Microbial Communities and Organic Matter Composition in Surface and Subsurface Sediments of the Helgoland Mud Area, North Sea

Impact of ibuprofen on nitrogen removal performance and its biotransformation in a coupled sulfur autotrophic denitrification and anammox system

Ibuprofen (IBU), a commonly used non-steroidal anti-inflammatory drug, is frequently detected in wastewater treatment systems, where it can interfere with nitrogen removal. This study investigated the effects of IBU on nitrogen removal performance and its biotransformation in a coupled sulfur autotrophic denitrification and anammox (SAD/A) system. Moreover, key parameters, such as nitrogen removal efficiency, microbial activity, community structure, and IBU degradation products, were carefully monitored. While IBU concentrations of up to 1 mg/L had negligible impacts on nitrogen removal efficiency due to the counteracting effects of slight inhibition on anammox and enhancement of sulfur autotrophic denitrification, a significant inhibition of ammonia removal occurred when the concentration increased to 10 mg/L. Quantum chemical analyses revealed that IBU underwent biotransformation through decarboxylation and hydroxylation pathways, leading to the formation of two biotransformation products with high ecological toxicity. This study is the first to elucidate the mechanisms by which IBU influences microbial communities and metabolic activities in SAD/A systems. In addition, it highlights the resilience of these systems in maintaining nitrogen removal efficiency under varying IBU concentrations, as well as the environmental risks posed by the biotransformation products of IBU.

Persistent functional and taxonomic groups dominate an 8,000-year sedimentary sequence from Lake Cadagno, Switzerland

Most of our knowledge of deep sedimentary life comes from marine environments; however, despite their relatively small volume, lacustrine sediments constitute one of the largest global carbon sinks and their deep sediments are largely unexplored. Here, we reconstruct the microbial functional and taxonomic composition of an 8,000-year Holocene sedimentary succession from meromictic Lake Cadagno (Switzerland) using shotgun metagenomics and 16S rRNA gene amplicon sequencing. While younger sediments (<1,000 years) are dominated by typical anaerobic surface sedimentary bacterial taxa (Deltaproteobacteria, Acidobacteria, and Firmicutes), older layers with lower organic matter concentrations and reduced terminal electron acceptor availability are dominated by taxa previously identified as "persistent populations" within deep anoxic marine sediments (Candidatus Bathyarchaeia, Chloroflexi, and Atribacteria). Despite these dramatic changes in taxonomic community composition and sediment geochemistry throughout the sediment core, higher-order functional categories and metabolic marker gene abundances remain relatively consistent and indicate a microbial community capable of carbon fixation, fermentation, dissimilatory sulfate reduction and dissimilatory nitrate reduction to ammonium. As the conservation of these metabolic pathways through changes in microbial community compositions helps preserve the metabolic pathway connectivity required for nutrient cycling, we hypothesize that the persistence of these functional groups helps enable the Lake Cadagno sedimentary communities persist amidst changing environmental conditions.

Mechanisms Driving Seasonal Succession and Community Assembly in Sediment Microbial Communities Across the Dali River Basin, the Loess Plateau, China

Microorganisms are instrumental in river ecosystems and participate in biogeochemical cycles. It is thought that dynamic hydrological processes in rivers influence microbial community assembly, but the seasonal succession and community assembly of river sediments on the Loess Plateau remain unclear. This study used high-throughput sequencing technology (16S and ITS) and the neutral community model to analyze seasonal succession and the assembly processes associated with microbial communities in the Dali River, a tributary of the Yellow River on the Loess Plateau. The results showed that sediment bacterial and fungal community diversity indexes in non-flood season were 1.03-3.15 times greater than those in flood season. There were obvious variations between non-flood and flood seasons in sediment microorganisms. The similarities among all, abundant, and rare microbial communities decreased as geographical distance increased. Proteobacteria (52.5-99.6%) and Ascomycota (22.0-34.2%) were the primary microbial phyla in all, abundant, and rare microbial communities. Sediment ammonia nitrogen, water temperature, and sediment organic carbon significantly affected (p < 0.05) the structure of all, abundant, and rare sediment microorganism communities. The ecological networks for the bacterial community of non-flood season and fungal community of flood season had complex topological parameters. The bacterial community in river sediments was driven by deterministic processes, while the fungal community was dominated by stochastic processes. These results expanded understanding about sediment microbial community characteristics in rivers on the Loess Plateau and provided insights into the assembly processes and the factors driving microbial communities in river networks.

Adaptation of Archaeal Communities to Summer Hypoxia in the Sediment of Bohai Sea

Understanding the adaptation of archaea to hypoxia is essential for deciphering the functions and mechanisms of microbes when suffering environmental changes. However, the dynamics and responses of archaea to the sedimentary hypoxia in Bohai Sea are still unclear. In this study, the diversity, composition, and distribution of archaeal community in sediment along an inshore-offshore transect across the oxygen-depleted area in the Bohai Sea were investigated in June, July, and August of 2021 by employing high-throughput sequencing of 16S rRNA gene. Results indicated that the archaeal communities were dominated by Thermoproteota (80.61%), Asgardarchaeota (8.70%), and Thermoplasmatota (5.27%). Dissolved oxygen (DO) and NO3 - were the two key factors shaping the distribution of archaeal communities, accounting for 49.5% and 38.3% of the total variabilities (p < 0.05), respectively. With the intensity of oxygen depletion, the diversity of archaeal communities increased significantly. Microbial networks revealed that Bathyarchaeia played a key role in interacting with both bacteria and other archaeal groups. Furthermore, adaptions to hypoxia of archaea were also displayed by variation in relative abundance of the predicted ecological functions and the metabolic pathways. The enrichment of specific nitrogen transformation enzymes showed the potential for nitrogen fixation and removal, which might contribute to the balance of N budget and thus facilitate the ecological restoration under eutrophication in Bohai Sea. Our results provided a new picture on ecological and metabolic adaptions to hypoxia by archaea, which will be beneficial to further investigations in extreme environments both theoretically and practically.

Bacterial Community Structure and Environmental Driving Factors in the Surface Sediments of Six Mangrove Sites from Guangxi, China

Mangroves, as blue carbon reservoirs, provide a unique habitat for supporting a variety of microorganisms. Among these, bacteria play crucial roles in the biogeochemical processes of mangrove sediments. However, little is known about their community composition, spatial distribution patterns, and environmental driving factors, particularly across the large geographical scales of mangrove wetlands. In this study, the composition and spatial distribution of the bacterial community structure and its response to fifteen physicochemical parameters (including temperature, pH, salinity, moisture, clay, silt, sand, organic carbon (OC), total nitrogen (TN), total phosphorus (TP), inorganic phosphorus (IP), organic phosphorus (OP), δ13C, δ15N, and carbon/nitrogen ratio (C/N ratio)) were characterized in 32 sampling locations of six different mangrove habitats from Guangxi, China, applying 16S rRNA gene high-throughput sequencing technology and correlation analysis. Our results indicated that the spatial distribution patterns in bacterial communities were significantly different among the six different mangrove sites, as evidenced by NMDS (non-metric multidimensional scaling), ANOSIM (analysis of similarity), and LDA (linear discriminant analysis) analysis. Composition analysis of bacterial communities showed that overall, Chloroflexi (8.3-31.6%), Proteobacteria (13.6-30.1%), Bacteroidota (5.0-24.6%), and Desulfobacterota (3.8-24.0%) were the most abundant bacterial phyla in the mangrove surface sediments. Redundancy analysis (RDA) further highlighted that salinity, δ13C, temperature, δ15N, and silt were the most critical environmental variables influencing the composition of bacterial communities across the whole mangrove samples. Notably, Chloroflexi, one of the most abundant bacterial phyla in the mangrove wetlands, displayed a significantly positive correlation with OC and a negative correlation with δ13C, suggesting its essential role in the degradation of terrestrial-derived organic carbon. These findings support the current understanding of the roles of the bacterial communities and their interactions with environmental factors in diverse mangrove ecosystems.

Metagenomic insights into microbial community, functional annotation, and antibiotic resistance genes in Himalayan Brahmaputra River sediment, India

Introduction

The Brahmaputra, a major transboundary river of the Himalayas flowing predominantly through Northeast India, particularly Assam, is increasingly endangered by contamination due to rapid urbanization and anthropogenic pressures. These environmental changes pose significant risks at the microbial level, affecting nutrient cycling and productivity, and thereby impacting river ecosystem health. The next-generation sequencing technology using a metagenomics approach has revolutionized our understanding of the microbiome and its critical role in various aquatic environments.

Methods

The present study aimed to investigate the structure of the bacterial community and its functional potentials within the sediments of the Brahmaputra River, India, using high-throughput shotgun metagenomics. Additionally, this study sought to explore the presence of antimicrobial resistance genes in the river's sediment.

Results and discussion

Shotgun metagenomics revealed a diverse bacterial community comprising 31 phyla, 52 classes, 291 families, 1,016 genera, and 3,630 species. Dominant phyla included Pseudomonadota (62.47-83.48%), Actinobacteria (11.10-24.89%), Bacteroidetes (0.97-3.82%), Firmicutes (0.54-3.94%), Cyanobacteria (0.14-1.70%), and Planctomycetes (0.30-0.78%). Functional profiling highlighted significant involvement in energy metabolism, amino acid and central carbon metabolism, stress response, and degradation pathways, emphasizing the microbial community's role in ecosystem functioning and resilience. Notably, 50 types of antibiotic resistance genes (ARGs) were detected, with resistance profiles spanning multidrug, aminoglycoside, β-lactam, fluoroquinolone, rifampicin, sulfonamide, and tetracycline classes. Network analysis underscored the intricate relationships among ARG subtypes, suggesting potential mechanisms of resistance propagation. Furthermore, plasmid-related genes and 185 virulence factor genes (VFGs) were identified, indicating additional layers of microbial adaptation and potential pathogenicity within the river sediments. This comprehensive microbial and functional profiling of the Brahmaputra's sediment metagenome provides crucial insights into microbial diversity, resistance potential, and ecological functions, offering a foundation for informed management and mitigation strategies to preserve river health and mitigate pollution impacts.

The hidden acceleration pump uncovers the role of shellfish in oceanic carbon sequestration

Whether shellfish mariculture should be included in the blue carbon profile as a strategy to combat climate change has been controversial. It is highly demanding not only to provide calibration quantitation, but also to provide an ecosystem-based mechanism. In this study, we chose mussel farms as a case study to evaluate their contributions to carbon sinks and their responses to sedimentary carbon fixation and sequestration. First, we quantified the air-sea CO2 flux in the mussel aquacultural zone and observed a weak carbon sink (-0.15 ± 0.07 mmol·m-2·d-1) during spring. Next, by analyzing the carbon composition in the sediment, we recorded a noticeable and unexpected increase in the sedimentary recalcitrant carbon (RC) content in the mussel farming case. To address this surprising sedimentary phenomenon, a long-term indoor experimental test was conducted to distinguish the consequences of mussel engagement with sedimentary RC. Our observational data support the idea that mussel engagement promotes accumulation of RC in sediments by 2.5-fold. Furthermore, the relative intensity of carboxylic-rich alicyclic molecule (CRAM)-like compounds (recalcitrant dissolved organic matter (RDOM)) increased by 451.4 % in the mussel-engaged sedimentary dissolved organic matter (DOM) in comparison to the initial state. Mussel engagement had a significantly positive effect on the abundance of sedimentary carbon-fixing genes. Therefore, we definitively conclude that mussel farming is blue carbon positive and propose a new alternative theory that mussel farming areas may have high carbon sequestration potential via an ecologically integrated "3 M" (microalgae-mussel-microbiota) consortium. The "mussel pump" accelerates carbon sequestration and enhances climate-related ecosystem services.

Capabilities of Microbial Consortia from Disparate Environment Matrices in the Decomposition of Nature Organic Matter by Biofiltration

Dissolved organic matter (DOM) plays a pivotal role in drinking water treatment, influencing the performance of unit processes and final water quality (e.g. disinfection byproduct risk). Biofiltration is an effective method of reducing DOM, but currently lacks a comprehensive appreciation of the association between microbial profiles and biofiltration performance. In this study, bench-scale biofiltration units inoculated with microbial consortia from river and soil matrices were operated successively for comparing their efficacy in terms of DOM removal. The results showed that biofiltration units receiving soil microbes were significantly superior (p < 0.05) to those receiving river inoculated microbes in terms of decomposing DOM recalcitrant fractions and reducing DBP formation potential, resulting in DOC and DBP precursor removals of up to 58.4 % and 87.9 %, respectively. Characterization of the taxonomic composition revealed that differences in the microbial assembly of the two biofilter groups were subject to deterministic rather than stochastic factors. Furthermore, more complicated interspecific relationships and niche structures in soil inoculated biofilters were deciphered by co-occurrence network, providing a plausible profile on a taxonomic division of labor in DOM stepwise degradation. Accordingly, the contribution of microbial compositions was found to be of greater importance than the GAC mass and biomass attached to the media. Thus, this study has advanced the understanding of microbial-mediated DOM decomposition in biofiltration, and also provided a promising strategy for enhancing the process for water use via developing appropriate engineered consortia of bacteria.

Exploring transformation of dissolved organic matters and dissolved organic nitrogen in full-scale anammox wastewater treatment: Temperature and microbial roles

Variation of dissolved organic matters (DOM) in mainstream anammox process has received limited attention. This study systematically characterized DOM and dissolved organic nitrogen (DON) in a full-scale mainstream anammox wastewater treatment plant (WWTP) using spectroscopy and Fourier transform-ion cyclotron resonance mass spectrometry. Roles of bacterial community structures related with temperatures on DOM and DON transformations were analyzed. Results indicated that the WWTP removed highly bioavailable, S-containing DOM while producing more unsaturated, aromatic, and N-containing DOM. Higher relative abundances of Proteobacteria and Chloroflexi at low temperature resulted in greater removal rates of proteins, SMP-like and humic acid-like substances. At high temperature, higher relative abundance of Actinobacteriota increased lignin production. Principal component analysis revealed that temperature significantly impacted DOM characteristics compared to DON. These findings are crucial for understanding DOM and DON transformation during mainstream anammox WWTP.

Cultivation of Diverse Novel Marine Bacteria from Deep Ocean Sediment Using Spent Culture Supernatant of Ca. Bathyarchaeia Enrichment

Most microorganisms resist pure cultivation under conventional laboratory conditions. One of the primary issues for this un-culturability is the absence of biologically produced growth-promoting factors in traditionally defined growth media. However, whether cultivating microbes by providing spent culture supernatant of pivotal microbes in the growth medium can be an effective approach to overcome this limitation is still an under-explored area of research. Here, we used the spent culture medium (SCM) method to isolate previously uncultivated marine bacteria and compared the efficiency of this method with the traditional cultivation (TC) method. In the SCM method, Ca. Bathyarchaeia-enriched supernatant (10%) was used along with recalcitrant organic substrates such as lignin, humic acid, and organic carbon mixture. Ca. Bathyarchaeia, a ubiquitous class of archaea, have the capacity to produce metabolites, making their spent culture supernatant a key source to recover new bacterial stains. Both cultivation methods resulted in the recovery of bacterial species from the phyla Pseudomonadota, Bacteroidota, Actinomycetota, and Bacillota. However, our SCM approach also led to the recovery of species from rarely cultivated groups, such as Planctomycetota, Deinococcota, and Balneolota. In terms of the isolation of new taxa, the SCM method resulted in the cultivation of 80 potential new strains, including one at the family, 16 at the genus, and 63 at the species level, with a novelty ratio of ~ 35% (80/219). In contrast, the TC method allowed the isolation of ~ 10% (19/171) novel strains at species level only. These findings suggest that the SCM approach improved the cultivation of novel and diverse bacteria.

Iron Promotes the Retention of Terrigenous Dissolved Organic Matter in Subtidal Permeable Sediments

Marine permeable sediments are important sites for organic matter turnover in the coastal ocean. However, little is known about their role in trapping dissolved organic matter (DOM). Here, we examined DOM abundance and molecular compositions (9804 formulas identified) in subtidal permeable sediments along a near- to offshore gradient in the German North Sea. With the salinity increasing from 30.1 to 34.6 PSU, the DOM composition in bottom water shifts from relatively higher abundances of aromatic compounds to more highly unsaturated compounds. In the bulk sediment, DOM leached by ultrapure water (UPW) from the solid phase is 54 ± 20 times more abundant than DOM in porewater, with higher H/C ratios and a more terrigenous signature. With 0.5 M HCl, the amount of leached DOM (enriched in aromatic and oxygen-rich compounds) is doubled compared to UPW, mainly due to the dissolution of poorly crystalline Fe phases (e.g., ferrihydrite and Fe monosulfides). This suggests that poorly crystalline Fe phases promote DOM retention in permeable sediments, preferentially terrigenous, and aromatic fractions. Given the intense filtration of seawater through the permeable sediments, we posit that Fe can serve as an important intermediate storage for terrigenous organic matter and potentially accelerate organic matter burial in the coastal ocean.

Response of sulfide autotrophic denitrification process and microbial community to oxytetracycline stress

The coexistence of antibiotics with sulfide and nitrate is common in sewage. Thus, this study explored the removal performance of nitrate and sulfide, and the response of extracellular polymer substances (EPS) and the microbial community to the sulfide autotrophic denitrification (SAD) process under oxytetracycline (OTC) stress. In Phase Ⅰ, the SAD system showed favouranle performance (nitrate removal rate ＞ 92.57%, sulfide removal rate ＞ 97.75%). However, in Phase Ⅳ, at OTC concentrations of 10, 15, and 20 mg/L, the NRE decreased to 76.13%, 40.71%, 11.37%, respectively, and the SRE decreased to 97.58%, 97.09%, 92.84%, respectively. At OTC concentrations of 0, 10, 15, and 20 mg/L, the EPS content were 1.62, 1.75, 2.03, and 1.42 mg/gVSS, respectively. The results showed that SAD performance gradually deteriorated under OTC stress. In particular, when the OTC concentration was 20 mg/L, the EPS content was lower than that of the control test, which could be attributed to the occurrence of microbial death. Finally, high-throughput sequencing results showed that OTC exposure led to gradual domination by heterotrophic denitrifying bacteria.

Unexpected carbon utilization activity of sulfate-reducing microorganisms in temperate and permanently cold marine sediments

Significant amounts of organic carbon in marine sediments are degraded, coupled with sulfate reduction. However, the actual carbon and energy sources used in situ have not been assigned to each group of diverse sulfate-reducing microorganisms (SRM) owing to the microbial and environmental complexity in sediments. Here, we probed microbial activity in temperate and permanently cold marine sediments by using potential SRM substrates, organic fermentation products at very low concentrations (15-30 μM), with RNA-based stable isotope probing. Unexpectedly, SRM were involved only to a minor degree in organic fermentation product mineralization, whereas metal-reducing microbes were dominant. Contrastingly, distinct SRM strongly assimilated 13C-DIC (dissolved inorganic carbon) with H2 as the electron donor. Our study suggests that canonical SRM prefer autotrophic lifestyle, with hydrogen as the electron donor, while metal-reducing microorganisms are involved in heterotrophic organic matter turnover, and thus regulate carbon fluxes in an unexpected way in marine sediments.

Organic matter stability and lability in terrestrial and aquatic ecosystems: A chemical and microbial perspective

Terrestrial and aquatic ecosystems have specific carbon fingerprints and sequestration potential, due to the intrinsic properties of the organic matter (OM), mineral content, environmental conditions, and microbial community composition and functions. A small variation in the OM pool can imbalance the carbon dynamics that ultimately affect the climate and functionality of each ecosystem, at regional and global scales. Here, we review the factors that continuously contribute to carbon stability and lability, with particular attention to the OM formation and nature, as well as the microbial activities that drive OM aggregation, degradation and eventually greenhouse gas emissions. We identified that in both aquatic and terrestrial ecosystems, microbial attributes (i.e., carbon metabolism, carbon use efficiency, necromass, enzymatic activities) play a pivotal role in transforming the carbon stock and yet they are far from being completely characterised and not often included in carbon estimations. Therefore, future research must focus on the integration of microbial components into carbon mapping and models, as well as on translating molecular-scaled studies into practical approaches. These strategies will improve carbon management and restoration across ecosystems and contribute to overcome current climate challenges.

Effect of ibuprofen on the sulfur autotrophic denitrification process and microbial toxic response mechanism

The effect of ibuprofen (IBU) on the sulfur autotrophic denitrification (SAD) process and microbial toxic response mechanism were investigated. Nitrate removal performance was inhibited by high IBU concentrations (10 and 50 mg/L), and the effect of low IBU concentrations (1 mg/L) on nitrate removal performance was negligible. The low IBU concentration induced basal oxidative stress for microbial self-protection, while the high IBU concentration induced high-intensity oxidative stress to damage the microbial cell membrane structure. Electrochemical characterization showed that the low IBU concentration stimulated the electron transfer efficiency, which was inhibited at the high IBU concentration. Moreover, the variation content of nicotinamide adenine dinucleotide (NADH) and nitrate reductase showed that metabolic activity increased at low IBU concentrations and decreased at high IBU concentrations during the sulfur autotrophic nitrate reduction process. This study proposed the hormesis toxic response mechanism of the SAD process to IBU exposure.

Molecular behavior and interactions with microbes during anaerobic degradation of bio-derived DOM in waste leachate

It is the key to control bio-derived dissolved organic matters (DOM) in order to reduce the effluent concentration of wastewater treatment, especially for waste leachate with high organic contaminants. In the present study, the anaerobic degradation of aerobically stabilized DOM was investigated with DOM substrate isolated through electrodialysis. The degradation of bio-derived DOM was confirmed by reduction of 15% of total organic carbon in 100 days. We characterized the molecular behavior of bio-derived DOM by coupling molecular and biological information analysis. Venn based Sankey diagram of mass features showed the transformation of bio-derived DOM mass features. Occurrence frequency analysis divided mass features into six categories so as to distinguish the fates of intermediate metabolites and persistent compounds. Reactivity continuum model and machine learning technologies realized the semi-quantitative determination on the kinetics of DOM mass features in the form of pseudo-first order, and confirmed the reduction of inert mass features. Furthermore, network analysis statistically establish relationship between DOM mass features and microbes to identify the active microbes that are able to utilize bio-derived DOM. This work confirmed the biological technology is still effective in controlling recalcitrant bio-derived DOM during wastewater treatment.

pH Drives Differences in Bacterial Community β-Diversity in Hydrologically Connected Lake Sediments

As microorganisms are very sensitive to changes in the lake environment, a comprehensive and systematic understanding of the structure and diversity of lake sediment microbial communities can provide feedback on sediment status and lake ecosystem protection. Xiao Xingkai Lake (XXL) and Xingkai Lake (XL) are two neighboring lakes hydrologically connected by a gate and dam, with extensive agricultural practices and other human activities existing in the surrounding area. In view of this, we selected XXL and XL as the study area and divided the area into three regions (XXLR, XXLD, and XLD) according to different hydrological conditions. We investigated the physicochemical properties of surface sediments in different regions and the structure and diversity of bacterial communities using high-throughput sequencing. The results showed that various nutrients (nitrogen, phosphorus) and carbon (DOC, LOC, TC) were significantly enriched in the XXLD region. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant bacterial phyla in the sediments, accounting for more than 60% of the entire community in all regions. Non-metric multidimensional scaling analysis and analysis of similarities confirmed that β-diversity varied among different regions. In addition, the assembly of bacterial communities was dominated by a heterogeneous selection in different regions, indicating the important influence of sediment environmental factors on the community. Among these sediment properties, the partial least squares path analysis revealed that pH was the best predictor variable driving differences in bacterial communities in different regions, with higher pH reducing beta diversity among communities. Overall, our study focused on the structure and diversity of bacterial communities in lake sediments of the Xingkai Lake basin and revealed that high pH causes the β-diversity of bacterial communities in the sediment to decrease. This provides a reference for further studies on sediment microorganisms in the Xingkai Lake basin in the future.

The majority of microorganisms in gas hydrate-bearing subseafloor sediments ferment macromolecules

BACKGROUND

Gas hydrate-bearing subseafloor sediments harbor a large number of microorganisms. Within these sediments, organic matter and upward-migrating methane are important carbon and energy sources fueling a light-independent biosphere. However, the type of metabolism that dominates the deep subseafloor of the gas hydrate zone is poorly constrained. Here we studied the microbial communities in gas hydrate-rich sediments up to 49 m below the seafloor recovered by drilling in the South China Sea. We focused on distinct geochemical conditions and performed metagenomic and metatranscriptomic analyses to characterize microbial communities and their role in carbon mineralization.

RESULTS

Comparative microbial community analysis revealed that samples above and in sulfate-methane interface (SMI) zones were clearly distinguished from those below the SMI. Chloroflexota were most abundant above the SMI, whereas Caldatribacteriota dominated below the SMI. Verrucomicrobiota, Bathyarchaeia, and Hadarchaeota were similarly present in both types of sediment. The genomic inventory and transcriptional activity suggest an important role in the fermentation of macromolecules. In contrast, sulfate reducers and methanogens that catalyze the consumption or production of commonly observed chemical compounds in sediments are rare. Methanotrophs and alkanotrophs that anaerobically grow on alkanes were also identified to be at low abundances. The ANME-1 group actively thrived in or slightly below the current SMI. Members from Heimdallarchaeia were found to encode the potential for anaerobic oxidation of short-chain hydrocarbons.

CONCLUSIONS

These findings indicate that the fermentation of macromolecules is the predominant energy source for microorganisms in deep subseafloor sediments that are experiencing upward methane fluxes. Video Abstract.

Characterization of the Sediment Bacterial Community Structure and Composition in Najafgarh Lake and Adjoining Dhansa Barrage

This study was undertaken to assess the changes in the community structure, diversity, and composition of sediment bacteria in a shallow lake, Najafgarh Lake (NL), that receives untreated sewage effluent through drains connected to it. These changes were analyzed by comparing the sediment bacterial community structure of NL to the sediment bacterial community structure of Dhansa Barrage (DB), which receives no such effluents. 16S rRNA amplicon was used for bacterial community analysis. Water and sediment samples were also analyzed and compared revealing high conductivity, ammonia, nitrite content, and low dissolved oxygen in NL. The organic matter content is also higher in the sediments of NL. Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria are the predominant phyla in both sites and account for 91% of total bacterial abundance in DB and only 77% in the case of NL. Proteobacteria have the highest relative abundance, accounting for around 42% of the total bacterial population in the case of DB and Firmicutes has the highest relative abundance in Najafgarh at 30%. The diversity analysis found significant differences in the community structure at the two sites. The variation in the bacterial communities in the two wetlands is significantly associated with two water parameters (conductivity and temperature) and two sediment parameters (Sediment Nitrogen and Sediment Organic Matter). Correlation Analysis showed that high ammonia, nitrite, and conductance in NL resulted in bacterial communities shifting towards phyla abundant in degraded ecosystems like Acidobacteria, Choloroflexi, Caldiserica, Aminicenantes, Thaumarchaeota, and Planctomycetes.

Increased food availability at offshore wind farms affects trophic ecology of plaice Pleuronectes platessa

Offshore wind farms (OWFs) and their associated cables, foundations and scour protection are often constructed in soft-sediment environments. This introduction of hard substrate has been shown to have similar effects as artificial reefs by providing food resources and offering increased habitat complexity, thereby aggregating fish around the turbines and foundations. However, as most studies have focused their efforts on fish species that are typically associated with reef structures, knowledge on how soft sediment species are affected by OWFs is still largely lacking. In this study, we analysed the trophic ecology and condition of plaice, a flatfish species of commercial interest, in relation to a Belgian OWF. The combination of a stomach and intestine content analysis with the use of biomarkers (i.e. fatty acids and stable isotopes) identified a clear shift in diet with increased occurrences of typical hard-substrate prey species for fish in the vicinity of the foundations and this both on the short and the long term. Despite some condition indices suggesting that the hard substrate provides increased food availability, no clear increases of overall plaice condition or fecundity were found. Samples from within the wind farm, however, contained larger fish and had a higher abundance of females compared to control areas, potentially indicating a refuge effect caused by the cessation of fisheries activities within the OWF. These results suggest that soft-sediment species can potentially benefit from the presence of an OWF, which could lead to fish production. However, more research is still needed to further elucidate the behavioral ecology of plaice within OWFs to make inferences on how they can impact fish populations on a larger spatial scale.

Geochemical properties of blue carbon sediments through an elevation gradient: study of an anthropogenically impacted coastal lagoon

Global research is showing that coastal blue carbon ecosystems are vulnerable to climate change driven threats including accelerated sea-level rise and prolonged periods of drought. Furthermore, direct anthropogenic impacts present immediate threats through deterioration of coastal water quality, land reclamation, long-term impact to sediment biogeochemical cycling. These threats will invariably alter the future efficacy of carbon (C) sequestration processes and it is imperative that currently existing blue carbon habitats be protected. Knowledge of underlying biogeochemical, physical and hydrological interactions occurring in functioning blue carbon habitats is essential for developing strategies to mitigate threats, and promote conditions to optimise C sequestration/storage. In this current work, we investigated how sediment geochemistry (0-10 cm depth) responds to elevation, an edaphic factor driven by long-term hydrological regimes consequently exerting control over particle sedimentation rates and vegetation succession. This study was performed in an anthropogenically impacted blue carbon habitat along a coastal ecotone encompassing an elevation gradient transect from intertidal sediments (un-vegetated and covered daily by tidal water), through vegetated salt marsh sediments (periodically covered by spring tides and flooding events), on Bull Island, Dublin Bay. We determined the quantity and distributions of bulk geochemical characteristics in sediments through the elevation gradient, including total organic carbon (TOC), total nitrogen (TN), total metals, silt, clay, and also, 16 individual polyaromatic hydrocarbon's (PAH's) as an indication of anthropogenic input. Elevation measurements for sample sites were determined on this gradient using a LiDAR scanner accompanied by an IGI inertial measurement unit (IMU) on board a light aircraft. Considering the gradient from the Tidal mud zone (T), through the low-mid marsh (M) to the most elevated upper marsh (H), there were significant differences between all zones for many measured environmental variables. The results of significance testing using Kruskal-Wallis analysis revealed, that %C, %N, PAH (µg/g), Mn (mg/kg), TOC:NH₄ ⁺ and pH are significantly different between all zones on the elevation gradient. The highest values for all these variables exists (excluding pH which followed a reverse trend) in zone H, decreasing in zone M and lowest in the un-vegetated zone T. TC content is 16 fold higher overall in vegetated (3.43 -21.84%) than uninhabited (0.21-0.56%) sediments. TN was over 50 times higher (0.24-1.76%), more specifically increasing in % mass on approach to the upper salt marsh with distance from the tidal flats sediments zone T (0.002-0.05%). Clay and silt distributions were greatest in vegetated sediments, increasing in % content towards upper marsh zones The retention of water, metals, PAHs, mud, chloride ions, NH₄ ⁺, PO₄ ^3- and SO₄ ^2- increased with elevated C concentrations, concurrently where pH significantly decreased. Sediments were categorized with respect to PAH contamination where all SM samples were placed in the high polluted category. The results highlight the ability of Blue C sediments to immobilise increasing levels of C, N, and metals, and PAH with over time and with both lateral and vertical expansion. This study provides a valuable data set for an anthropogenically impacted blue carbon habitat predicted to suffer from sea-level rise and exponential urban development.

GRAPHICAL ABSTRACT

Summarized results from this study demonstrating the geochemical changes through an elevation gradient, with a transect encompassing intertidal sediments through supratidal salt marsh sediments within Bull Island's blue carbon lagoon zones.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10533-022-00974-0.

Spatial and temporal dynamics of microbial community composition and factors influencing the surface water and sediments of urban rivers

The temporal and spatial characteristics of urban river bacterial communities help us understand the feedback mechanism of bacteria to changes in the aquatic environment. The Fuhe River plays an important role in determining the water ecological environment of Baiyangdian Lake. 16S rRNA gene sequencing was used to study the microbial distribution characteristics in the Fuhe River in different seasons. The results showed that some environmental factors of the surface water (ammonia nitrogen (NH₃-N), total nitrogen (TN), and total phosphorus (TP)) were different on the spatial and temporal scales. Moreover, there were no seasonal differences in the contents of TN, TP, total organic carbon (TOC), or heavy metals in the sediments. The distributions of Cyanobacteria, Actinomycetes and Firmicutes in the water and Actinomycetes and Planctomycetes in the sediments differed significantly among seasons (P < 0.05). There were significant spatial differences in bacteria in the surface water, with the highest abundance of Proteobacteria recorded in the river along with the highest nutrient concentration, while the abundance of Bacteroidetes was higher in the upstream than the downstream. Microbial communities in the water were most sensitive to temperature (T) and the TP concentration (P < 0.01). Moreover, differences in the bacterial community were better explained by the content of heavy metals in the sediments than by the chemical characteristics. A PICRUSt metabolic inference analysis showed that the effect of high summer temperatures on the enzyme action led to an increase in the abundances of the metabolic-related genes of the river microorganisms.

Stable carbon isotope values of syndepositional carbonate spherules and micrite record spatial and temporal changes in photosynthesis intensity

Marine and lacustrine carbonate minerals preserve carbon cycle information, and their stable carbon isotope values (δ¹³ C) are frequently used to infer and reconstruct paleoenvironmental changes. However, multiple processes can influence the δ¹³ C values of bulk carbonates, confounding the interpretation of these values in terms of conditions at the time of mineral precipitation. Co-existing carbonate forms may represent different environmental conditions, yet few studies have analyzed δ¹³ C values of syndepositional carbonate grains of varying morphologies to investigate their origins. Here, we combine stable isotope analyses, metagenomics, and geochemical modeling to interpret δ¹³ C values of syndepositional carbonate spherules (>500 μm) and fine-grained micrite (<63 μm) from a ~1600-year-long sediment record of a hypersaline lake located on the coral atoll of Kiritimati, Republic of Kiribati (1.9°N, 157.4°W). Petrographic, mineralogic, and stable isotope results suggest that both carbonate fractions precipitate in situ with minor diagenetic alterations. The δ¹³ C values of spherules are high compared to the syndepositional micrite and cannot be explained by mineral differences or external perturbations, suggesting a role for local biological processes. We use geochemical modeling to test the hypothesis that the spherules form in the surface microbial mat during peak diurnal photosynthesis when the δ¹³ C value of dissolved inorganic carbon is elevated. In contrast, we hypothesize that the micrite may precipitate more continuously in the water as well as in sub-surface, heterotrophic layers of the microbial mat. Both metagenome and geochemical model results support a critical role for photosynthesis in influencing carbonate δ¹³ C values. The down-core spherule-micrite offset in δ¹³ C values also aligns with total organic carbon values, suggesting that the difference in the δ¹³ C values of spherules and micrite may be a more robust, inorganic indicator of variability in productivity and local biological processes through time than the δ¹³ C values of individual carbonate forms.

Catabolic protein degradation in marine sediments confined to distinct archaea

Metagenomic analysis has facilitated prediction of a variety of carbon utilization potentials by uncultivated archaea including degradation of protein, which is a wide-spread carbon polymer in marine sediments. However, the activity of detrital catabolic protein degradation is mostly unknown for the vast majority of archaea. Here, we show actively executed protein catabolism in three archaeal phyla (uncultivated Thermoplasmata, SG8-5; Bathyarchaeota subgroup 15; Lokiarchaeota subgroup 2c) by RNA- and lipid-stable isotope probing in incubations with different marine sediments. However, highly abundant potential protein degraders Thermoprofundales (MBG-D) and Lokiarchaeota subgroup 3 were not incorporating ¹³C-label from protein during incubations. Nonetheless, we found that the pathway for protein utilization was present in metagenome associated genomes (MAGs) of active and inactive archaea. This finding was supported by screening extracellular peptidases in 180 archaeal MAGs, which appeared to be widespread but not correlated to organisms actively executing this process in our incubations. Thus, our results have important implications: (i) multiple low-abundant archaeal groups are actually catabolic protein degraders; (ii) the functional role of widespread extracellular peptidases is not an optimal tool to identify protein catabolism, and (iii) catabolic degradation of sedimentary protein is not a common feature of the abundant archaeal community in temperate and permanently cold marine sediments.

The metabolic core of the prokaryotic community from deep-sea sediments of the southern Gulf of Mexico shows different functional signatures between the continental slope and abyssal plain

Marine sediments harbor an outstanding level of microbial diversity supporting diverse metabolic activities. Sediments in the Gulf of Mexico (GoM) are subjected to anthropic stressors including oil pollution with potential effects on microbial community structure and function that impact biogeochemical cycling. We used metagenomic analyses to provide significant insight into the potential metabolic capacity of the microbial community in Southern GoM deep sediments. We identified genes for hydrocarbon, nitrogen and sulfur metabolism mostly affiliated with Alpha and Betaproteobacteria, Acidobacteria, Chloroflexi and Firmicutes, in relation to the use of alternative carbon and energy sources to thrive under limiting growth conditions, and metabolic strategies to cope with environmental stressors. In addition, results show amino acids metabolism could be associated with sulfur metabolism carried out by Acidobacteria, Chloroflexi and Firmicutes, and may play a crucial role as a central carbon source to favor bacterial growth. We identified the tricarboxylic acid cycle (TCA) and aspartate, glutamate, glyoxylate and leucine degradation pathways, as part of the core carbon metabolism across samples. Further, microbial communities from the continental slope and abyssal plain show differential metabolic capacities to cope with environmental stressors such as oxidative stress and carbon limiting growth conditions, respectively. This research combined taxonomic and functional information of the microbial community from Southern GoM sediments to provide fundamental knowledge that links the prokaryotic structure to its potential function and which can be used as a baseline for future studies to model microbial community responses to environmental perturbations, as well as to develop more accurate mitigation and conservation strategies.

Microbial consortia adaptation to substrate changes in anaerobic digestion

Renewable natural gas (RNG) produced from anaerobic digestion (AD) of agricultural residues is emerging a serious biofuel alternative. Complex nature of lignocellulosic biomass residues coupled with complex biochemical transformations involving a large spectrum of microbial communities make anaerobic digestion of biomass difficult to understand and control. The present work aims at studying adaptation of microbial consortia in AD to substrates changes and correlating these to biogas generation. The double edged study deals with (a) using a common starting culture inoculum on different fractions of pretreated lignocellulosic biomass (LBM) fractions; and (b) using different starter inocula for gas generation from simple glucose substrate. Taxonomic analysis using 16S amplicon sequencing is shown to highlight changes in microbial community structure and predominance, majorly in hydrolytic bacterial populations. Observed variations in the rate of digestion with different starter inocula could be related to differences in microbial community structure and relative abundance. Results with different treated biomass fractions as substrates indicated that AD performance could be related to abundance of substrate-specific microbial communities. The work is a step to a deeper understanding of AD processes that may lead to better control and operation of AD for super-scale production of RNG from biomass feedstocks.

Microbial Roles in Dissolved Organic Matter Transformation in Full-Scale Wastewater Treatment Processes Revealed by Reactomics and Comparative Genomics

Understanding the degradation of dissolved organic matter (DOM) is vital for optimizing DOM control. However, the microbe-mediated DOM transformation during wastewater treatment remains poorly characterized. Here, microbes and DOM along full-scale biotreatment processes were simultaneously characterized using comparative genomics and high-resolution mass spectrometry-based reactomics. Biotreatments significantly increased DOM's aromaticity and unsaturation due to the overproduced lignin and polyphenol analogs. DOM was diversified by over five times in richness, with thousands of nitrogenous and sulfur-containing compounds generated through microbe-mediated oxidoreduction, functional group transfer, and C-N and C-S bond formation. Network analysis demonstrated microbial division of labor in DOM transformation. However, their roles were determined by their functional traits rather than taxa. Specifically, network and module hubs exhibited rapid growth potentials and broad substrate affinities but were deficient in xenobiotics-metabolism-associated genes. They were mainly correlated to liable DOM consumption and its transformation to recalcitrant compounds. In contrast, connectors and peripherals were potential degraders of recalcitrant DOM but slow in growth. They showed specialized associations with fewer DOM molecules and probably fed on metabolites of hub microbes. Thus, developing technologies (e.g., carriers) to selectively enrich peripheral degraders and consequently decouple the liable and recalcitrant DOM transformation processes may advance DOM removal.

Metagenomic analysis reveals genetic insights on biogeochemical cycling, xenobiotic degradation, and stress resistance in mudflat microbiome

Mudflats are highly productive coastal ecosystems that are dominated by halophytic vegetation. In this study, the mudflat sediment microbiome was investigated from Nalabana Island, located in a brackish water coastal wetland of India; Chilika, based on the MinION shotgun metagenomic analysis. Bacterial, archaeal, and fungal communities were mostly composed of Proteobacteria (38.3%), Actinobacteria (20.7%), Euryarchaeota (76.1%), Candidatus Bathyarchaeota (6.8%), Ascomycota (47.2%), and Basidiomycota (22.0%). Bacterial and archaeal community composition differed significantly between vegetated mudflat and un-vegetated bulk sediments. Carbon, nitrogen, sulfur metabolisms, oxidative phosphorylation, and xenobiotic biodegradation were the most common microbial functionalities in the mudflat metagenomes. Furthermore, genes involved in oxidative stresses, osmotolerance, secondary metabolite synthesis, and extracellular polymeric substance synthesis revealed adaptive mechanisms of the microbiome in mudflat habitat. Mudflat metagenome also revealed genes involved in the plant growth and development, suggesting that microbial communities could aid halophytic vegetation by providing tolerance to the abiotic stresses in a harsh mudflat environment. Canonical correspondence analysis and co-occurrence network revealed that both biotic (vegetation and microbial interactions) and abiotic factors played important role in shaping the mudflat microbiome composition. Among abiotic factors, pH accounted for the highest variance (20.10%) followed by available phosphorus (19.73%), total organic carbon (9.94%), salinity (8.28%), sediment texture (sand) (6.37%) and available nitrogen (5.53%) in the mudflat microbial communities. Overall, this first metagenomic study provided a comprehensive insight on the community structure, potential ecological interactions, and genetic potential of the mudflat microbiome in context to the cycling of organic matter, xenobiotic biodegradation, stress resistance, and in providing the ecological fitness to halophytes. These ecosystem services of the mudflat microbiome must be considered in the conservation and management plan of coastal wetlands. This study also advanced our understanding of fungal diversity which is understudied from the coastal lagoon ecosystems.

Cross-Shore and Depth Zonations in Bacterial Diversity Are Linked to Age and Source of Dissolved Organic Matter across the Intertidal Area of a Sandy Beach

Microbial communities and dissolved organic matter (DOM) are intrinsically linked within the global carbon cycle. Demonstrating this link on a molecular level is hampered by the complexity of both counterparts. We have now investigated this connection within intertidal beach sediments, characterized by a runnel-ridge system and subterranean groundwater discharge. Using datasets generated by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and Ilumina-sequencing of 16S rRNA genes, we predicted metabolic functions and determined links between bacterial communities and DOM composition. Four bacterial clusters were defined, reflecting differences within the community compositions. Those were attributed to distinct areas, depths, or metabolic niches. Cluster I was found throughout all surface sediments, probably involved in algal-polymer degradation. In ridge and low water line samples, cluster III became prominent. Associated porewaters indicated an influence of terrestrial DOM and the release of aromatic compounds from reactive iron oxides. Cluster IV showed the highest seasonality and was associated with species previously reported from a subsurface bloom. Interestingly, Cluster II harbored several members of the candidate phyla radiation (CPR) and was related to highly degraded DOM. This may be one of the first geochemical proofs for the role of candidate phyla in the degradation of highly refractory DOM.

Seasonal Sampling of a Microbial Community in the Sediment of Geoje-Hansan Bay, Republic of Korea

Several oyster farms are concentrated in Geoje-Hansan Bay, Republic of Korea, and there is concern about marine pollution. Hence, we monitored the sediment at this site for a year using 16S rRNA gene sequencing. The predominant phyla were Proteobacteria (69.9 to 79.1%) and Bacteroidetes (8.2 to 10.6%) in all seasons.

Vertical Stratification of Dissolved Organic Matter Linked to Distinct Microbial Communities in Subtropic Estuarine Sediments

Dissolved organic matter (DOM) provides carbon substrates and energy sources for sediment microbes driving benthic biogeochemical processes. The interactions between microbes and DOM are dynamic and complex and require the understanding based on fine-scale microbial community and physicochemical profiling. In this study, we characterized the porewater DOM composition in a 300-cm sediment core from the Pearl River estuary, China, and examined the interactions between DOM and archaeal and bacterial communities. DOM composition were highly stratified and associated with changing microbial communities. Compared to bacteria, the amplicon sequence variants of archaea showed significant Pearson correlations (r ≥ 0.65, P < 0.01) with DOM molecules of low H/C ratios, high C number and double bond equivalents, indicating that the distribution of archaea was closely correlated to recalcitrant DOM while bacteria were associated with relatively labile compounds. This was supported by the presence of auxiliary enzyme families essential for lignin degradation and bcrABCD, UbiX genes for anaerobic aromatic reduction in metagenome-assembled genomes of Bathyarchaeia. Our study demonstrates that niche differentiation between benthic bacteria and archaea may have important consequences in carbon metabolism, particularly for the transformation of recalcitrant organic carbon that may be predominant in aged marine sediments.

Bacterial community structure and functional profiling of high Arctic fjord sediments

Kongsfjorden, an Arctic fjord is significantly affected by the glacier melt and Atlantification, both the processes driven by accelerated warming in the Arctic. This has lead to changes in primary production, carbon pool and microbial communities, especially that in the sediment. In this study, we have examined the bacterial community structure of surface (0-2 cm) and subsurface (3-9 cm) sediments of Kongsfjorden using the high throughput sequencing analysis. Results revealed that bacterial community structure of Kongsfjorden sediments were dominated by phylum Proteobacteria followed by Bacteroidetes and Epsilonbacteraeota. While α- and γ-Proteobacterial class were dominant in surface sediments; δ-Proteobacteria were found to be predominant in subsurface sediments. The bacterial community structure in the surface and subsurface sediments showed significant variations (p ≤ 0.05). Total organic carbon could be one of the major parameters controlling the bacterial diversity in the surface and subsurface sediments. Functional prediction analysis indicated that the bacterial community could be involved in the degradation of complex organic compounds such as glycans, glycosaminoglycans, polycyclic aromatic hydrocarbons and also in the biosynthesis of secondary metabolites.

Crystalline iron oxides stimulate methanogenic benzoate degradation in marine sediment-derived enrichment cultures

Elevated dissolved iron concentrations in the methanic zone are typical geochemical signatures of rapidly accumulating marine sediments. These sediments are often characterized by co-burial of iron oxides with recalcitrant aromatic organic matter of terrigenous origin. Thus far, iron oxides are predicted to either impede organic matter degradation, aiding its preservation, or identified to enhance organic carbon oxidation via direct electron transfer. Here, we investigated the effect of various iron oxide phases with differing crystallinity (magnetite, hematite, and lepidocrocite) during microbial degradation of the aromatic model compound benzoate in methanic sediments. In slurry incubations with magnetite or hematite, concurrent iron reduction, and methanogenesis were stimulated during accelerated benzoate degradation with methanogenesis as the dominant electron sink. In contrast, with lepidocrocite, benzoate degradation, and methanogenesis were inhibited. These observations were reproducible in sediment-free enrichments, even after five successive transfers. Genes involved in the complete degradation of benzoate were identified in multiple metagenome assembled genomes. Four previously unknown benzoate degraders of the genera Thermincola (Peptococcaceae, Firmicutes), Dethiobacter (Syntrophomonadaceae, Firmicutes), Deltaproteobacteria bacteria SG8_13 (Desulfosarcinaceae, Deltaproteobacteria), and Melioribacter (Melioribacteraceae, Chlorobi) were identified from the marine sediment-derived enrichments. Scanning electron microscopy (SEM) and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) images showed the ability of microorganisms to colonize and concurrently reduce magnetite likely stimulated by the observed methanogenic benzoate degradation. These findings explain the possible contribution of organoclastic reduction of iron oxides to the elevated dissolved Fe²⁺ pool typically observed in methanic zones of rapidly accumulating coastal and continental margin sediments.

Seafloor deposition of water-based drill cuttings generates distinctive and lengthy sediment bacterial community changes

The spatial extent and persistence of bacterial change caused by deposition of water-based drill cuttings on the seafloor were explored by a community-wide approach. Ten centimeter sediment cores were sampled along transects extending from ≤15 m to 250 m from three nearby drilling sites in the southern Barents Sea. Eight months, 8 years and 15 years, respectively, had passed since the completion of the drillings. At locations heavily affected by drill cuttings, the two most recent sites showed distinct, corresponding deviances from native Barents Sea bacterial community profiles. Otherwise marginal groups, including Mollicutes and Clostridia, showed significant increases in relative abundance. Beyond 100 m from the boreholes the microbiotas appeared undisturbed, as they did at any distance from the 15-years old borehole. The extent of the biological distortion, as indicated by the present microbial study, agreed with previously published macrofaunal surveys at the same drilling sites.

Subgroup level differences of physiological activities in marine Lokiarchaeota

Asgard is a recently discovered archaeal superphylum, closely linked to the emergence of eukaryotes. Among Asgard archaea, Lokiarchaeota are abundant in marine sediments, but their in situ activities are largely unknown except for Candidatus 'Prometheoarchaeum syntrophicum'. Here, we tracked the activity of Lokiarchaeota in incubations with Helgoland mud area sediments (North Sea) by stable isotope probing (SIP) with organic polymers, 13C-labelled inorganic carbon, fermentation intermediates and proteins. Within the active archaea, we detected members of the Lokiarchaeota class Loki-3, which appeared to mixotrophically participate in the degradation of lignin and humic acids while assimilating CO2, or heterotrophically used lactate. In contrast, members of the Lokiarchaeota class Loki-2 utilized protein and inorganic carbon, and degraded bacterial biomass formed in incubations. Metagenomic analysis revealed pathways for lactate degradation, and involvement in aromatic compound degradation in Loki-3, while the less globally distributed Loki-2 instead rely on protein degradation. We conclude that Lokiarchaeotal subgroups vary in their metabolic capabilities despite overlaps in their genomic equipment, and suggest that these subgroups occupy different ecologic niches in marine sediments.

Application of Fourier transform ion cyclotron resonance mass spectrometry in deciphering molecular composition of soil organic matter: A review

Swiftly deciphering soil organic matter (SOM) composition is critical for research on soil degradation and restoration. Recent advances in analytical techniques (e.g., optical methods and mass spectrometry) have expanded our understanding of the composition, origin, and evolution of SOM. In particular, the use of Fourier transform ion cyclotron resonance mass spectrometers (FTICR-MS) makes it possible to interpret SOM compositions at the molecular level. In this review, we discuss extraction, enrichment, and purification methods for SOM using FTICR-MS analysis; summarize ionization techniques, FTICR-MS mechanisms, data analysis methods, and molecular compositions of SOM in different environments (providing new insights into its origin and evolution); and discuss factors affecting its molecular diversity. Our results show that digenesis, combustion, pyrolysis, and biological metabolisms jointly contribute to the molecular diversity of SOM molecules. The SOM thus formed can further undergo photodegradation during transportation from land to fresh water (and subsequently oceans), resulting in the formation of dissolved organic matter (DOM). Better understanding the molecular features of DOM therefore accelerates our understanding of SOM evolution. In addition, we assess the degradation potential of SOM in different environments to better inform soil remediation methods. Finally, we discuss the merits and drawbacks of applying FTICR-MS on the analysis of SOM molecules, along with existing gaps in knowledge, challenges, and new opportunities for research in FTICR-MS applications and SOM identification.

Spectral Characterization of Dissolved Organic Matter in Seawater and Sediment Pore Water from the Arctic Fjords (West Svalbard) in Summer

Fjords in the high Arctic, as aquatic critical zones at the interface of land-ocean continuum, are undergoing rapid changes due to glacier retreat and climate warming. Yet, little is known about the biogeochemical processes in the Arctic fjords. We measured the nutrients and the optical properties of dissolved organic matter (DOM) in both seawater and sediment pore water, along with the remote sensing data of the ocean surface, from three West Svalbard fjords. A cross-fjord comparison of fluorescence fingerprints together with downcore trends of salinity, Cl−, and PO43− revealed higher impact of terrestrial inputs (fluorescence index: ~1.2–1.5 in seawaters) and glaciofluvial runoffs (salinity: ~31.4 ± 2.4 psu in pore waters) to the southern fjord of Hornsund as compared to the northern fjords of Isfjorden and Van Mijenfjorden, tallying with heavier annual runoff to the southern fjord of Hornsund. Extremely high levels of protein-like fluorescence (up to ~4.5 RU) were observed at the partially sea ice-covered fjords in summer, in line with near-ubiquity ice-edge blooms observed in the Arctic. The results reflect an ongoing or post-phytoplankton bloom, which is also supported by the higher levels of chlorophyll a fluorescence at the ocean surface, the very high apparent oxygen utilization through the water column, and the nutrient drawdown at the ocean surface. Meanwhile, a characteristic elongated fluorescence fingerprint was observed in the fjords, presumably produced by ice-edge blooms in the Arctic ecosystems. Furthermore, alkalinity and the humic-like peaks showed a general downcore accumulation trend, which implies the production of humic-like DOM via a biological pathway also in the glaciomarine sediments from the Arctic fjords.

Effect of salinity and algae biomass on mercury cycling genes and bacterial communities in sediments under mercury contamination: Implications of the mercury cycle in arid regions

Lakes in arid regions are experiencing mercury pollution via air deposition and surface runoff, posing a threat to ecosystem safety and human health. Furthermore, salinity and organic matter input could influence the mercury cycle and composition of bacterial communities in the sediment. In this study, the effects of salinity and algae biomass as an important organic matter on the genes (merA and hgcA) involved in the mercury cycle under mercury contamination were investigated. Archaeal merA and hgcA were not detected in sediments of lake microcosms, indicating that bacteria rather than archaea played a crucial role in mercury reduction and methylation. The high content of mercury (300 ng g^-1) could reduce the abundance of both merA and hgcA. The effects of salinity and algae biomass on mercury cycling genes depended on the gene type and dose. A higher input of algae biomass (250 mg L^-1) led to an increase of merA abundance, but a decrease of hgcA abundance. All high inputs of mercury, salinity, and algae biomass decreased the richness and diversity of bacterial communities in sediment. Further analysis indicated that higher mercury (300 ng g^-1) led to an increased relative abundance of mercury methylators, such as Ruminococcaceae, Bacteroidaceae, and Veillonellaceae. Under saline conditions (10 and 30 g L^-1), the richness of specific bacteria associated with mercury reduction (Halomonadaceae) and methylation (Syntrophomonadaceae) increased compared to the control. The input of algae biomass led to an increase in the specific bacterial communities associated with the mercury cycle and the richness of bacteria involved in the decomposition of organic matter. These results provide insight into mercury cycle-related genes and bacterial communities in the sediments of lakes in arid regions.

Linkage between water soluble organic matter and bacterial community in sediment from a shallow, eutrophic lake, Lake Chaohu, China

Lacustrine sediment played important roles in migration and transformation of its water soluble organic matter (WSOM), and the source and composition of WSOM would affect water trophic status and the fate of pollutants. However, we know little about the pathway of WSOM transformation and its driving bacterial communities in lacustrine sediment. In the present study, we investigated the spatial distribution patterns of sediment WSOM and its fluorescent fractions across Lake Chaohu using fluorescence spectroscopy, and explored WSOM compositional structure through our proposed calculated ratios. In addition, we also analyzed sediment bacterial community using Illumina sequencing technology, and probed the possible pathway of sediment WSOM transformation under the mediate of indigenous bacteria. Our results showed that the inflowing rivers affected the spatial distribution patterns of WSOM and its five fractions (including tyrosine-, tryptophan-, fulvic acid-, humic acid-like substances and soluble microbial productions), and sediment WSOM originated from fresh algae detritus or bacterial sources. In parallel, we also found that Proteobacteria (mainly γ-Proteobacteria and δ-Proteobacteria), Firmicutes (mainly Bacilli), Chloroflexi, Acidobacteria, Planctomycetes and Actinobacteria dominate sediment bacterial community. Furthermore, these dominant bacteria triggered sediment WSOM transformation, specifically, the humic acid-like substances could be converted into fulvic acid-like substances, and further degraded into aromatic protein-like and SMP substances. In addition, our proposed ratios (P-L:H-L, Ar-P:SMP and H-L ratio), as supplementary tool, were effective to reveal WSOM composition structure. These results figured out possible pathway of WSOM transformation, and revealed its microbial mechanism in lacustrine sediment.

Defining the sediment prokaryotic communities of the Indian River Lagoon, FL, USA, an Estuary of National Significance

The Indian River Lagoon, located on the east coast of Florida, USA, is an Estuary of National Significance and an important economic and ecological resource. The Indian River Lagoon faces several environmental pressures, including freshwater discharges through the St. Lucie Estuary; accumulation of anoxic, fine-grained, organic-rich sediment; and metal contamination from agriculture and marinas. Although the Indian River Lagoon has been well-studied, little is known about its microbial communities; thus, a two-year 16S amplicon sequencing study was conducted to assess the spatiotemporal changes of the sediment bacterial and archaeal groups. In general, the Indian River Lagoon exhibited a prokaryotic community that was consistent with other estuarine studies. Statistically different communities were found between the Indian River Lagoon and St. Lucie Estuary due to changes in porewater salinity causing microbes that require salts for growth to be higher in the Indian River Lagoon. The St. Lucie Estuary exhibited more obvious prokaryotic seasonality, such as a higher relative abundance of Betaproteobacteriales in wet season and a higher relative abundance of Flavobacteriales in dry season samples. Distance-based linear models revealed these communities were more affected by changes in total organic matter and copper than changes in temperature. Anaerobic prokaryotes, such as Campylobacterales, were more associated with high total organic matter and copper samples while aerobic prokaryotes, such as Nitrosopumilales, were more associated with low total organic matter and copper samples. This initial study fills the knowledge gap on the Indian River Lagoon bacterial and archaeal communities and serves as important data for future studies to compare to determine possible future changes due to human impacts or environmental changes.

Global diversity of microbial communities in marine sediment

Marine sediment covers 70% of Earth’s surface and harbors as much biomass as seawater. However, the global taxonomic diversity of marine sedimentary communities, and the spatial distribution of that diversity remain unclear. We investigated microbial composition from 40 globally distributed sampling locations, spanning sediment depths of 0.1 to 678 m. Statistical analysis reveals that oxygen presence or absence and organic carbon concentration are key environmental factors for defining taxonomic composition and diversity of marine sedimentary communities. Global marine sedimentary taxonomic richness predicted by species–area relationship models is 7.85 × 10³ to 6.10 × 10⁵ for Archaea and 3.28 × 10⁴ to 2.46 × 10⁶ for Bacteria as amplicon sequence variants, which is comparable to the richness in seawater and that in topsoil.

Microbial life in marine sediment contributes substantially to global biomass and is a crucial component of the Earth system. Subseafloor sediment includes both aerobic and anaerobic microbial ecosystems, which persist on very low fluxes of bioavailable energy over geologic time. However, the taxonomic diversity of the marine sedimentary microbial biome and the spatial distribution of that diversity have been poorly constrained on a global scale. We investigated 299 globally distributed sediment core samples from 40 different sites at depths of 0.1 to 678 m below the seafloor. We obtained ∼47 million 16S ribosomal RNA (rRNA) gene sequences using consistent clean subsampling and experimental procedures, which enabled accurate and unbiased comparison of all samples. Statistical analysis reveals significant correlations between taxonomic composition, sedimentary organic carbon concentration, and presence or absence of dissolved oxygen. Extrapolation with two fitted species–area relationship models indicates taxonomic richness in marine sediment to be 7.85 × 10³ to 6.10 × 10⁵ and 3.28 × 10⁴ to 2.46 × 10⁶ amplicon sequence variants for Archaea and Bacteria, respectively. This richness is comparable to the richness in topsoil and the richness in seawater, indicating that Bacteria are more diverse than Archaea in Earth’s global biosphere.

Molecular Evidence of Arsenic Mobility Linked to Biodegradable Organic Matter

Molecular characteristics of natural organic matter (NOM) and their potential connections to arsenic enrichment processes remain poorly understood. Here, we examine dissolved organic matter (DOM) in groundwater and water-soluble organic matter (WSOM) in aquifer sediments being depth-matched with groundwater samples from a typical arid-semiarid basin (Hetao Basin, China) hosting high arsenic groundwater. We used Fourier transform ion cyclotron resonance mass spectrometry to determine molecular characteristics of DOM and WSOM and evaluate potential roles of biodegradable compounds in microbially mediated arsenic mobility at the molecular level. High-arsenic groundwater DOM was generally enriched in recalcitrant molecules (including lignins and aromatic structures). Although potential contribution of recalcitrant compounds to arsenic enrichment cannot be ruled out, preferential degradation of the labile molecules coupled with reduction of Fe(III) (oxyhydr)oxides seemed to dominate arsenic mobilization. Both the number and the intensity of biodegradable compounds (including aliphatic/proteins and carbohydrates) were higher in WSOM than those in DOM in depth-matched high-arsenic groundwater (arsenic >0.67 μmol/L or 50 μg/L). Groundwater arsenic concentration generally increased with the increase in the number and the intensity of unique biodegradable compounds (especially N-containing compounds) in WSOM at matched depths. Anoxic incubations of sediments and deionized water show that more arsenic and Fe(II) were released from aquifer sediments with greater numbers and intensities of consumed biodegradable compounds in WSOM (especially N-containing compounds), with a higher proportion of microbially derived compounds produced. These observations indicate that the biodegradation of aliphatic/proteins and carbohydrates (especially CHON formulas) in WSOM fueling the reductive dissolution of Fe(III) (oxyhydr)oxides predominantly promotes arsenic release from aquifer solids. Our unique data present a better understanding of arsenic mobilization shaped by microbial degradation of labile organic compounds in anoxic aquifers at the molecular level.

A continental scale spatial investigation of lake sediment organic compositions using sedimentomics

Sedimentomics is a new method used to investigate carbon cycling in sediment organic matter. This untargeted method, based on metabolomics workflows, was used to investigate the molecular composition of sediment organic matter across northern Canada (Nunavut and Northwest Territories). Unique "lake districts" were defined using unsupervised clustering based on changes in sediment organic carbon compositions across space. Supervised machine learning analyses were used to compare the "lake districts" to commonly used regional classification systems like the treeline, ecozones, and/or georegions. Treeline was the best model to explain the compositional variance of sediment organic carbon from lakes across Canada, closely followed by the georegions model. A novel sediment metaphenomics analysis was also applied to determine how well environmental constraints explain the variation of sediment organic matter composition across a continent. We determined that sedimentomics is more informative than traditional measurements (such as total organic carbon) and can be integrated with other "omics" techniques.

Contrasting bacterial and archaeal distributions reflecting different geochemical processes in a sediment core from the Pearl River Estuary

Microbial community structure and metabolic activities have profound impacts on biogeochemical processes in marine sediments. Functional bacteria such as nitrate- and sulfate-reducing bacteria respond to redox gradients by coupling specific reactions amenable to relevant energy metabolisms. However, similar functional patterns have not been observed for sedimentary archaea (except for anaerobic methanotrophs and methanogens). We coupled taxonomic composition with comprehensive geochemical species to investigate the participation of distinct bacteria and archaea in sedimentary geochemical cycles in a sediment core (300 cm) from Pearl River Estuary (PRE). Geochemical properties (NO₃⁻, dissolved Mn and Fe, SO₄²⁺, NH₄⁺; dissolved inorganic carbon (DIC), δ¹³C_DIC, dissolved organic carbon (DOC), total organic carbon (TOC), δ¹³C_TOC, and fluorescent dissolved organic matter (FDOM)) exhibited strong depth variability of different trends. Bacterial 16S rRNA- and dsrB gene abundance decreased sharply with depth while archaeal and bathyarchaeotal 16S rRNA gene copies were relatively constant. This resulted in an increase in relative abundance of archaea from surface (11.6%) to bottom (42.8%). Network analysis showed that bacterial groups of Desulfobacterales, Syntrophobacterales and Gammaproteobacteria were significantly (P < 0.0001) associated with SO₄²⁻ and dissolved Mn while archaeal groups of Bathyarchaeota, Group C3 and Marine Benthic Group D (MBGD) showed close positive correlations (P < 0.0001) with NH₄⁺, δ¹³C_TOC values and humic-like FDOM. Our study suggested that these bacterial groups dominated in redox processes relevant to sulfate or metal oxides, while the archaeal groups are more like to degrade recalcitrant organic compounds in anaerobic sediments.

Fluoride contributes to the shaping of microbial community in high fluoride groundwater in Qiji County, Yuncheng City, China

As a toxic element, excessive amounts of fluoride in environment can be harmful because of its antimicrobial activity, however little is known about the relationship between fluoride and the bacterial community in groundwater systems. Here, we use samples from a typical fluorosis area to test the hypothesis that fluoride concentration is a fundamental structuring factor for bacterial communities in groundwater. Thirteen groundwater samples were collected; high-throughput 16S rRNA gene sequencing and statistical analysis were conducted to compare the bacterial community composition in individual wells. The results showed that Proteobacteria, with most relative abundance in groundwater, decreased along the groundwater fluoride concentration. Additionally, relative abundances of 12 families were also statistically correlated with fluoride concentration. The bacterial community was significantly explained by TOC (P = 0.045) and fluoride concentration (P = 0.007) of groundwater. This suggests that fluoride and TOC likely plays an important role in shaping the microbial community structure in these groundwater systems. Our research suggest that fluoride concentration should be taken into consideration in future when evaluating microbial response to environmental conditions in groundwater system, especially for fluoride rich groundwater.

Gas seepage pockmark microbiomes suggest the presence of sedimentary coal seams in the Öxarfjörður graben of northeastern Iceland

Natural gas seepage pockmarks are found off- and onshore in the Öxarfjörður graben, Iceland. The bacterial communities of two onshore seepage sites were analysed by 16S rRNA gene amplicon sequencing; the geochemical characteristics, hydrocarbon content, and the carbon isotope composition of the sites were also determined. While one site was found to be characterised by biogenic origin of methane gas, with a carbon isotope ratio (δ¹³C (‰)) of -63.2, high contents of organic matter and complex hydrocarbons, the other site showed a mixed origin of the methane gas (δ¹³C (‰) = -26.6) with geothermal characteristics and lower organic matter content. While both sites harboured Proteobacteria as the most abundant bacterial phyla, the Deltaproteobacteria were more abundant at the geothermal site and the Alphaproteobacteria at the biogenic site. The Dehalococcoidia class of phylum Chloroflexi was abundant at the geothermal site while the Anaerolineae class was more abundant at the biogenic site. Bacterial strains from the seepage pockmarks were isolated on a variety of selective media targeting bacteria with bioremediation potential. A total of 106 strains were isolated and characterised, including representatives from the phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. This article describes the first microbial study on gas seepage pockmarks in Iceland.

Nagasaki sediments reveal that long-term fate of plutonium is controlled by select organic matter moieties

Forecasting the long-term fate of plutonium (Pu) is becoming increasingly important as more worldwide military and nuclear-power waste is being generated. Nagasaki sediments containing bomb-derived Pu that was deposited in 1945 provided a unique opportunity to explore the long-term geochemical behavior of Pu. Through a combination of selective extractions and molecular characterization via electrospray ionization Fourier-transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS), we determined that 55 ± 3% of the bomb-derived ^239,240Pu was preferentially associated with more persistent organic matter compounds in Nagasaki sediments, particularly those natural organic matter (NOM) stabilized by Fe oxides (NOM_Fe-oxide). Other organic matter compounds served as a secondary sink of these bomb-derived ^239,240Pu (31 ± 2% on average), and <20% of the ^239,240Pu was immobilized by inorganic mineral particles. In a narrow, ^239,240Pu-enriched layer of only 9-cm depth (total core depth was 600 cm), N-containing carboxyl aliphatic and/or alicyclic molecules (CCAM) in NOM_Fe-oxide and other NOM fractions immobilized the majority of ^239,240Pu. Among the cluster of N-containing CCAM moieties, hydroxamate siderophores, the strongest known Pu chelators in nature, were further detected in these "aged" Nagasaki bomb residue-containing sediments. While present long-term disposal and environmental remediation modeling assume that solubility limits and sorption to mineral surfaces control Pu subsurface mobility, our observations suggest that NOM, which is present in essentially all subsurface systems, undoubtedly plays an important role in sequestrering Pu. Ignoring the role of NOM in controlling Pu fate and transport is not justified in most environmental systems.

Characterisation of microbial communities of drill cuttings piles from offshore oil and gas installations

Drill cuttings (DC) are produced during hydrocarbon drilling operations and are composed of subsurface rock coated with hydrocarbons and drilling fluids. Historic disposal of DC at sea has resulted in the formation of large piles on the seabed that may be left in situ following infrastructure decommissioning. This study provides a first insight into the microbial abundance, diversity and community structure of two DC piles from North Sea oil and gas installations. The abundance of both bacteria and archaea was lower in DC than in surrounding natural sediments. Microbial diversity and richness within DC were low but increased with distance from the piles. Microbial community structure was significantly different in DC piles compared to nearby natural sediments. DC bacterial communities were dominated by Halomonas, Dietzia and Dethiobacter. The presence of such organisms suggests a potential function of hydrocarbon degradation ability and may play an active role in DC pile remediation.