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ABSTRACT Microbial communities play a fundamental role in biogeochemical cycling within salt and brackish marsh ecosystems, yet fungal‐prokaryotic interactions in these environments remain poorly understood. This study employed metabarcoding of the 16S and 28S rRNA genes to investigate prokaryotic and fungal communities across four locations in sediments and surface waters of the North Inlet salt marsh and Winyah Bay brackish marsh (South Carolina, USA) over four time points from 2020 to 2021. Co‐occurrence network analyses were used to identify potential microbial interactions and their ecological implications. Distinct fungal and prokaryotic communities were observed between the two marsh types. From the 16S prokaryotic primer set, Proteobacteria, Bacteroidota, and Cyanobacteriota dominated both marshes. Early diverging fungi and Actinomycetota (bacteria) were prevalent in the brackish marsh, whereas salt marsh communities were primarily composed of Dikarya fungi (Ascomycota and Basidiomycota) and Desulfobacteria. Network analyses revealed contrasting interactions between surface water and sediment. In brackish marsh sediments, fungi and prokaryotes exhibited nearly exclusively negative connections, suggesting strong resource competition. In contrast, Dikarya fungi in brackish marsh surface water displayed numerous positive connections with bacteria, suggesting potential cross‐feeding interactions. In the salt marsh, fungi and prokaryotes exhibited potential cooperative and competitive/antagonistic interactions. Ascomycota were positively connected with Desulfobacteria, suggesting a role in complex organic matter degradation. Conversely, negative connections between Chytridiomycota (early diverging fungi) and Cyanobacteriota (bacteria) implied parasitic interactions. These findings highlight the dynamic nature of fungal‐prokaryotic interactions in coastal ecosystems. By analyzing potential microbial relationships in salt and brackish marshes, this study provides new insights into the ecological roles of fungi in estuarine environments, particularly their contributions to nutrient cycling and organic matter decomposition. Understanding these interactions is crucial for generating hypotheses and predicting microbial responses to environmental changes—such as shifts in salinity and nutrient availability—and their potential impacts on marsh ecosystem functioning. 

Abstract Marine microorganisms are drivers of biogeochemical cycles in the world’s oceans, including oxygen minimum zones (OMZs). Using a metabarcoding survey of the 16S rRNA gene, we investigated prokaryotic communities, as well as their potential interactions with fungi, at the coastal, offshore, and peripheral OMZ of the eastern tropical North Pacific. Water samples were collected along a vertical oxygen gradient, and large volumes were filtered through three size fractions, 0.22, 2, and 22 µm. The changes in community composition along the oxygen gradient were driven by Planctomycetota, Bacteroidota, Verrucomicrobiota, and Gammaproteobacteria; most are known degraders of marine polysaccharides and usually associated with the large particle-associated (LPA) community. The relative abundance of Nitrososphaerota, Alphaproteobacteria, Actinomycetota, and Nitrospinota was high in free-living and small particle-associated (SPA) communities. Network analyses identified putative interactions between fungi and prokaryotes in the particle-associated fractions, which have been largely overlooked in the ocean. In the SPAnetwork analysis, fungal amplicon sequence variants (ASVs) had exclusively negative connections with SAR11 nodes. In the LPA network analysis, fungal ASVs displayed both negative and positive connections with Pseudomonadota, SAR324, and Thermoplasmatota. Our findings demonstrate the utility of three-stage size-fractioned filtration in providing novel insights into marine microbial ecology. 

Abstract. Despite long-standing interest in the biogeochemistry of the Santa Barbara Basin (SBB), there are no direct rate measurements of different nitrogen transformation processes. We investigated benthic nitrogen cycling using in situ incubations with 15NO3- addition and quantified the rates of total nitrate (NO3-) uptake, denitrification, anaerobic ammonia oxidation (anammox), N2O production, and dissimilatory nitrate reduction to ammonia (DNRA). Denitrification was the dominant NO3- reduction process, while anammox contributed 0 %–27 % to total NO3- reduction. DNRA accounted for less than half of NO3- reduction except at the deepest station at the center of the SBB where NO3- concentration was lowest. NO3- availability and sediment total organic carbon content appeared to be two key controls on the relative importance of DNRA. The increasing importance of fixed N retention via DNRA relative to fixed N loss as NO3- deficit intensifies suggests a negative feedback loop that potentially contributes to stabilizing the fixed N budget in the SBB. Nitrous oxide (N2O) production as a fraction of total NO3- reduction ranged from 0.2 % to 1.5 %, which was higher than previous reports from nearby borderland basins. A large fraction of NO3- uptake was unaccounted for by NO3- reduction processes, suggesting that intracellular storage may play an important role. Our results indicate that the SBB acts as a strong sink for fixed nitrogen and potentially a net source of N2O to the water column. 

ABSTRACT Marine macroalgae produce abundant and diverse polysaccharides, which contribute substantially to the organic matter exported to the deep ocean. Microbial degradation of these polysaccharides plays an important role in the turnover of macroalgal biomass. Various members of thePlanctomycetes-Verrucomicrobia-Chlamydia(PVC) superphylum are degraders of polysaccharides in widespread anoxic environments. In this study, we isolated a novel anaerobic bacterial strain NLcol2^Tfrom microbial mats on the surface of marine sediments offshore Santa Barbara, CA, USA. Based on 16S ribosomal RNA (rRNA) gene and phylogenomic analyses, strain NLcol2^Trepresents a novel species within thePontiellagenus in theKiritimatiellotaphylum (within the PVC superphylum). Strain NLcol2^Tis able to utilize various monosaccharides, disaccharides, and macroalgal polysaccharides such as agar and ɩ-carrageenan. A near-complete genome also revealed an extensive metabolic capacity for anaerobic degradation of sulfated polysaccharides, as evidenced by 202 carbohydrate-active enzymes (CAZymes) and 165 sulfatases. Additionally, its ability of nitrogen fixation was confirmed by nitrogenase activity detected during growth on nitrogen-free medium, and the presence of nitrogenases (nifDKH) encoded in the genome. Based on the physiological and genomic analyses, this strain represents a new species of bacteria that may play an important role in the degradation of macroalgal polysaccharides and with relevance to the biogeochemical cycling of carbon, sulfur, and nitrogen in marine environments. Strain NLcol2^T(= DSM 113125^T= MCCC 1K08672^T) is proposed to be the type strain of a novel species in thePontiellagenus, and the namePontiella agarivoranssp. nov. is proposed.IMPORTANCEGrowth and intentional burial of marine macroalgae is being considered as a carbon dioxide reduction strategy but elicits concerns as to the fate and impacts of this macroalgal carbon in the ocean. Diverse heterotrophic microbial communities in the ocean specialize in these complex polymers such as carrageenan and fucoidan, for example, members of theKiritimatiellotaphylum. However, only four type strains within the phylum have been cultivated and characterized to date, and there is limited knowledge about the metabolic capabilities and functional roles of related organisms in the environment. The new isolate strain NLcol2^Texpands the known substrate range of this phylum and further reveals the ability to fix nitrogen during anaerobic growth on macroalgal polysaccharides, thereby informing the issue of macroalgal carbon disposal. 

Abstract. The Santa Barbara Basin naturally experiences transient deoxygenation due to its unique geological setting in the southern California Borderland and seasonal changes in ocean currents. Long-term measurements of the basin showed that anoxic events and subsequent nitrate exhaustion in the bottom waters have been occurring more frequently and lasting longer over the past decade. One characteristic of the Santa Barbara Basin is the seasonal development of extensive mats of benthic nitrate-reducing sulfur-oxidizing bacteria, which are found at the sediment–water interface when the basin's bottom waters reach anoxia but still provide some nitrate. To assess the mat's impact on the benthic and pelagic redox environment, we collected biogeochemical sediment and benthic flux data in November 2019, after anoxia developed in the deepest waters of the basin and dissolved nitrate was depleted (down to 9.9 µM). We found that the development of mats was associated with a shift from denitrification to dissimilatory nitrate reduction to ammonium. The zone of sulfate reduction appeared near the sediment–water interface in sediment hosting these ephemeral white mats. We found that an exhaustion of iron oxides in the surface sediment was an additional prerequisite for mat proliferation. Our research further suggests that cycles of deoxygenation and reoxygenation of the benthic environment result in extremely high benthic fluxes of dissolved iron from the basin's sediment. This work expands our understanding of nitrate-reducing sulfur-oxidizing mats and their role in sustaining and potentially expanding marine anoxia. 

Fungi in terrestrial environments are known to play a key role in carbon and nitrogen biogeochemistry and exhibit high diversity. In contrast, the diversity and function of fungi in the ocean has remained underexplored and largely neglected. In the eastern tropical North Pacific oxygen minimum zone, we examined the fungal diversity by sequencing the internal transcribed spacer region 2 (ITS2) and mining a metagenome dataset collected from the same region. Additionally, we coupled 15N-tracer experiments with a selective inhibition method to determine the potential contribution of marine fungi to nitrous oxide (N2O) production. Fungal communities evaluated by ITS2 sequencing were dominated by the phyla Basidiomycota and Ascomycota at most depths. However, the metagenome dataset showed that about one third of the fungal community belong to early-diverging phyla. Fungal N2O production rates peaked at the oxic–anoxic interface of the water column, and when integrated from the oxycline to the top of the anoxic depths, fungi accounted for 18–22% of total N2O production. Our findings highlight the limitation of ITS-based methods typically used to investigate terrestrial fungal diversity and indicate that fungi may play an active role in marine nitrogen cycling. 

Abstract. As a key biogeochemical pathway in the marine nitrogen cycle, nitrification (ammonia oxidation and nitrite oxidation) converts the most reduced form of nitrogen – ammonium–ammonia (NH4+–NH3) – into the oxidized species nitrite (NO2-) and nitrate (NO3-). In the ocean, these processes are mainly performed by ammonia-oxidizing archaea (AOA) and bacteria (AOB) and nitrite-oxidizing bacteria (NOB). By transforming nitrogen speciation and providing substrates for nitrogen removal, nitrification affects microbial community structure; marine productivity (including chemoautotrophic carbon fixation); and the production of a powerful greenhouse gas, nitrous oxide (N2O). Nitrification is hypothesized to be regulated by temperature, oxygen, light, substrate concentration, substrate flux, pH and other environmental factors. Although the number of field observations from various oceanic regions has increased considerably over the last few decades, a global synthesis is lacking, and understanding how environmental factors control nitrification remains elusive. Therefore, we have compiled a database of nitrification rates and nitrifier abundance in the global ocean from published literature and unpublished datasets. This database includes 2393 and 1006 measurements of ammonia oxidation and nitrite oxidation rates and 2242 and 631 quantifications of ammonia oxidizers and nitrite oxidizers, respectively. This community effort confirms and enhances our understanding of the spatial distribution of nitrification and nitrifiers and their corresponding drivers such as the important role of substrate concentration in controlling nitrification rates and nitrifier abundance. Some conundrums are also revealed, including the inconsistent observations of light limitation and high rates of nitrite oxidation reported from anoxic waters. This database can be used to constrain the distribution of marine nitrification, to evaluate and improve biogeochemical models of nitrification, and to quantify the impact of nitrification on ecosystem functions like marine productivity and N2O production. This database additionally sets a baseline for comparison with future observations and guides future exploration (e.g., measurements in the poorly sampled regions such as the Indian Ocean and method comparison and/or standardization). The database is publicly available at the Zenodo repository: https://doi.org/10.5281/zenodo.8355912 (Tang et al., 2023). 

Abstract Changes in the sequence of an organism’s genome, i.e., mutations, are the raw material of evolution. The frequency and location of mutations can be constrained by specific molecular mechanisms, such as diversity-generating retroelements (DGRs). DGRs have been characterized from cultivated bacteria and bacteriophages, and perform error-prone reverse transcription leading to mutations being introduced in specific target genes. DGR loci were also identified in several metagenomes, but the ecological roles and evolutionary drivers of these DGRs remain poorly understood. Here, we analyze a dataset of >30,000 DGRs from public metagenomes, establish six major lineages of DGRs including three primarily encoded by phages and seemingly used to diversify host attachment proteins, and demonstrate that DGRs are broadly active and responsible for >10% of all amino acid changes in some organisms. Overall, these results highlight the constraints under which DGRs evolve, and elucidate several distinct roles these elements play in natural communities.