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ABSTRACT Anaerolineae, particularly uncultured representatives, are one of the most abundant microbial groups in coastal salt marshes, dominating the belowground rhizosphere, where over half of plant biomass production occurs. However, this class generally remains poorly understood, particularly in a salt marsh context. Here, novelAnaerolineaemetagenome-assembled genomes (MAGs) were generated from the salt marsh rhizosphere representingAnaerolineales,Promineifilales, JAAYZQ01, B4-G1, JAFGEY01, UCB3, andCaldilinealesorders. Metagenome and metatranscriptome reads were mapped to annotated MAGs, revealing nearly allAnaerolineaeencoded and transcribed genes required for oxidation of carbon compounds ranging from simple sugars to complex polysaccharides, fermentation, and carbon fixation. Furthermore, the majority ofAnaerolineaeexpressed genes involved in anaerobic and aerobic respiration and secondary metabolite production. The data revealed that the belowground salt marshAnaerolineaein the rhizosphere are important players in carbon cycling, including degradation of simple carbon compounds and more recalcitrant plant material, such as cellulose, using a diversity of electron acceptors and represent an unexplored reservoir of novel secondary metabolites.IMPORTANCEGiven that coastal salt marshes are recognized as biogeochemical hotspots, it is fundamentally important to understand the functional role of the microbiome in this ecosystem. In particular,Anaerolineaeare abundant members of the salt marsh rhizosphere and have been identified as core microbes, suggesting they play an important functional role. Yet, little is known about the metabolic pathways encoded and expressed in this abundant salt marsh clade. Using an ‘omics-based approach, we determined thatAnaerolineaeare capable of oxidizing a range of carbon compounds, including simple sugars to complex carbon compounds, while also encoding fermentation and carbon fixation. Surprisingly,Anaerolineaeencoded and transcribed genes involved in aerobic respiration, which was unexpected given the reduced nature of the salt marsh rhizosphere. Finally, the majority ofAnaerolineaeappear to be involved in secondary metabolite production, suggesting that this group represents an unexplored reservoir of novel and important secondary metabolites. 

Abstract Plants have evolved numerous strategies for surviving the harsh conditions of the Arctic. One strategy for Arctic evergreen and semi‐evergreen species is to photosynthesize beneath the snow during spring. However, the prevalence of this photosynthesis and how recent photosynthates are used is still unknown. Here we ask,how is newly acquired carbon beneath the snow allocated?To answer this question, we delivered isotopically labeled¹³CO₂to tussock tundra plants before snowmelt. Soluble sugars and starches were preferentially enriched with¹³C in all five species tested, with lipids having comparatively low¹³C enrichment. These results provide evidence of the recovery of metabolites used over the long winter. Additionally, these new soluble sugars may function in photoprotection and cold tolerance as plants release from snow cover. Climate change, by reducing the duration of subnivean photosynthesis of these species, will limit metabolite production before snowmelt, which may lead to a reduction in the ability of these species to compete effectively during the growing season, potentially leading to changes in community structure. 

ABSTRACT Sulfur-cycling microbial communities in salt marsh rhizosphere sediments mediate a recycling and detoxification system central to plant productivity. Despite the importance of sulfur-cycling microbes, their biogeographic, phylogenetic, and functional diversity remain poorly understood. Here, we use metagenomic data sets from Massachusetts (MA) and Alabama (AL) salt marshes to examine the distribution and genomic diversity of sulfur-cycling plant-associated microbes. Samples were collected from sediments underSporobolus alterniflorusandSporobolus pumilusin separate MA vegetation zones, and underS. alterniflorusandJuncus roemerianusco-occuring in AL. We grouped metagenomic data by plant species and site and identified 38 MAGs that included pathways for sulfate reduction or sulfur oxidation. Phylogenetic analyses indicated that 29 of the 38 were affiliated with uncultivated lineages. We showed differentiation in the distribution of MAGs between AL and MA, betweenS. alterniflorusandS. pumilusvegetation zones in MA, but no differentiation betweenS. alterniflorusandJ. roemerianusin AL. Pangenomic analyses of eight ubiquitous MAGs also detected site- and vegetation-specific genomic features, including varied sulfur-cycling operons, carbon fixation pathways, fixed single-nucleotide variants, and active diversity-generating retroelements. This genetic diversity, detected at multiple scales, suggests evolutionary relationships affected by distance and local environment, and demonstrates differential microbial capacities for sulfur and carbon cycling in salt marsh sediments. IMPORTANCESalt marshes are known for their significant carbon storage capacity, and sulfur cycling is closely linked with the ecosystem-scale carbon cycling in these ecosystems. Sulfate reducers are key for the decomposition of organic matter, and sulfur oxidizers remove toxic sulfide, supporting the productivity of marsh plants. To date, the complexity of coastal environments, heterogeneity of the rhizosphere, high microbial diversity, and uncultured majority hindered our understanding of the genomic diversity of sulfur-cycling microbes in salt marshes. Here, we use comparative genomics to overcome these challenges and provide an in-depth characterization of sulfur-cycling microbial diversity in salt marshes. We characterize communities across distinct sites and plant species and uncover extensive genomic diversity at the taxon level and specific genomic features present in MAGs affiliated with uncultivated sulfur-cycling lineages. Our work provides insights into the partnerships in salt marshes and a roadmap for multiscale analyses of diversity in complex biological systems. 

Quantifying and characterizing groundwater flow and discharge from barrier islands to coastal waters is crucial for assessing freshwater resources and contaminant transport to the ocean. In this study, we examined the groundwater hydrological response, discharge, and associated nutrient fluxes in Dauphin Island, a barrier island located in the northeastern Gulf of Mexico. We employed radon ( 222 Rn) and radium (Ra) isotopes as tracers to evaluate the temporal and spatial variability of fresh and recirculated submarine groundwater discharge (SGD) in the nearshore waters. The results from a 40-day continuous 222 Rn time series conducted during a rainy season suggest that the coastal area surrounding Dauphin Island was river-dominated in the days after storm events. Groundwater response was detected about 1 week after the precipitation and peak river discharge. During the period when SGD was a factor in the nutrient budget of the coastal area, the total SGD rates were as high as 1.36 m day –1 , or almost three times higher than detected fluxes during the river-dominated period. We found from a three-endmember Ra mixing model that most of the SGD from the barrier island was composed of fresh groundwater. SGD was driven by marine and terrestrial forces, and focused on the southeastern part of the island. We observed spatial variability of nutrients in the subterranean estuary across this part of the island. Reduced nitrogen (i.e., NH 4 + and dissolved organic nitrogen) fluxes dominated the eastern shore with average rates of 4.88 and 5.20 mmol m –2 day –1 , respectively. In contrast, NO 3 – was prevalent along the south-central shore, which has significant tourism developments. The contrasting nutrient dynamics resulted in N- and P-limited coastal water in the different parts of the island. This study emphasizes the importance of understanding groundwater flow and dynamics in barrier islands, particularly those urbanized, prone to storm events, or located near large estuaries. 

Summary Marine oil spills are catastrophic events that cause massive damage to ecosystems at all trophic levels. While most of the research has focused on carbon‐degrading microorganisms, the potential impacts of hydrocarbons on microbes responsible for nitrification have received far less attention. Nitrifiers are sensitive to hydrocarbon toxicity: ammonia‐oxidizing bacteria and archaea being 100 and 1000 times more sensitive than typical heterotrophs respectively. Field studies have demonstrated the response of nitrifiers to hydrocarbons is highly variable and the loss of nitrification activity in coastal ecosystems can be restored within 1–2 years, which is much shorter than the typical recovery time of whole ecosystems (e.g., up to 20 years). Since the denitrification process is mainly driven by heterotrophs, which are more resistant to hydrocarbon toxicity than nitrifiers, the inhibition of nitrification may slow down the nitrogen turnover and increase ammonia availability, which supports the growth of oil‐degrading heterotrophs and possibly various phototrophs. A better understanding of the ecological response of nitrification is paramount in predicting impacts of oil spills on the nitrogen cycle under oil spill conditions, and in improving current bioremediation practices.