Effects of plastispheres and pristine microplastics on sediment microbial communities and nitrogen cycling under global warming.

Mechanisms of hydrophilic and hydrophobic dissolved organic matter influencing nitrogen dynamics in sediments.

Hypoxia impacts sediment nitrogen (N) cycling, yet its effects remain poorly constrained and exhibit strong cross-system inconsistency. We investigate these mechanisms through observations and mass-balance analysis of the Pearl River Estuary region, a typical estuarine coastal system under diverse environmental regimes. Our results show that low-oxygen conditions in the bottom waters increased sediment ammonium efflux. Under well-oxygenated bottom waters, 75% of the ammonium released from organic matter was oxidized within the sediments, with the remaining 25% entering the water column. Under low-oxygen conditions, ammonium efflux increased to 55% of that from organic matter, and only 45% of remineralized ammonium was oxidized through nitrification. With reduced sediment nitrification under hypoxia, denitrification decreased, removing only 53% of remineralized organic N in sediments compared to 76% under high bottom-oxygen conditions. This is because denitrification depends heavily on nitrate supply by nitrification, while nitrate concentrations in bottom waters were too low to support adequate nitrate influx to the sediments. Using a mass-balance analysis, we further demonstrate that this mechanism operates in many coastal systems with low-to-moderate nitrate levels. Thus, bottom-water hypoxia likely enhances sediment N recycling and reduces N removal on a broader scale, creating amplifying feedback to eutrophication in coastal N-limiting systems.

Global warming and microplastics (MPs) pollution are emerging stressors that threaten coastal ecosystems, yet their combined impacts on biogeochemical cycles remain poorly resolved. Here, we integrated a factorial microcosm experiment with stable isotope tracing and molecular techniques to disentangle how warming and MPs jointly regulate nitrogen (N) cycling in coastal sediments. We demonstrate that warming and MPs interacted nonadditively to reshape nitrification, denitrification, and associated nitrous oxide (N2O) production dynamics. Warming reversed the stimulatory effect of polyethylene (PE) on nitrification, turning it inhibitory, and amplified the suppressive impact of poly(butylene adipate-co-terephthalate) (PBAT), primarily through synergistic intensification of anoxic stress. In contrast, warming strengthened PE-driven stimulation of denitrification and mitigated PBAT-induced inhibition, likely due to the selective enrichment of nirS- and nosZ-harboring denitrifiers. Moreover, warming overturned the stimulatory effects of both PE and PBAT on N2O production, shifting toward inhibition through nitrifier denitrification, as substantiated by dual-isotope (15N-18O) tracing and genomic evidence. Collectively, these findings provide novel mechanistic insights into how warming interacts with MPs to reconfigure sedimentary N cycling, with broad implications for predicting the responses and evolution of coastal ecosystems under accelerating global change.

Influence of algal deposition-decay on nitrification/denitrification in shallow eutrophic lakes: ecological interactions and mechanisms of nitrifiers and denitrifiers.

Salinity-driven shifts in potential ammonia oxidation rates and microbial community dynamics in estuarine mangrove sediments.

BackgroundStream hyporheic zones represent a unique ecosystem at the interface of stream water and surrounding sediments, characterized by high heterogeneity and accelerated biogeochemical activity. These zones—represented by the top sediment layer in this study—are increasingly impacted by anthropogenic stressors and environmental changes at a global scale, directly altering their microbiomes. Despite their importance, the current body of literature lacks a systematic understanding of active nitrogen and sulfur cycling across stream sediment and surface water microbiomes, particularly across geographic locations and in response to environmental factors.ResultsBased on previously published and unpublished datasets, 363 stream metagenomes were combined to build a comprehensive MAG and gene database from stream sediments and surface water including a full-factorial mesocosm experiment which had been deployed to unravel microbial stress response. Metatranscriptomic data from 23 hyporheic sediment samples collected across North America revealed that microbial activity in sediments was distinct from the activity in surface water, contrasting similarly encoded metabolic potential across the two compartments. The expressed energy metabolism of the hyporheic zone was characterized by increased cycling of sulfur and nitrogen compounds, governed by Nitrospirota and Desulfobacterota lineages. While core metabolic functions like energy conservation were conserved across sediments, temperature and stream order change resulted in differential expression of stress response genes previously observed in mesocosm studies.ConclusionsThe hyporheic zone is a microbial hotspot in stream ecosystems, surpassing the activity of overlaying riverine surface waters. Metabolic activity in the form of sulfur and nitrogen cycling in hyporheic sediments is governed by multiple taxa interacting through metabolic handoffs. Despite the spatial heterogeneity of streams, the hyporheic sediment microbiome encodes and expresses conserved stress responses to anthropogenic stressors, e.g., temperature, in streams of separate continents. The high number of uncharacterized differentially expressed genes as a response to tested stressors is a call-to-action to deepen the study of stream systems.Video Supplementary InformationThe online version contains supplementary material available at 10.1186/s40168-025-02236-1.

Microplastics modify the relationship between benthic animals and their environment and can alter ecosystem functioning in seafloor habitats. We experimentally investigated shifts in the functional roles of 2 large deposit feeders that influence biogeochemical processes in marine sediments, the tellinid bivalve Macomona liliana and the maldanid worm Macroclymenella stewartensis , as well as a combination of these 2 species. We measured the particle mixing capacity as a proxy for interactions between macrofauna and their environment when exposed to microplastics. Increasing microplastic concentrations (polypropylene, diameter of <500 µm) impaired the deep-burrowing behaviour of M. stewartensis . Particle mixing by M. liliana was not significantly affected by microplastics. Contamination levels of microplastics also modified the relationship between the 2 species. Our study shows that microplastics influence the process of macrofauna transporting particulate resources and regulating nutrient cycling. The degree to which microplastics influence benthic fluxes (oxygen and nitrogen) varies with the functional traits of the macrofaunal species and the concentrations of the microplastics.

Hydrilla-derived organic matter dominates sediment nitrogen mineralization in Poyang Lake.

Effect of Perfluorobutane Sulfonic Acid On Microbial Community and Functional Enzyme of Nitrogen Cycling in Coastal Sediment

Aging behaviors intensify the impacts of microplastics on nitrate bioreduction-driven nitrogen cycling in freshwater sediments.

Copper contamination determined the impact of phages on microbially-driven nitrogen cycling in coastal wetland sediments.

Microplastics affect organic nitrogen in sediment: The response of organic nitrogen mineralization to microbes and benthic animals.

Mangroves are one of the most productive marine ecosystems with high ecosystem service value. The sediment microbial communities contribute to pivotal ecological functions in mangrove ecosystems. However, the study of mangrove sediment microbiomes is limited. Here, we applied metagenome sequencing analysis of microbial communities in mangrove sediments across Southeast China from 2014 to 2020. This genome dataset includes 966 metagenome-assembled genomes with ≥50% completeness and ≤10% contamination generated from 6 groups of samples. Phylogenomic analysis and taxonomy classification show that mangrove sediments are inhabited by microbial communities with high species diversity. Thermoplasmatota, Thermoproteota, and Asgardarchaeota in archaea, as well as Proteobacteria, Desulfobacterota, Chloroflexota, Acidobacteriota, and Gemmatimonadota in bacteria, dominate the mangrove sediments across Southeast China. Functional analyses suggest that the microbial communities may contribute to carbon, nitrogen, and sulfur cycling in mangrove sediments. These combined microbial genomes provide an important complement of global mangrove genome datasets and may serve as a foundational resource for enhancing our understanding of the composition and functions of mangrove sediment microbiomes.

Microbially-driven phosphorus cycling and its coupling mechanisms with nitrogen cycling in mangrove sediments.

BackgroundThe ecosystems of marine ranching have enhanced marine biodiversity and ecological balance and have promoted the natural recovery and enhancement of fishery resources. The microbial communities of these ecosystems, including bacteria, fungi, protists, and viruses, are the drivers of biogeochemical cycles. Although seasonal changes in microbial communities are critical for ecosystem functioning, the current understanding of microbial-driven metabolic properties and their viral communities in marine sediments remains limited. Here, we employed amplicon (16S and 18S) and metagenomic approaches aiming to reveal the seasonal patterns of microbial communities, bacterial-eukaryotic interactions, whole metabolic potential, and their coupling mechanisms with carbon (C), nitrogen (N), and sulfur (S) cycling in marine ranching sediments. Additionally, the characterization and diversity of viral communities in different seasons were explored in marine ranching sediments.ResultsThe current study demonstrated that seasonal variations dramatically affected the diversity of microbial communities in marine ranching sediments and the bacterial-eukaryotic interkingdom co-occurrence networks. Metabolic reconstruction of the 113 medium to high-quality metagenome-assembled genomes (MAGs) was conducted, and a total of 8 MAGs involved in key metabolic genes and pathways (methane oxidation - denitrification - S oxidation), suggesting a possible coupling effect between the C, N, and S cycles. In total, 338 viral operational taxonomic units (vOTUs) were identified, all possessing specific ecological characteristics in different seasons and primarily belonging to Caudoviricetes, revealing their widespread distribution and variety in marine sediment ecosystems. In addition, predicted virus-host linkages showed that high host specificity was observed, with few viruses associated with specific hosts.ConclusionsThis finding deepens our knowledge of element cycling and viral diversity in fisheries enrichment ecosystems, providing insights into microbial-virus interactions in marine sediments and their effects on biogeochemical cycling. These findings have potential applications in marine ranching management and ecological conservation.DRyDF7ykR-XALqAtu34uZtVideo

Synergetic effects of chlorinated paraffins and microplastics on microbial communities and nitrogen cycling in deep-sea cold seep sediments

Unveiling microplastic's role in nitrogen cycling: Metagenomic insights from estuarine sediment microcosms

The Okinawa Trough (OT) is a back-arc basin with a wide distribution of active cold seep systems. However, our understanding of the metabolic function of microbial communities in the cold seep sediments of the OT remains limited. In this study, we investigated the vertical profiles of functional genes involved in methane, nitrogen, and sulphur cycling in the cold seep sediments of the OT. Furthermore, we explored the possible coupling mechanisms between these biogeochemical cycles. The study revealed that the majority of genes associated with the nitrogen and sulphur cycles were most abundant in the surface sediment layers. However, only the key genes responsible for sulphur disproportionation (sor), nitrogen fixation (nifDKH), and methane metabolism (mcrABG) were more prevalent within sulfate-methane transition zone (SMTZ). Significant positive correlations (P < 0.05) were observed between functional genes involved in sulphur oxidation, thiosulphate disproportionation with denitrification, and dissimilatory nitrate reduction to ammonium (DNRA), as well as between AOM/methanogenesis and nitrogen fixation, and between sulphur disproportionation and AOM. A genome of Filomicrobium (class Alphaproteobacteria) has demonstrated potential in chemoautotrophic activities, particularly in coupling DNRA and denitrification with sulphur oxidation. Additionally, the characterized sulfate reducers such as Syntrophobacterales have been found to be capable of utilizing nitrate as an electron acceptor. The predominant methanogenic/methanotrophic groups in the OT sediments were identified as H2-dependent methylotrophic methanogens (Methanomassiliicoccales and Methanofastidiosales) and ANME-1a. This study offered a thorough understanding of microbial ecosystems in the OT cold seep sediments, emphasizing their contribution to nutrient cycling.IMPORTANCEThe Okinawa Trough (OT) is a back-arc basin formed by extension within the continental lithosphere behind the Ryukyu Trench arc system. Cold seeps are widespread in the OT. While some studies have explored microbial communities in OT cold seep sediments, their metabolic potential remains largely unknown. In this study, we used metagenomic analysis to enhance comprehension of the microbial community's role in nutrient cycling and proposed hypotheses on the coupling process and mechanisms involved in biogeochemical cycles. It was revealed that multiple metabolic pathways can be performed by a single organism or microbes that interact with each other to carry out various biogeochemical cycling. This data set provided a genomic road map on microbial nutrient cycling in OT sediment microbial communities.

The urgent need to reduce phosphorus discharges for sustainable mangrove wetland management