Abstract. Salinization, a widespread threat to the structure and ecological functioning of inland and coastal wetlands, is currently occurring at an unprecedented rate and geographic scale. The causes of salinization are diverse and include alterations to freshwater flows, land-clearance, irrigation, disposal of wastewater effluent, sea level rise, storm surges, and applications of de-icing salts. Climate change and anthropogenic modifications to the hydrologic cycle are expected to further increase the extent and severity of wetland salinization. Salinization alters the fundamental physicochemical nature of the soil-water environment, increasing ionic concentrations and altering chemical equilibria and mineral solubility. Increased concentrations of solutes, especially sulfate, alter the biogeochemical cycling of major elements including carbon, nitrogen, phosphorus, sulfur, iron, and silica. The effects of salinization on wetland biogeochemistry typically include decreased inorganic nitrogen removal (with implications for water quality and climate regulation), decreased carbon storage (with implications for climate regulation and wetland accretion), and increased generation of toxic sulfides (with implications for nutrient cycling and the health/functioning of wetland biota). Indeed, increased salt and sulfide concentrations induce physiological stress in wetland biota and ultimately can result in large shifts in wetland communities and their associated ecosystem functions. The productivity and composition of freshwater species assemblages will be highly altered, and there is a high potential for the disruption of existing interspecific interactions. Although there is a wealth of information on how salinization impacts individual ecosystem components, relatively few studies have addressed the complex and often non-linear feedbacks that determine ecosystem-scale responses or considered how wetland salinization will affect landscape-level processes. Although the salinization of wetlands may be unavoidable in many cases, these systems may also prove to be a fertile testing ground for broader ecological theories including (but not limited to): investigations into alternative stable states and tipping points, trophic cascades, disturbance-recovery processes, and the role of historical events and landscape context in driving community response to disturbance.

To better understand the distribution of soil microbial communities at multiple spatial scales, a survey was conducted to examine the spatial organization of community structure in a wheat field in eastern Virginia (USA). Nearly 200 soil samples were collected at a variety of separation distances ranging from 2.5 cm to 11 m. Whole-community DNA was extracted from each sample, and community structure was compared using amplified fragment length polymorphism (AFLP) DNA fingerprinting. Relative similarity was calculated between each pair of samples and compared using geostatistical variogram analysis to study autocorrelation as a function of separation distance. Spatial autocorrelation was found at scales ranging from 30 cm to more than 6 m, depending on the sampling extent considered. In some locations, up to four different correlation length scales were detected. The presence of nested scales of variability suggests that the environmental factors regulating the development of the communities in this soil may operate at different scales. Kriging was used to generate maps of the spatial organization of communities across the plot, and the results demonstrated that bacterial distributions can be highly structured, even within a habitat that appears relatively homogeneous at the plot and field scale. Different subsets of the microbial community were distributed differently across the plot, and this is thought to be due to the variable response of individual populations to spatial heterogeneity associated with soil properties.

Climate change-associated sea level rise is expected to cause saltwater intrusion into many historically freshwater ecosystems. Of particular concern are tidal freshwater wetlands, which perform several important ecological functions including carbon sequestration. To predict the impact of saltwater intrusion in these environments, we must first gain a better understanding of how salinity regulates decomposition in natural systems. This study sampled eight tidal wetlands ranging from freshwater to oligohaline (0-2 ppt) in four rivers near the Chesapeake Bay (Virginia). To help isolate salinity effects, sites were selected to be highly similar in terms of plant community composition and tidal influence. Overall, salinity was found to be strongly negatively correlated with soil organic matter content (OM%) and C : N, but unrelated to the other studied environmental parameters (pH, redox, and above- and below-ground plant biomass). Partial correlation analysis, controlling for these environmental covariates, supported direct effects of salinity on the activity of carbon-degrading extracellular enzymes (β-1, 4-glucosidase, 1, 4-β-cellobiosidase, β-D-xylosidase, and phenol oxidase) as well as alkaline phosphatase, using a per unit OM basis. As enzyme activity is the putative rate-limiting step in decomposition, enhanced activity due to salinity increases could dramatically affect soil OM accumulation. Salinity was also found to be positively related to bacterial abundance (qPCR of the 16S rRNA gene) and tightly linked with community composition (T-RFLP). Furthermore, strong relationships were found between bacterial abundance and/or composition with the activity of specific enzymes (1, 4-β-cellobiosidase, arylsulfatase, alkaline phosphatase, and phenol oxidase) suggesting salinity's impact on decomposition could be due, at least in part, to its effect on the bacterial community. Together, these results indicate that salinity increases microbial decomposition rates in low salinity wetlands, and suggests that these ecosystems may experience decreased soil OM accumulation, accretion, and carbon sequestration rates even with modest levels of saltwater intrusion.

Abstract. Environmental perturbations in wetlands affect the integrated plant-microbial-soil system, causing biogeochemical responses that can manifest at local to global scales. The objective of this study was to determine how saltwater intrusion affects carbon mineralization and greenhouse gas production in coastal wetlands. Working with tidal freshwater marsh soils that had experienced ∼ 3.5 yr of in situ saltwater additions, we quantified changes in soil properties, measured extracellular enzyme activity associated with organic matter breakdown, and determined potential rates of anaerobic carbon dioxide (CO 2 ) and methane (CH 4 ) production. Soils from the field plots treated with brackish water had lower carbon content and higher C : N ratios than soils from freshwater plots, indicating that saltwater intrusion reduced carbon availability and increased organic matter recalcitrance. This was reflected in reduced activities of enzymes associated with the hydrolysis of cellulose and the oxidation of lignin, leading to reduced rates of soil CO 2 and CH 4 production. The effects of long-term saltwater additions contrasted with the effects of short-term exposure to brackish water during three-day laboratory incubations, which increased rates of CO 2 production but lowered rates of CH 4 production. Collectively, our data suggest that the long-term effect of saltwater intrusion on soil CO 2 production is indirect, mediated through the effects of elevated salinity on the quantity and quality of autochthonous organic matter inputs to the soil. In contrast, salinity, organic matter content, and enzyme activities directly influence CH 4 production. Our analyses demonstrate that saltwater intrusion into tidal freshwater marshes affects the entire process of carbon mineralization, from the availability of organic carbon through its terminal metabolism to CO 2 and/or CH 4 , and illustrate that long-term shifts in biogeochemical functioning are not necessarily consistent with short-term disturbance-type responses.

Background: Environmental metagenomic analysis is typically accomplished by assigning taxonomy and/or function from whole genome sequencing or 16S amplicon sequences. Both of these approaches are limited, however, by read length, among other technical and biological factors. A nanopore-based sequencing platform, MinION™, produces reads that are ≥1 × 104 bp in length, potentially providing for more precise assignment, thereby alleviating some of the limitations inherent in determining metagenome composition from short reads. We tested the ability of sequence data produced by MinION (R7.3 flow cells) to correctly assign taxonomy in single bacterial species runs and in three types of low-complexity synthetic communities: a mixture of DNA using equal mass from four species, a community with one relatively rare (1%) and three abundant (33% each) components, and a mixture of genomic DNA from 20 bacterial strains of staggered representation. Taxonomic composition of the low-complexity communities was assessed by analyzing the MinION sequence data with three different bioinformatic approaches: Kraken, MG-RAST, and One Codex. Results: Long read sequences generated from libraries prepared from single strains using the version 5 kit and chemistry, run on the original MinION device, yielded as few as 224 to as many as 3497 bidirectional high-quality (2D) reads with an average overall study length of 6000 bp. For the single-strain analyses, assignment of reads to the correct genus by different methods ranged from 53.1% to 99.5%, assignment to the correct species ranged from 23.9% to 99.5%, and the majority of misassigned reads were to closely related organisms. A synthetic metagenome sequenced with the same setup yielded 714 high quality 2D reads of approximately 5500 bp that were up to 98% correctly assigned to the species level. Synthetic metagenome MinION libraries generated using version 6 kit and chemistry yielded from 899 to 3497 2D reads with lengths averaging 5700 bp with up to 98% assignment accuracy at the species level. The observed community proportions for “equal” and “rare” synthetic libraries were close to the known proportions, deviating from 0.1% to 10% across all tests. For a 20-species mock community with staggered contributions, a sequencing run detected all but 3 species (each included at <0.05% of DNA in the total mixture), 91% of reads were assigned to the correct species, 93% of reads were assigned to the correct genus, and >99% of reads were assigned to the correct family. Conclusions: At the current level of output and sequence quality (just under 4 × 103 2D reads for a synthetic metagenome), MinION sequencing followed by Kraken or One Codex analysis has the potential to provide rapid and accurate metagenomic analysis where the consortium is comprised of a limited number of taxa. Important considerations noted in this study included: high sensitivity of the MinION platform to the quality of input DNA, high variability of sequencing results across libraries and flow cells, and relatively smal...