Impacts of antiscalants used for seawater desalination on benthic bacteria, seagrass and their microbial epiphytes.

Artificial reef age reshapes benthic microbial communities and modulates the genetic potential for nitrogen and sulfur cycling.

Abstract. This study examines the sedimentary and microbial responses offshore the Marche Region (Italy) to the September 2022 flood, one of the most severe recent hydrological events, which delivered large amounts of sediment and anthropogenic contaminants to the Adriatic Sea. We employed a multidisciplinary approach integrating sedimentology, geochemistry, organic matter analysis, pollutant assessments (Polycyclic Aromatic Hydrocarbons, PAHs and Poly- and Perfluorinated alkyl substances, PFASs), and benthic microbial community structure. Sediments collected just five days after the event offshore river mouths reveal that flood deposits, ranging from fine sand to coarse silt, remained substantially confined to the nearshore zone, whereas finer clay particles were dispersed further offshore and down to the 15 m isobath. This distribution reflects intense riverine inputs and a brief windstorm-enhanced coastal circulation that generated patchy, temporary sediment accumulations mainly in the prodelta sector. Simultaneously, the flood forced a strong spatial heterogeneity in benthic bacterial communities, through the introduction of short-distance shifts in sediment texture and organic matter content. Freshwater taxa became prominent in prodelta deposits, highlighting riverine sedimentary imprints. Heavy metal concentrations remained below regulatory thresholds, whereas organic pollutants, heterogeneously distributed, reach peak concentrations offshore urban and industrial zones. PAH signatures indicate mixed pyrogenic and petrogenic sources, while next-generation PFASs (6:2 FTS) showed localized but severe contamination linked to upstream industrial activities. Despite the flood's magnitude onshore, its offshore sedimentary signatures resulted ephemeral and spatially limited. These findings underscore the ecological significance of episodic sediment and contaminant input, while highlighting the challenges in detecting such transient events in the marine stratigraphic record.

Introduction Coral reef resilience is strongly influenced by microbial communities associated with diverse benthic substrates. However, microbiomes beyond corals remain poorly characterized in the Indian Ocean. This study provides the first cross-substrate microbial baseline from Palk Bay, southeast India. Methods We used 16S rRNA gene amplicon sequencing to characterize bacterial communities associated with corals, crustose coralline algae (CCA), rubble, sediments, and seawater. Alpha and beta diversity metrics, taxonomic composition, and genus-level co-occurrence network analyses were performed to compare microbial assemblages across substrates. Results Bacterial alpha diversity was broadly similar among substrates, whereas beta diversity showed strong compositional segregation (PERMANOVA, Bray–Curtis: F = 5.35, R² = 0.742, p = 0.001). Each substrate harbored distinct microbial assemblages. Corals displayed host-linked signatures (e.g., Favia enriched in Ruegeria ), sediments were dominated by Woeseia and Desulfovibrio , seawater by pelagic taxa ( Pelagibacterales , Synechococcus ), and CCA by Rhodobacteraceae members ( Roseospira , Labrenzia , Ruegeria ). CCA-associated Rhodobacteraceae , known to produce larval settlement inducers, suggest a potential role in coral recruitment. Environmental substrates, particularly sediment and rubble, contained the highest number of unique genera, indicating their function as microbial reservoirs. Only a few generalist taxa, notably Pelagibius , were shared across all substrates. Network analysis identified CCA as a highly connected node within the benthic microbial community. Discussion These findings demonstrate that reef microbial communities are strongly substrate-specific rather than defined by a conserved core microbiome. The results establish a regional microbial baseline for Indian reefs and highlight the ecological significance of CCA-associated microbial assemblages in supporting reef resilience and potential coral recruitment processes.

Urbanization reshapes planktonic and benthic microbial communities and networks along a river continuum

Microorganisms, as the foundation of deep-sea ecosystems, are crucial for maintaining the structure and stability of polymetallic nodule field environments. To investigate the community structure and distributional patterns of benthic microorganisms in such environments, this study used high-throughput sequencing to analyze the composition, diversity, and environmental correlations of bacteria, archaea, and fungi in the BPC (Beijing Pioneer Hi-tech Development Corporation Ltd., Beijing, China). Furthermore, microbial communities from BPC were compared with those from UK-1 (UK Seabed Resources, Southampton, UK) in terms of community structure and co-occurrence network characteristics. The results revealed that in the BPC, the bacterial communities were dominated by Proteobacteria and Chloroflexi, while Crenarchaeota represented the overwhelmingly dominant group. Fungal communities were primarily composed of Ascomycota and Basidiomycota. Correlation Analysis suggested that water depth, TOC (Total organic carbon), TN (Total nitrogen), and δ15N emerged as the key environmental drivers of microbial community variation. Comparative analysis showed microbial groups exhibited certain similarities but also some differences at the phylum, class, and order levels, with the differences becoming increasingly pronounced at finer taxonomic resolutions between BPC and UK-1. Co-occurrence network analyses indicated the microbial networks with higher density and node connectivity in the BPC, whereas the UK-1 exhibited greater modularity and clustering coefficients. Microbial interactions were weaker in the UK-1, but its resilience to benthic disturbance was expected to be higher than in the BPC.

Response of microbial communities in sediments from marine artificial and natural habitats to seasonal variations.

Hydro-environmental and ecological effects of drop structure in urban river system

Microbial communities and environmental conditions are closely linked to ecosystem functions and directly govern the biodegradation of pollutants in aquatic environments. However, the role of multi-trophic interactions and their spatiotemporal dynamics in these processes remains poorly understood. Here, we examined how seasonal and spatial variations, mediated by trophic interactions within benthic microbial communities, influence their composition, functional capacity, and collective potential to degrade a diverse array of organic pollutants in rivers. By characterizing both prokaryotic (i.e. archaea and bacteria) and eukaryotic taxa (i.e. algae, fungi, protists, and metazoans), and inferring metabolic pathways, we explored the connections between community composition and pollutant degradation in wastewater-receiving rivers across four seasons. Mediation analysis revealed that variation in multi-trophic community structure statistically mediates the total effect of environmental factors on the biodegradation profiles of 96 organic pollutants, with prokaryotic communities explaining 60% of the total environmental influence. Eukaryotic groups also showed significant indirect mediation effects, with fungal, protistan, algal, and metazoan communities accounting for 56%, 53%, 26%, and 38% of the mediated effect, respectively. Across the two rivers studied, spatial variation explained more of the variance in community composition than seasonality did over the sampled year. Together, these results provide ecosystem-level insights into how multi-trophic microbial community organization is associated with pollutant biodegradation potential in dynamic river environments and support the development of predictive frameworks for sustainable water management.

Organic carbon and metal concentrations shape surficial benthic microbial communities in Arctic fjords.

The end of a winding path: The anaerobic ciliate Spirorhynchus is a member of the class Muranotrichea.

Biological systems face multiple stressors that impact biodiversity and ecosystem functions, with complex interactions that vary spatially and temporally leading to unpredictable outcomes. In freshwater ecosystems, benthic microbial communities underpin vital functions like decomposition and primary productivity, but are threatened by stressors such as salinization and nutrient enrichment, which are intensifying and increasingly co‐occurring due to climate change. We experimentally tested how stressor repetition and different orders of stressor exposure affect freshwater benthic microbial community responses over time. Communities established on tiles in 1000 L open freshwater ponds established more than 10 years ago in the field were exposed to elevated salinity and nutrient enrichment, either once or repeatedly, independently or in combination, and under different orders. Repeated exposure to nutrient enrichment led to stronger functional changes than the single exposure, while repeated exposure to elevated salinity resulted in weaker changes compared to a single exposure. Critically, we found that the sequence in which stressors occurred was a major determinant of microbial responses, driving interaction outcomes in opposing directions. When exposure to nutrient enrichment preceded elevated salinity, gross primary productivity was halved and carbon metabolic rates increased by 50% compared to communities treated in the reverse order. This study is among the first in a complex, outdoor freshwater system to demonstrate that stressor sequence can strongly shape multiple stressor effects, highlighting the order of stressor exposure as a key but often overlooked dimension of global change ecology. These findings suggest that microbial functions, including productivity and carbon cycling, will fluctuate more dramatically as stressors increasingly occur in different sequences under global change.

Deep-sea polymetallic nodule provinces harbor rich benthic microbial communities that underpin biogeochemical cycles and sustain abyssal ecosystem functions. Recent studies have begun to map their abundance, diversity and community structure, emphasizing the role of environmental gradients and spatial heterogeneity. Yet the spatiotemporal dynamics and assembly mechanisms of these microbes remain largely unresolved. Mining-induced sediment plumes further complicate the picture: they modify microbial biomass, activity and composition, but the trajectories of community succession and the functional consequences of disturbance are still unclear. Thresholds used to gauge plume impacts also differ markedly among studies, hampering consistent risk assessments. In summary, a stark contrast exists between the limited in situ observational data, the widely varying impact thresholds reported across studies, and the pressing need for unified standards in environmental impact assessments for deep-sea mining. It recommends future work that integrates multi-omics, time-series in situ monitoring, cross-regional comparisons and standardized evaluation frameworks to refine microbial indicators and ecological thresholds for deep-sea mining impact assessments.

Glyphosate, the active ingredient in many broad-spectrum herbicides, is extensively used in agriculture but has come under increasing scrutiny due to its potential impacts on non-target microbial communities. To investigate these effects within a controlled yet ecologically relevant framework, Winogradsky columns, self-contained sediment-based ecosystems, were employed as a model system. A novel, non-destructive sampling approach was introduced using macroporous elastomeric silicone foam (MESIF) integrated in stainless-steel frames to enable spatiotemporal monitoring of benthic microbial communities. These MESIF-loaded frames were vertically embedded in columns filled with lake sediment and subjected to varying experimental conditions, including light exposure and glyphosate treatment. Microbial colonization of the MESIF was assessed via amplicon sequencing at defined time points. Glyphosate-treated columns exhibited delayed microbial stratification and diminished development of characteristic pigmentation associated with functional groups such as iron-oxidizing and sulfate-reducing bacteria. Although within-column alpha diversity remained relatively constant, glyphosate exposure led to distinct shifts in community composition, including an increased abundance of taxa potentially involved in glyphosate degradation. These findings demonstrate the effectiveness of combining Winogradsky columns with MESIF-based sampling for studying environmental stressors and underscore glyphosate's influence on microbial succession and functional diversity in sediment ecosystems.

ABSTRACTMicrobial communities play a crucial role in the functioning of freshwater ecosystems but are continuously threatened by climate change and anthropogenic activities. Elevated temperatures and salinisation are particularly challenging for freshwater habitats, but little is known about how microbial communities respond to the simultaneous exposure to these stressors. Here, we use mesocosm experiments and amplicon sequencing data to investigate the responses of pelagic and benthic microbial communities to temperature and salinity increases, both individually and in combination. Our results highlight the varying responses of freshwater microbial communities, with sediment communities exhibiting greater stability in response to environmental changes compared to water column communities, and salinisation having a more pronounced impact on microeukaryotes compared to prokaryotes. Simultaneous exposure to elevated temperature and salinity reduced the impact of salinisation on prokaryotes, while microeukaryotes were similarly affected by the combined treatments and salinisation alone. These findings emphasise the complexity of microbial responses to single and multiple stressors, underscoring the need to consider both individual and interactive effects when predicting ecosystem responses to environmental changes.

Wastewater treatment plant (WWTP) effluent can be a point source of pharmaceuticals and personal care products (PPCPs) to surface waters, and these biologically active compounds have the potential to select for resistant traits and taxa within aquatic microbial communities. The goals of this study were to determine if WWTP effluent is a point source of PPCPs to urban streams; to determine if effluent inputs affect benthic microbial community composition; and to determine if effluent inputs increase the abundance of antibiotic resistance determinants within benthic microbial communities. We collected water and sediment from three streams in the Chicago metro area: two urban streams that receive WWTP effluent and one rural stream that does not receive effluent. We quantified concentrations of a suite of 45 common PPCPs in water samples from each stream, including sites upstream and downstream of effluent inputs to the urban streams, analyzed benthic bacterial community composition, and quantified the abundance of intI1, a gene linked to antibiotic resistance. A stream receiving 80% of its flow from effluent showed higher concentrations of ten PPCPs, including several antibiotics, downstream of the effluent input, as well as decreased abundance of photosynthetic organisms and shifts in bacterial community composition, implicating effluent as the driver of these changes. We did not observe differences between upstream and downstream sites in a stream receiving only 13% of its flow from effluent. The intI1 gene did not differ in abundance within streams in response to effluent input, but intI1 abundance and PPCP concentrations were higher in the urban streams than in the rural stream. These results indicate that watershed-scale anthropogenic impacts were the driver of intI1 abundance and that non-point sources contributed to PPCP pollution.

Abstract High hydrostatic pressure is characteristic of the deep ocean and is presumed to influence microbial functions and viability. However, marine microbial processes are typically measured only at atmospheric pressure (0.1 MPa), limiting our understanding of pressure effects on the activities of microbes that sink as part of the biological carbon pump, as well as those that reside in the deep ocean. To test pressure effects on microbial functions, we measured extracellular enzymatic activities—the first step in organic matter remineralization—of a moderate piezophile ( Photobacterium profundum SS9), as well as of microbial communities in waters and sediments from shallow to abyssal (5500 m) depths and their cell‐free enzymes (< 0.2 μ m). Activities were measured at 0.1–100 MPa to assess the pressure effects across the nearly full range of oceanic depths. Photobacterium profundum SS9 enzymes show varying pressure effects, from considerable stimulation at optimal pressure (28 MPa) to near complete inhibition (100 MPa). Pressure effects were measured for diverse protein‐ and carbohydrate‐degrading and phosphorus‐acquiring enzymes among pelagic and benthic microbial communities. The most common pressure effect was partial activity inhibition, indicating a dampening of the initial step of carbon remineralization at increasing pressures. However, the retention of cell‐free enzymatic activities at higher pressures was occasionally observed even for enzymes from surface‐originating assemblages, indicating functionality down to hadal depths and their potential for piezotolerance. These variable pressure effects must be considered when quantifying degradation rates of sinking and deposited particulate matter at increasing pressures in the deep ocean.

Pipeline misconnections in separated sewer systems worsen urban river ecological status through stormwater discharge.

Benthic microbial communities are a vital component of coastal subtidal zones, playing an essential role in nutrient cycling and energy flow, and are fundamental to maintaining the stability and functioning of marine ecosystems. However, the response of benthic prokaryotic and eukaryotic microbial communities to environmental changes remains poorly understood. Herein, we conducted a nearly semimonthly annual sampling survey to investigate the temporal patterns and underlying mechanisms of benthic prokaryotic and eukaryotic microbial communities in the subtidal sediments of Sanshan Island, situated in the eastern Laizhou Bay of the Bohai Sea, China. The results showed that the temporal variations in benthic microbial communities followed a distinct seasonal pattern, with turnover playing a more dominant role in community succession. Nonetheless, contrasting temporal variations were observed in the alpha diversity of benthic prokaryotic and eukaryotic microbial communities, as well as in the dominant taxa across different microbial communities. Water temperature, dissolved oxygen, electrical conductivity, salinity, total nitrogen (TN), NH4+, and PO43- were identified as the predominant environmental drivers. The assembly of benthic microbial communities was driven by different ecological processes, in which stochastic processes mainly shaped the benthic prokaryotic communities, while deterministic processes dominated the assembly of benthic eukaryotic microbial communities. Interactions within benthic microbial communities were primarily characterized by mutualistic or cooperative relationships, but the ability of prokaryotic and eukaryotic microbial communities to maintain stability under environmental disturbances showed notable differences. These results shed light on the temporal dynamics and potential driving mechanisms of benthic prokaryotic and eukaryotic microbial communities under environmental disturbances, highlighting the distinct roles of prokaryotic and eukaryotic communities in coastal subtidal zones and providing valuable insights for the management and conservation of coastal subtidal marine ecosystems.

About 80% of the biosphere is constantly exposed to temperatures below 5 °C in cold environments. Microorganisms in cold environments can grow and decompose various organic compounds at sub-zero temperatures despite exposure to conditions that are harmful to their survival, such as sub-zero temperatures and low nutrient and water availability. The present study was designed to investigate metagenomic insights into the microbial diversity in (Al-Lawz Mountains / Trojena Mountains) Saudi Arabia. Metagenomic data sets are obtained by high-throughput sequencing of environmental soil samples and provide an aggregation of all the conceptually genetic materials of the intended area of this project. This study easily overcomes the bottlenecks associated with conventional molecular methods of retrieving genetic information and the unscientific shortage of microbial biodiversity research at Tabuk. High throughput bioinformatic analysis has been highlighted as the accurate exploration of the abundance and diversity of bacterial communities. Environmental DNA can be sequenced to identify the recent presence, relative abundance & distribution of a prokaryotic species or whole communities of bacteria. A total of 333 bacterial metagenomes were sequenced over two seasons, fall and winter. The 16S rRNA genes were quantified during this period. The most significant species regarding the relative abundance and diversity were in the location of sample1 by, Klebsiella michiganensis (251), stenotrophomonass maltophilia (110), Escherichia coli USML2 (88), Zhongshania aliphaticivorans (40), Acidibrevibacterium fodinaquatile (12) Calothrix spp. & Nibribacter ruber (10) Bacillus spp (10) respectively. On the other hand, the lowest abundances were in sample 4 location with Pseudomonas fluorescens (5) and Corynebacterium glutamicum (3) with (NA) species. This means these were unidentified yet. All these species have a growing demand for microbial biodiversity evaluations, given the pronounced impact of climate change in this region (Al-Lawz Mountains/Trojena Mountain). Benthic microbial communities are to be considered, given they have a potential role in CO2 and nitrogen fixation, which is related to plant growth-promoting properties. They can resist salinity, radiation, low-temperature adaptation, and biocontrol properties. Thus, eDNA cold-mountain biodiversity is a fraction of the time it costs to conduct conventional ecological monitoring.