowed by 21 ± 10% and 55 ± 8%, respectively, between 1- and 5- days following exudate pulses. Respiration rates immediately following and between pulses increased over time, suggesting that microbes capitalize on and may acclimate to patchy resources. Starvation caused oxygen consumption and sulfide production to fall 28% and 78% in oxic and anoxic treatments. Smaller decreases in oxygen consumption following pulses could suggest greater access to secondary carbon sources and that sulfate reducers were more reliant on exudates. Soil organic carbon was not the likely secondary source because porewater dissolved inorganic carbon δ13C values did not change during transit through the reactors, despite a ∼26‰ difference between the supplied seawater and marsh soil. Interpretation of oxygen consumption rates is complicated by non-respiratory oxidation of reduced inorganic compounds and possibly significant lithoautotrophy. Exudate pulses elicited rapid and ephemeral respiratory responses, particularly under anoxia, but non-respiratory oxidation of reduced compounds obscured the impact of oxygen availability in our experimental system. Despite this, greater aerobic respiration rates suggest that oxygen availability has more potential to regulate carbon mineralization in coastal wetlands than root exudates. • Respiration rates immediately following and between carbon pulses increased over time. • Respiratory responses to carbon pulses and starvation were greater under anoxia. • Non-respiratory oxidation of reduced compounds obscured oxygen availability effects. • Carbon mineralization may be more sensitive to oxygen than root exudates in wetlands. [ABSTRACT FROM AUTHOR]

Abstract: Runaway expansion of shallow ponds can catalyze the conversion of vegetated marshes into open water environments. Predicting how this transition affects ecosystem functioning is difficult because little is known about pond biogeochemistry. We characterized sediment organic matter sources and transformations in three ponds with different plant communities, over alternating periods of tidal isolation and flushing, during summer and fall, using a combination of stable isotopes, lipid biomarkers, and benthic fluxes. Sediment respiration rates (1.66 ± 0.09 mmol C m−2 d−1 to 28.53 ± 7.76 mmol C m−2 d−1) were comparable to shallow estuaries and driven by sulfate reduction. Rates varied across ponds, reflecting differences in summertime Ruppia maritima and macroalgae abundances, but were similar between seasons. Interactions between aboveground plant and sediment bacterial communities translated into distinct biogeochemical processes across the three ponds. Tidal isolation and summer weather intensified plant and bacterial community effects on pond carbon dynamics, resulting in algal biomass and lipid δ13C values that were 3–12‰ enriched, compared to nearby habitats. Surface sediment organic matter mainly derived from pond microalgae and was compositionally distinct from tidal creeks and marshes. Surprisingly, sediment bacteria were not tightly coupled to benthic microalgae but decomposed multiple carbon sources in surface sediments and became increasingly reliant on buried peat at deeper horizons. Pond development over time could largely be explained by sediment respiration and the simultaneous accretion of the surrounding marsh platform. The role of decomposition in pond expansion is consistent with previous assessments based on whole‐pond metabolism rates. Consequently, future pond expansion could alter ecosystem biogeochemistry and reduce carbon storage. [ABSTRACT FROM AUTHOR]

To test how benthic biogeochemistry responds to changing nutrient availability and estuary trophic state, I conducted mesocosm and field experiments. In the mesocosm experiment, sediment cores from eutrophic and oligotrophic estuaries were incubated under high or low nutrient levels. Net production rates were greater in eutrophic vs. oligotrophic cores while respiration rates were greater in high nutrient treatments, indicating that sediment metabolism was affected by trophic history and nutrient availability. Sediment organic matter (SOM) composition was insensitive to the nutrient treatments but varied with trophic history as carbon : nitrogen ratios were lower, δ15N was higher, and algal and bacterial fatty acids (FAs) were more abundant in eutrophic sediments. In the field experiment, intact cores were reciprocally transplanted between eutrophic and oligotrophic estuaries and changes in SOM composition were followed over four months. SOM responses were more dramatic in cores transplanted to the oligotrophic vs. eutrophic estuary. In sediments moved from the eutrophic to oligotrophic estuary, carbon and nitrogen content as well as abundances of algal and bacterial FAs fell within one month. Conversely, sediment δ15N increased sharply while algal and bacterial FAs rose slightly in cores transplanted from the oligotrophic to eutrophic estuary. Different SOM responses between the experiments were likely due to direct vs. indirect effects of nutrient enrichment. Nutrient levels were manipulated in the mesocosm experiment while the estuaries differed in nutrients, macroalgal biomass, benthic animal communities, and oxygen levels. Consequently, sediment biogeochemical responses to watershed nutrient mitigation will likely follow broader changes in estuary habitat quality. [ABSTRACT FROM AUTHOR]

1. Aquatic ecologists use mesocosm experiments to understand mechanisms driving ecological processes. Comparisons across experiments, and extrapolations to larger scales, are complicated by the use of mesocosms with varying dimensions. We conducted a mesocosm experiment over a volumetric scale spanning five orders of magnitude (from 4 L to whole ponds) to determine the generality of algal responses to nutrient enrichment. Recognising that mesocosm dimensions may affect algal growth, we also manipulated the ratio of mesocosm surface area to volume (SA : V) over two levels (high versus low). We used mesocosm tanks of similar size and construction to those commonly used in aquatic experiments to increase the generality of our results. 2. Volume was generally a stronger determinant of algal responses than mesocosm shape (i.e. SA : V). However, the effects of both volume and shape on algae were weak and explained a small portion of the variance in response variables. In addition, there was no consistent, directional relationship (positive or neutral) between mesocosm volume and algal abundance (estimated by chlorophyll concentration). Combined, our findings suggest that results from small-scale experiments, examining the direct response of algae to nutrient enrichment, can probably be 'moved on up' and applied to larger, more natural aquatic systems. 3. Algal response to nutrient enrichment (e.g. nutrient use efficiency and effect size) varied strongly with time. This underscores the importance of choosing an experimental timescale appropriate to the biological and/or ecological process of interest. 4. We compared our results to those from a recent meta-analysis of nutrient-limitation studies that included 359 freshwater pelagic experiments, spanning a wide range of volumetric and temporal scales. Similar findings between this experiment and the meta-analysis indicate that algal response to nutrient enrichment varies little across spatial scales. Therefore, it is probable that results from small-scale pelagic algal nutrient-limitation experiments are relevant to large-scale processes, such as eutrophication. [ABSTRACT FROM AUTHOR]

Background: Food web composition and resource levels can influence ecosystem properties such as productivity and elemental cycles. In particular, herbivores occupy a central place in food webs as the species richness and composition of this trophic level may simultaneously influence the transmission of resource and predator effects to higher and lower trophic levels, respectively. Yet, these interactions are poorly understood. Methodology/Principal Findings: Using an experimental seagrass mesocosm system, we factorially manipulated water column nutrient concentrations, food chain length, and diversity of crustacean grazers to address two questions: (1) Does food web composition modulate the effects of nutrient enrichment on plant and grazer biomasses and stoichiometry? (2) Do ecosystem fluxes of dissolved oxygen and nutrients more closely reflect above-ground biomass and community structure or sediment processes? Nutrient enrichment and grazer presence generally had strong effects on biomass accumulation, stoichiometry, and ecosystem fluxes, whereas predator effects were weaker or absent. Nutrient enrichment had little effect on producer biomass or net ecosystem production but strongly increased seagrass nutrient content, ecosystem flux rates, and grazer secondary production, suggesting that enhanced production was efficiently transferred from producers to herbivores. Gross ecosystem production (oxygen evolution) correlated positively with above-ground plant biomass, whereas inorganic nutrient fluxes were unrelated to plant or grazer biomasses, suggesting dominance by sediment microbial processes. Finally, grazer richness significantly stabilized ecosystem processes, as predators decreased ecosystem production and respiration only in the zero- and one- species grazer treatments. Conclusions/Significance: Overall, our results indicate that consumer presence and species composition strongly influence ecosystem responses to nutrient enrichment, and that increasing herbivore diversity can stabilize ecosystem flux rates in the face of perturbations. [ABSTRACT FROM AUTHOR]

We tested the singular and interactive effects of resource availability (light) and community composition (food chain length and herbivore species richness) on eelgrass (Zostera marina) ecosystem properties and functioning with an experimental mesocosm system. Food chain length was manipulated through the presence or absence of blue crab (Callinectes sapidus) predators, whereas grazer species richness varied across three levels (zero, two, or four crustacean species). We found important and interacting effects of bottom-up and top-down forcings on sediment organic matter (SOM) composition. Light increased eelgrass and algal biomass and sediment organic carbon and nitrogen content. Increasing grazer diversity generally decreased algal biomass and ecosystem production but interacted with food chain length (i.e., presence of predatory crabs) and light. Predators generally increased algal biomass and ecosystem production through a trophic cascade, which was stronger at high grazer diversity and under ambient light. SOM composition, determined with fatty acid (FA) biomarkers, was sensitive to all manipulated variables. Increasing grazer species richness often decreased the contributions of FAs derived from plant and algal sources, whereas increasing light had the opposite effect. Food chain length was generally a less important determinant of SOM composition than light, although predators did increase FAs representative of heterotrophic bacteria. Overall, resource availability and epibenthic community composition strongly influenced organic matter cycling, SOM composition, and the bacterial community in seagrass-bed sediments. [ABSTRACT FROM AUTHOR]

Disturbances are one of the most important processes affecting natural systems, but there is a gap between simple conceptual models of disturbance and complex empirical studies. We studied the perturbation caused by headward‐eroding creeks in southeastern USA salt marshes. We measured disturbance responses (magnitude and recovery trajectory) of 19 variables. Some variables (shoot density, root biomass, snail density, soil pH, soil strength, soil temperature, elevation) declined sharply, while other variables (crab burrow density, soil organic matter, soil redox) increased sharply, in response to the burrowed and grazed conditions at the creek head. These variables recovered over subsequent years or decades. Other variables (shoot height, aboveground biomass, rhizome biomass, light interception) declined sharply in the creek head, then overshot control values before recovering. Some variables (benthic algae, soil salinity) did not appear to be disturbed by the creek head. As hypothesized, plants recovered before soils and snails. Disturbance magnitude and time to recovery were often greater directly adjacent to the new creekbank than for the same variables in a parallel transect further away from the creekbank, and in some cases variables never converged with control values, indicating a persistent state change. Reducing the dimensionality of the data set into principal component axes obscured the diverse ways in which different aspects of the system responded to and recovered from the perturbation. Our study illustrates the challenges in moving from simple conceptual models of disturbance to empirical studies in which multiple variables are likely to be affected differently and follow different recovery trajectories. [ABSTRACT FROM AUTHOR]

Salt marsh survival with sea‐level rise (SLR) increasingly relies on soil organic carbon (SOC) accumulation and preservation. Using a novel combination of geochemical approaches, we characterized fine SOC (≤1 mm) supporting marsh elevation maintenance. Overlaying thermal reactivity, source (δ13C), and age (F14C) information demonstrates several processes contributing to soil development: marsh grass production, redeposition of eroded material, and microbial reworking. Redeposition of old carbon, likely from creekbanks, represented ∼9%–17% of shallow SOC (≤26 cm). Soils stored marsh grass‐derived compounds with a range of reactivities that were reworked over centuries‐to‐millennia. Decomposition decreases SOC thermal reactivity throughout the soil column while the decades‐long disturbance of ponding accelerated this shift in surface horizons. Empirically derived estimates of SOC turnover based on geochemical composition spanned a wide range (640–9,951 years) and have the potential to inform predictions of marsh ecosystem evolution. Plain Language Summary: Salt marsh survival with rising sea levels increasingly depends on the accumulation and preservation of buried organic carbon. Marsh soil organic carbon development reflects at least three processes: burial of differently reactive compounds that derive from local grasses, redeposition of old carbon (9%–17%), and microbial reworking. Decomposition results in a progressive decrease in the thermal reactivity of soil organic carbon, and disturbances such as ponding can accelerate this shift. Modeled rates of geochemically defined soil organic carbon pools turnover on the order of centuries‐to‐millennia and can refine predictions of salt marsh sustainability. Key Points: Salt marsh soils preserved compounds with a range of reactivities that were derived from local grasses9%–17% of surface soil carbon was old, likely reflecting redeposition of eroded creekbank materialDecomposition decreases soil organic carbon thermal reactivity, and disturbances accelerate this shift, particularly in surface horizons [ABSTRACT FROM AUTHOR]

High‐throughput sequencing has enabled robust shotgun metagenomic sequencing that informs our understanding of the genetic basis of important biogeochemical processes. Slower to develop, however, are the application of these tools in a controlled experimental framework that pushes the field beyond exploratory analysis toward hypothesis‐driven research. We performed flow‐through reactor experiments to examine how salt marsh sediments from varying depths respond to nitrate addition and linked biogeochemical processes to this underlying genetic foundation. Understanding the mechanistic basis of carbon and nitrogen cycling in salt marsh sediments is critical for predicting how important ecosystem services provided by marshes, including carbon storage and nutrient removal, will respond to global change. Prior to the addition of nitrate, we used metagenomics to examine the functional potential of the sediment microbial community that occurred along a depth gradient, where organic matter reactivity changes due to decomposition. Metagenomic data indicated that genes encoding enzymes involved in respiration, including denitrification, were higher in shallow sediments, and genes indicative of resource limitation were greatest at depth. After 92 d of nitrate enrichment, we measured cumulative increases in dissolved inorganic carbon production, denitrification, and dissimilatory nitrate reduction to ammonium; these rates correlated strongly with genes that encode essential enzymes in these important pathways. Our results highlight the importance of controlled experiments in linking biogeochemical rates to underlying genetic pathways. Furthermore, they indicate the importance of nitrate as an electron acceptor in fueling microbial respiration, which has consequences for carbon and nitrogen cycling and fate in coastal marine systems. [ABSTRACT FROM AUTHOR]

Classic bottom-up theory predicts that increased resource availability (for example, nutrients) at the base of the food web will stimulate primary production and, in turn, secondary production. Recent studies, however, indicate that bottom-up controls on food web production can be modified by other factors, such as landscape configuration and continuity. As part of a 10-year ecosystem-scale experiment in a New England salt marsh, we investigated the response of secondary consumers, specifically a fish, the mummichog (Fundulus heteroclitus), to nutrient enrichment. In the first 6 years, we observed a classic bottom-up response of increased production of algae, invertebrate prey, and mummichogs. After the sixth year, however, mummichog biomass declined to below reference levels by the eighth year. This decline in mummichog biomass coincided with nutrient-induced collapse of the low-marsh habitat. Based on stable isotope analyses, field surveys, and small-scale experiments, we suggest that the geomorphic changes induced a trophic decoupling between creek and marsh habitats, thereby reducing mummichog access to prey in the intermittently flooded marsh. Thus, despite continued stimulation of algal and invertebrate prey production, fish abundances declined to below pre-enrichment levels. Our results demonstrate how geomorphic controls can override classic bottom-up control and emphasize the importance of long-term studies in detecting the response of slow-turnover phenomena (for example, changing landscapes). [ABSTRACT FROM AUTHOR]

Salt marshes, due to their capability to bury soil carbon (C), are potentially important regional C sinks. Efforts to restore tidal flow to former salt marshes have increased in recent decades in New England (USA), as well as in some other parts of the world. In this study, we investigated plant biomass and carbon dioxide (CO 2) fluxes at four sites where restoration of tidal flow occurred five to ten years prior to the study. Site elevation, aboveground biomass, CO 2 flux, and porewater chemistry were measured in 2015 and 2016 in both restored marshes and adjacent marshes where tidal flow had never been restricted. We found that the elevation in restored marsh sites was 2–16 cm lower than their natural references. Restored marshes where porewater chemistry was similar to the natural reference had greater plant aboveground biomass, gross ecosystem production, ecosystem respiration, as well as net ecosystem CO 2 exchange (NEE) than the natural reference, even though they had the same plant species. We also compared respiration rates in aboveground biomass (AR) and soil (BR) during July 2016, and found that restored marshes had higher AR and BR fluxes than natural references. Our findings indicated that well-restored salt marshes can result in greater plant biomass and NEP, which has the potential to enhance rates of C sequestration at 10-yrs post restoration. Those differences were likely due to lower elevation and greater flooding frequency in the recently restored marshes than the natural marsh. The inverse relationship between elevation and productivity further suggests that, where sea-level rise rate does not surpass the threshold of plant survival, the restoration of these salt marshes may lead to enhanced organic and mineral sedimentation, extending marsh survival under increased sea level, and recouping carbon stocks that were lost during decades of tidal restriction. The photos showing the tidal channel before (A) and after restoration (B) at Bass creek, Barnstable, MA, USA. Our study indicated that successful restoration of salt marshes leads to greater rates of C sequestration for a decade, at minimum. Moreover, the negative relationship between elevation and plant productivity suggested that sea level rise may lead to enhanced sedimentation, extending marsh survival under the increased sea level, and recouping carbon stocks that were lost during tidal restriction periods. Unlabelled Image • Coastal wetlands are important regional C sinks. • The plant biomass and CO 2 fluxes was compared in restored marsh and reference. • The recently restored salt marsh had higher plant aboveground biomass and NEE than the natural marsh. • Negative feedbacks between plant productivity and sea levels rise help salt marsh survival. [ABSTRACT FROM AUTHOR]