This chapter briefly presents the most important microbially mediated redox reactions in ecosystems. The chapter introduces redox reactions and their terminology, electron donors and acceptors, and energy yields from redox reactions. It then describes some of the most important microbially mediated redox reactions and the environments in which each typically occurs. The chapter presents the sequence in which redox reactions typically occur as electron acceptors are successively depleted, and briefly discusses why microbially mediated redox reactions are important in ecosystem element cycles.

We use a 32-year dataset from a rural, southeastern New York stream to describe the effect of long-term road salt use on concentrations of sodium (Na+) and chloride (Cl−). Mean annual stream Na+ and Cl− concentrations initially increased, reached a plateau, and then increased again. Trends in summer and winter stream concentrations were similar but summer concentrations were higher than winter, indicating that salt entered the stream via groundwater discharge. Seasonal and inter-annual variability in stream Na+ and Cl− concentrations and export were high in the latter years of the study and can be explained by increased variability in stream discharge. Stream water Na+ and Cl− concentrations were positively correlated with conductivity, and conductivity was negatively correlated with discharge during all seasons (p < 0.001). We used road salt application data from a local agency to examine effects of best management practices. Despite reductions in salt application, there was no commensurate decrease in stream water Na+ and Cl− concentrations. We estimate that the legacy of long-term salt accumulation in groundwater and soils may delay a decline in stream water Na+ and Cl− concentrations by 20–30 years. Continued research to develop road salt reduction practices is important to mitigate impacts on freshwater ecosystems and drinking water supplies.

Large river ecosystems (LRE) are important components of global cycles, influence large parts of the earth's surface, and provide many services in support of human civilization. However, understanding their condition, functioning, and trajectory of change is difficult in part due to their scale and diversity of forcing factors but also due to multiple and potentially conflicting human uses. Although these challenges are generally applicable and probably true to some degree for any large river ecosystem, there are also attributes of LRE that foster scientific understanding, can lead to knowledge‐based management, and may catalyse their interaction. The absolute size of LRE means they will be complex, unique and the water quality, physical character, or habitat availability at any particular point may be the result of drivers acting further up the basin or legacies from previous times. On the bright side however, their absolute size also means there will be existing information on many important features, not least land cover and hydrology. Moreover, it is highly likely there will be a sizeable human population in the basin that derives some benefits from the river even if just in a narrow anthropocentric fashion and so there will be some motivation for understanding characteristics and potential change. Large size also suggests that the LRE will be viewed (perhaps with some basis in law) as a national or regional resource making it (at least nominally) worthy of study and management. I provide some examples of how science and management of the Hudson River in New York, USA, have benefitted from some of these perceived difficulties perhaps offering optimism for application in other systems.

The overall mass of sodium chloride salt used to treat icy roads can be significantly reduced by pretreating roads or prewetting dry rock salt with concentrated brine solutions. Brine solutions can be made from rock salt; however, an alternative source of brine for some communities is brine that is a waste product of oil and gas extraction. This study compares contaminant chemistry of brine made from rock salt with literature data on oil and gas well brine from conventional and unconventional wells. In addition to reviewing existing literature, this paper analyzes four rock salt samples for a suite of chemical constituents. Maximum reported levels of some harmful contaminants are higher for well brines than for rock salt brines and are higher for unconventional than for conventional well brines. Because the regulatory structure for using well brines varies among states, the authors recommend a consistent approval process for permitting the use of waste brines that includes specific maximum allowable limits for potentially harmful contaminants, and that each batch of solution be tested before use. Although the use of brine, including waste brine, can reduce the overall amount of salt needed for snow and ice control, adequate steps should be taken to ensure the safety of the brine solutions before they are used.

Non-native species are among the most important drivers of the structure and function of modern ecosystems. The ecological impacts of a non-native species ought to depend on the size and characteristics of its population, but the exact nature of this population-impacts relationship is rarely defined. Both the mathematical form of this relationship (e.g., linear, exponential, and threshold) and the attributes of the invading population (e.g., density, biomass, and body size) that most efficiently describe its impacts could vary greatly across invaders, ecosystems, and ecological variables. Knowing the shape of this relationship could improve management and help to infer mechanisms of interaction between the invader and ecosystem. We used a long-term data set on the invasion of the Hudson River ecosystem by two species of Dreissena (the zebra mussel, Dreissena polymorpha, and the quagga mussel, Dreissena rostriformis) to explore the shape of the population-impacts relationship for selected ecological variables, including seston, phytoplankton, and several taxa of zooplankton. Most population-impacts relationships appeared to follow a negative exponential form, but we also found apparent thresholds and scatterplots for some variables. Including information on the traits of Dreissena (body size and filtration rate) often substantially improved models of impacts. We found only slight evidence that the resistance of the Hudson River ecosystem to the Dreissena invasion might be increasing over time. Our results suggest important refinements to widely used conceptual models of invasive species impact, and indicate that defining the population-effects relationship will be essential in understanding and managing the impacts of non-native species.

We used a GIS analysis of sodium and chloride concentrations in private water wells in a southeastern New York township to describe the pattern of distribution of road salt in aquifers tapped for drinking water. The primary source of road salt was sodium chloride, and sodium and chloride concentrations were significantly correlated ( = 0.80, < 0.01). Chloride concentrations in wells increased as the percentage of impervious surface cover (ISC) within a 250-m radius around wells increased ( = 0.87, < 0.01) and declined with increasing distance to the nearest road ( = 0.76, < 0.01). Wells that were located lower in elevation than the nearest road had higher concentrations of chloride than wells that were higher than the nearest road, but this occurred only when the nearest road was >30 m from the wells ( < 0.01). Chloride concentrations were not affected by well depth or adjacent road type (major or minor roads). Surface geology and hydrologic soil class had significant effects ( < 0.01) on chloride concentrations in wells, with porous surface geology types and well-drained soils having higher concentrations; these effects may be confounded by the fact that ISC was more likely to occur on these permeable surface geology and soil types. Hot and cold spot analysis revealed substantial unevenness in chloride concentrations. Results for sodium were similar to those for chloride. Overall, these results indicate that road salt contamination of groundwater is unevenly distributed and is affected by landscape factors that can be used to guide well testing and best management practices of deicing salt distribution.

This article investigates the mechanics of loss of Hudson River Vallisneria americana after the high volume storms at the end of the 2011 growing season, when two severe weather events-Tropical Storm Irene and the remnants of Tropical Storm Leestruck the Hudson River watershed. In 2012, the distribution of the most common species of submerged aquatic vegetation (SAV), Vallisneria americana (wild celery, water celery, or tape grass), in the Hudson River estuary declined by more than 90%, with no appreciable recovery in 2013 and 2014. Because of its important habitat value for aquatic life and for increasing dissolved oxygen, managers and scientists have begun discussing the reasons for the loss, as well as how to assist its recovery through assisted restoration efforts in the estuary. Supported by in situ and in vitro experiments, the article posits the hypothesis that sediment, washed into the river by the storm, buried overwintering tubers of the plant, thus reducing sprouting success. Sprouting was as low as 50% with sediment depth between 2 and 5cm; sprouting did not occur with sediment depth greater than 10cm. Field experiments found no support for the hypothesis that herbivory inhibited regrowth of the plant after the storm events. These results suggest that future assisted restoration of Vallisneria americana and SAV in general may require attention to system-specific factors.

This chapter synthesizes the multitude of interactions that affect Dissolved Organic Matter (DOM) generation, reactivity, consumption, and transport into a unified framework using interactivity as the core theme. DOM experiences highly variable dynamics as it moves through ecosystem subunits—namely, wetlands, soil horizons, and across major system boundaries, such as terrestrial to aquatic and freshwater to marine. DOM is "refractory" or "conservative," as the DOM turnover was slow in relation to microbial dynamics and hydrologic retention times. Within the system, the abiotic interactions of DOM affect the transparency of water, the microscale structure of the aqueous medium, and the availability, and mobility of inorganic nutrients and other compounds. At the same time, interactions between DOM and the microbial community underlie system metabolism and influence the composition of DOM exported to linked ecosystems. The interaction of DOM with physical processes is often viewed in one direction— the physical environment imposing constraints on DOM supply, retention, and reactivity. DOM-microbe interactions are intense in both directions. DOM characteristics influence microbial community structure and function, while microbial community metabolism and composition influence DOM production, characteristics, and fate. The synthesis is classified into two broad categories: (1) DOM-microbial and (2) DOM-physicochemical interactions. Although these categories are fairly distinct at large scales, they become increasingly difficult to parse at fine scales.

Burial of aboveground plant litter by animals reduces the amount available for surface transport and places it into a different environment, affecting decomposition rates and fluxes of organic matter to adjacent ecosystems. Here we show that in a Southwestern Atlantic salt marsh the burrowing crab Neohelice granulata buries aboveground plant litter at rates (0.5–8 g m−2 day−1) comparable to those of litter production (3 g m−2 day−1). Buried litter has a low probability (0.6%) of returning to the marsh surface. The formation of burrow excavation mounds on the marsh surface is responsible for most litter burial, whereas litter trapped in burrows was an order of magnitude lower than rates of burial under excavation mounds. Crab exclusion markedly increased surface litter accumulation (3.5-fold in just 21 days). Tides with the potential to transport significant amounts of surface litter are infrequent; hence, most litter is buried before it can be transported elsewhere or decomposes on the surface. Crab litter burial can account for the observed low levels of surface litter accumulation in this ecosystem and likely drives organic matter transformation and export. The impacts of ecosystem engineering by this crab species are therefore substantial and comparable in magnitude to the large effects found for tropical crabs and other litter-burying organisms, such as anecic earthworms.

Establishing relationships between biodiversity and ecosystem function is an ongoing endeavor in contemporary ecosystem and community ecology, with important practical implications for conservation and the maintenance of ecosystem services. Removal of invasive plant species to conserve native diversity is a common management objective in many ecosystems, including wetlands. However, substantial changes in plant community composition have the potential to alter sediment characteristics and ecosystem services, including permanent removal of nitrogen from these systems via microbial denitrification. A balanced assessment of costs associated with keeping and removing invasive plants is needed to manage simultaneously for biodiversity and pollution targets. We monitored small-scale removals of Phragmites australis over four years to determine their effects on potential denitrification rates relative to three untreated Phragmites sites and adjacent sites dominated by native Typha angustifolia. Sediment ammonium increased following the removal of vegetation from treated sites, likely as a result of decreases in both plant uptake and nitrification. Denitrification potentials were lower in removal sites relative to untreated Phragmites sites, a pattern that persisted at least two years following removal as native plant species began to re-colonize treated sites. These results suggest the potential for a trade-off between invasive-plant management and nitrogen-removal services. A balanced assessment of costs associated with keeping versus removing invasive plants is needed to adequately manage simultaneously for biodiversity and pollution targets.

Riprapped revetments are a common shore defense along lakes, rivers, estuaries, and the ocean, but little is known about the ecology of these structures. We studied the amount and composition of vascular vegetation on riprapped revetments along the freshwater tidal Hudson River, New York. Cover, species richness, and species composition of vegetation varied greatly across the 21 study sites, from nearly barren sites to densely vegetated sites. The flora was split about equally between native and nonnative species, and vines were especially well represented. Vegetation cover and composition were correlated with the age, slope, particle size, and roughness of revetments, as well as site exposure and local management practices. We suggest that the ecological functions provided by revetment vegetation vary enormously from site to site along the Hudson, and could be enhanced by deliberate design and management.

Quantifying the role that freshwater ecosystems play in the global carbon cycle requires accurate measurement and scaling of dissolved organic carbon (DOC) removal in river networks. We reviewed reach-scale measurements of DOC uptake from experimental additions of simple organic compounds or leachates to inform development of aquatic DOC models that operate at the river network, regional, or continental scale. Median DOC uptake velocity (v(f)) across all measurements was 2.28 mm min(-1). Measurements using simple compound additions resulted in faster vf (2.94 mm min(-1)) than additions of leachates (1.11 mm min(-1)). We also reviewed published data of DOC bioavailability for ambient stream water and leaf leachate DOC from laboratory experiments. We used these data to calculate and apply a correction factor to leaf leachate uptake velocity to estimate ambient stream water DOC uptake rates at the reach scale. Using this approach, we estimated a median ambient stream DOC vf of 0.26 mm min(-1). Applying these DOC vf values (0.26, 1.11, 2.28, and 2.94 mm min(-1)) in a river network inverse model in seven watersheds revealed that our estimated ambient DOC vf value is plausible at the network scale and 27 to 45% of DOC input was removed. Applying the median measured simple compound or leachate vf in whole river networks would require unjustifiably high terrestrial DOC inputs to match observed DOC concentrations at the basin mouth. To improve the understanding and importance of DOC uptake in fluvial systems, we recommend using a multiscale approach coupling laboratory assays, with reach-scale measurements, and modeling.

Invasive species like Phragmites australis are notorious for thriving in drastically different environments. This expansion into new habitats could be assisted by phenotypic plasticity. Phenotypic plasticity may be partially driven by epigenetic changes. Epigenetics, the study how markers on DNA effect transcription, is characterized in part by the patterns of methyl and acetyl groups that attach to either the DNA or histones, thus affecting gene transcription. Phragmites australis is a well-known invasive plant in wetland habitats that has been expanding its range in the Hudson River estuary including higher salt concentrations. To investigate the potential relationship of Phragmites australis and its epigenetic patterns in varying salinities, I sampled six populations in the Hudson River estuary, from three different salinity ranges. Assays quantifying the amount of methylated DNA were conducted with DNA samples extracted from these populations. Three different tests produced varying results. The only significant results displayed methylation levels that decrease with increased salinity concentrations. Though the other two tests had similar overall trends, neither was statistically significant. These results indicate the need for further examination into environmental epigenetics, to better determine any potential relationship between epigenetics and phenotypic plasticity and understand what may be driving Phragmites australis rapid adaptation into saltier waters. Further studies would include investigation into region specific methylation of Phragmites australis, as well as studying any changes of methylation while raising clones in varying salinities.

EDITORIAL article Front. Microbiol., 02 December 2015Sec. Aquatic Microbiology Volume 6 - 2015 | https://doi.org/10.3389/fmicb.2015.01364

A better understanding is needed of how hydrological and biogeochemical processes control dissolved organic carbon (DOC) concentrations and dissolved organic matter (DOM) composition from headwaters downstream to large rivers. We examined a large DOM dataset from the National Water Information System of the US Geological Survey, which represents approximately 100 000 measurements of DOC concentration and DOM composition at many sites along rivers across the United States. Application of quantile regression revealed a tendency towards downstream spatial and temporal homogenization of DOC concentrations and a shift from dominance of aromatic DOM in headwaters to more aliphatic DOM downstream. The DOC concentration–discharge (C-Q) relationships at each site revealed a downstream tendency towards a slope of zero. We propose that despite complexities in river networks that have driven many revisions to the River Continuum Concept, rivers show a tendency towards chemostasis (C-Q slope of zero) because of a downstream shift from a dominance of hydrologic drivers that connect terrestrial DOM sources to streams in the headwaters towards a dominance of instream and near-stream biogeochemical processes that result in preferential losses of aromatic DOM and preferential gains of aliphatic DOM.

Rising sea levels and stronger storm surges may expose tidal freshwater wetlands to saline waters, possibly leading to increased sulfate reduction and higher sulfide (H2S) concentrations. To better understand the effects of salinity on nitrogen cycling, porewater chemistry and sediment profiles of H2S and dissolved oxygen (O2) were measured along a salinity gradient in the Hudson River (New York, USA). Additionally, laboratory experiments exposed freshwater sediments to varying salinities after which sediment O2 and H2S dynamics along with nitrification and denitrification were measured. Overall, sites with higher salinities had lower oxygen availability (both as concentration and oxic sediment depth) and higher sulfide concentrations. Both nitrification and denitrification were depressed at higher salinities suggesting that exposure to saline water may alter nitrogen cycling of tidally influenced wetlands in the brackish region of the Hudson River estuary which may result in reduced retention of nitrogen.

Population growth in cities has resulted in the rapid expansion of urbanized land. Most research and management of stream ecosystems affected by urban expansion has focused on the maintenance and restoration of biotic communities rather than their basal resources. We examined the potential for urbanization to induce bottom‐up ecosystem effects by looking at its influence on dissolved organic matter (DOM) composition and bioavailability and microbial enzyme activity. We selected 113 headwater streams across a gradient of urbanization in central and southern Maine and used elemental and optical analyses, including parallel factor analysis of excitation‐emission matrices, to characterize DOM composition. Results show that fluorescent and stoichiometric DOM composition changed significantly across the rural to urban gradient. Specifically, the proportion of humic‐like allochthonous DOM decreased while that of more bioavailable autochthonous DOM increased in the more urbanized streams. In laboratory incubations, increased autochthonous DOM was associated with a doubling in the decay rate of dissolved organic carbon as well as increased activity of C‐acquiring enzymes. These results suggest that urbanization replaces upstream humic material with more local sources of DOM that turnover more rapidly and may drive bottom‐up changes in microbial communities and affect the quality and quantity of downstream DOM delivery.