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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]

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]

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]

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]