Bacteria In Sediments Research Articles

Spatiotemporal Distribution of nirS-Type Denitrifiers in Cascade Reservoir Sediments of the Qinghai Plateau

Compared to single damming, the impact of cascade damming on nitrogen-related microorganisms in river ecosystems exhibits greater complexity. However, there is still a lack of research on the response of denitrifiers to the construction of cascade reservoirs. A study was conducted on 10 cascade reservoirs in the upper reaches of the Yellow River to investigate the impact of cascade reservoir construction on nirS-type denitrifying bacteria in sediments. Sediment samples were collected in May (dry season) and August (wet season) of 2023. The spatiotemporal characteristics of the nirS-type denitrifying bacterial community and gene abundance were analyzed using Illumina high-throughput sequencing and real-time fluorescence quantification PCR (qPCR). Redundancy analysis (RDA) and variation partitioning (VP) were utilized to assess the impact of environmental factors on these communities. The results showed the following: (1) Proteobacteria was the predominant phylum of nirS-type denitrifying bacteria in cascade reservoir sediments. At the genus level, unclassified Proteobacteria (69.51–95.64%) showed the highest relative abundance, followed by Paracoccus, Rhodanobacter, and Pseudomonas, indicating that unclassified Proteobacteria may dominate denitrification in these reservoir sediments. (2) The α and β diversity indices of nirS-type denitrifying bacteria were higher in the dry season than in the wet season, and also higher in young reservoirs compared to old reservoirs (p < 0.05). (3) Temporally, the abundance of the nirS gene was significantly higher in the wet season (12.71 × 107 copies/g dry sediment) compared to the dry season (66.35 × 105 copies/g dry sediment). Spatially, the abundance of the nirS gene was higher in the central region, while relatively lower at both ends. (4) RDA and VP analysis indicated that the community structure and abundance of nirS-type denitrifying bacteria were significantly influenced by the total nitrogen in sediments (19.31%) and water temperature (14.13%). Spearman correlation analysis showed that organic carbon significantly affected the diversity of nirS-type denitrifying bacteria (p < 0.05). The results contribute to a better understanding of the nitrogen-related microbial community in cascade reservoir sediments of the Yellow River, providing a scientific basis for reservoir management.

The Source of Thermophilic Bacteria in Lake Baikal Cold Sediments – Coastal Hydrotherms or Deep Fluids?

The sources of thermophilic bacteria revealed in cold Lake Baikal sediments are considered. Comparative analysis of the taxonomic position of thermophilic microorganisms from four terrestrial hot springs at Lake Baikal coast and from the bottom sediments associated with hydrocarbon discharge was carried out. The sequences of thermophilic microorganisms with the same taxonomic position were revealed both in the hot springs and bottom sediments. Some microbial species occurred only in the hydrotherm samples or only in those from the sediments. Gas-saturated fluids from the hydrocarbon generation zone at the depth of 4‒6 km are the most probable source of thermophilic microorganisms in the bottom sediments.

The diversity and biogeography of bacterial communities in lake sediments across different climate zones

Bacteria are diverse and play important roles in biogeochemical cycling of aquatic ecosystems, but the global distribution patterns of bacterial communities in lake sediments across different climate zones are still obscure. Here we integrated the high-throughput sequencing data of 750 sediment samples from published literature to investigate the distribution of bacterial communities in different climate zones and the potential driving mechanisms. The obtained results indicated that the diversity and richness of bacterial community were notably higher in temperate and cold zones than those in other climate zones. In addition, the bacterial community composition varied significantly in different climate zones, which further led to changes in bacterial functional groups. Specifically, the relative abundance of nitrogen cycling functional groups in polar zones was notably higher compared to other climate zones. Regression analysis revealed that climate (mean annual precipitation, MAP; and mean annual temperature, MAT), vegetation, and geography together determined the diversity pattern of sediment bacterial community on a global scale. The results of partial least squares path modeling further demonstrated that climate was the most significant factor affecting the composition and diversity of bacterial communities, and MAP was the most important climate factor affecting the composition of bacteria community (R2 = 0.443, P < 0.001). It is worth noting that a strong positive correlation was observed between the abundance of the dominant bacterial group uncultured_f_Anaerolineaceae and the normalized difference vegetation index (NDVI; P < 0.001), suggesting that vegetation could affect bacterial community diversity by influencing dominant bacterial taxa. This study enhances our understanding of the global diversity patterns and biogeography of sediment bacteria.

Temperature, sediment resuspension, and salinity drive the prevalence of Vibrio vulnificus in the coastal Baltic Sea

ABSTRACT The number of Vibrio -related infections in humans, e.g., by Vibrio vulnificus , has increased along the coasts of the Baltic Sea. Due to climate change, vibriosis risk is expected to increase. It is, therefore, pertinent to design a strategy for mitigation of the vibriosis threat in the Baltic Sea area, but a prerequisite is to identify the environmental conditions promoting the occurrence of pathogenic Vibrio spp., like V. vulnificus . To address this, we sampled three coastal Baltic sites in Finland, Germany, and Denmark with salinities between 6 and 21 from May to October 2022. The absolute and relative abundances of Vibrio spp. and V. vulnificus in water were compared to environmental conditions, including the presence of the eelgrass Zostera marina , which has been suggested to reduce pathogenic Vibrio species abundance. In the water column, V. vulnificus only occurred at the German station between July and August at salinity 8.1–11.2. Temperature and phosphate (PO 4 3– ) were identified as the most influencing factors for Vibrio spp. and V. vulnificus . The accumulation of Vibrio spp. in the sediment and the co-occurrence with sediment bacteria in the water column indicate that sediment resuspension contributed to V. vulnificus abundance. Interestingly, V. vulnificus co-occurred with specific cyanobacteria taxa, as well as specific bacteria associated with cyanobacteria. Although we found no reduction in Vibrio spp. or V. vulnificus associated with eelgrass beds, our study underscores the importance of extended heatwaves and sediment resuspension, which may elevate the availability of PO 4 3– , for Vibrio species levels at intermediate salinities in the Baltic Sea. IMPORTANCE Elevated sea surface temperatures are increasing the prevalence of pathogenic Vibrio at higher latitudes. The recent increase in Vibrio -related wound infections and deaths along the Baltic coasts is, therefore, of serious health concern. We used culture-independent data generated from three Baltic coastal sites in Denmark, Germany, and Finland from May to October (2022), with a special focus on Vibrio vulnificus , and combined it with environmental data. Our temporal model shows that temperature, combined with sediment resuspension, drives the prevalence of V. vulnificus at intermediate salinities in the coastal Baltic Sea.

Understanding the mechanisms behind the antibacterial activity of magnesium hydroxide nanoparticles against sulfate-reducing bacteria in sediments

Nanomaterials, with their small size, surface characteristics, and antibacterial properties, are extensively employed across environmental, energy, biomedical, agricultural, and other industries. This study examined the antibacterial efficacy of magnesium hydroxide (Mg(OH)2) nanoparticles (NPs) against sulfate-reducing bacteria (SRB) within sediments. The inhibitory effects of two types of Mg(OH)2 NPs with distinct particle sizes (20.3 and 29.6 nm) and concentrations (0–10.0 mg/mL) were examined under optimal treatment conditions. The antibacterial mechanisms of Mg(OH)2 NPs through direct contact and dissolution effects were determined. The results revealed a correlation between the concentration, particle size, and inhibitory activity, with the smallest NPs (20.3 nm) at the highest concentration (10.0 mg/mL) substantially reducing SRB counts from 8.77 ± 0.18 to 6.48 ± 0.13 log10 colony forming units/mL after 6 h treatment. Treatment with high concentrations of Mg(OH)2 NPs induced cellular damage, reduced intracellular lactate dehydrogenase activity, and elevated intracellular catalase activity and H2O2 content, suggesting that the contact effect of NPs stimulated SRB. This leads to oxidative stress response and structural damage to the cell membrane, which has emerged as the primary driver of the antibacterial action of Mg(OH)2 NPs. This study presents a novel nanomaterial that can inhibit and control SRB in natural sedimentary environments.

The effects and mechanism of organic matter degradation in river sediment driven by humic-reducing bacteria

The reduction of organic pollutants in sediments is essential for controlling the rebound of black-odor waterbodies. Humic-reducing bacteria are promising in the anaerobic remediation of river sediments. However, the material conditions and environmental factors influencing organic matter (OM) degraded by humic-reducing bacteria in river sediment remain unclear. In this study, humic-reducing bacteria agents (HRBs) were used to remediate sediments with different contamination levels. The result indicated that HRBs remove light fraction organic matter (LFOM) in sediment with a high active organic matter (ATOM) content and can remove heavy fraction organic matter (HFOM) in sediment with a high degree of humification. Correlation analysis showed that OM removal was significantly correlated with fluorescein diacetate (FDA) hydrolase activity (R = 0.89, P ≤ 0.01) and acidified volatile sulfides (AVS) content (R = 0.81, P ≤ 0.05), respectively. Combined analyses of changes in iron morphology and FDA hydrolase activity revealed that HRBs mediated the reduction process of iron minerals, leading to an increase in Fe(II) content in sediment. HFOM complexed with iron minerals was released and could be further decomposed and utilized by FDA hydrolases. In addition, the process of OM degraded by HRBs can induce the accumulation of Fe(II) and AVS. The work helps to understand the mechanism of OM degraded by HRBs in sediment and the applicable conditions for the effective removal of OM by HRBs to control the rebound of black-odor waterbodies caused by endogenous pollution.

Mobilization of phosphorus in sediments of eutrophic lakes induced by elevated sulfate levels

Elevated sulfate levels in eutrophic lakes have been observed to induce the release of endogenous phosphorus. While previous studies have predominantly examined its impact on iron-bound phosphorus (FeP), the influence on organic phosphorus (OP), a crucial active phosphorus component in sediments, remains poorly understood. In this study, mesocosms were established with lactate supplementation and varying sulfate concentrations to explore sulfate reduction and its impacts on phosphorus mobilization in freshwater sediments. Lactate addition induced hypoxia and provided substrates, thereby stimulating sulfate reduction with a decline of sulfate levels, an increase of sulfide concentrations, and fluctuations of sulfate-reducing bacteria. Meanwhile, concentrations of total dissolved phosphorus and phosphate were dramatically promoted during lactate decomposition, with a higher sulfate concentration associated with greater phosphorus elevation, correlating with the decrease of total phosphorus in sediment. The increase in phosphorus of the overlying water was partly attributed to FeP release from the sediment, confirmed by a decrease in its sediment content. FeP release was ascribed to dissimilatory reduction of iron oxides or chemical reduction mediated by sulfides in anoxic sediments, leading to the desorption and subsequent release of phosphorus. Evidences included the proliferation of iron-reducing bacteria, a decrease in Fe(II) concentrations in sediment pore- water, and the continuous accumulation of solid iron sulfides in surface sediments. Furthermore, OP mineralization in sediment also contributed to the increase in phosphorus in water columns, confirmed by a reduction in its content and the abundance of fermentation bacteria in surface sediment. Notably, the decrease in OP content accounted for >80 % of the total phosphorus reduction in surface sediment in the end. Thus, sulfur cycling plays a critical role in iron and phosphorus cycling, significantly stimulating not only the mobilization of FeP but also OP in sediments, with OP mineralization potentially being the primary contributor to endogenous phosphorus release.

Environmental Adaptability and Roles in Ammonia Oxidation of Aerobic Ammonia-Oxidizing Microorganisms in the Surface Sediments of East China Sea.

This study investigated the community characteristics and environmental influencing factors of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the surface sediments of the East China Sea. The research found no consistent pattern in the richness and diversity of AOA and AOB with respect to the distance from the shore, indicating a complex interplay of factors. The expression levels of AOA amoA gene and AOB amoA gene in the surface sediments of the East China Sea ranged from 4.49 × 102 to 2.17 × 106 copies per gram of sediment and from 6.6 × 101 to 7.65 × 104 copies per gram of sediment, respectively. Salinity (31.77 to 34.53 PSU) and nitrate concentration (1.51 to 10.12 μmol/L) were identified as key environmental factors significantly affecting the AOA community, while salinity and temperature (13.71 to 19.50°C) were crucial for the AOB community. The study also found that AOA, dominated by the Nitrosopumilaceae family, exhibited higher gene expression levels than AOB, suggesting a more significant role in ammonia oxidation. The expression of AOB was sensitive to multiple environmental factors, indicating a responsive role in nitrogen cycles and ecosystem health. The findings contribute to a better understanding of the biogeochemical processes and ecological roles of ammonia-oxidizing microorganisms in marine sediments.

Long-distance electron transport in multicellular freshwater cable bacteria.

Filamentous multicellular cable bacteria perform centimeter-scale electron transport in a process that couples oxidation of an electron donor (sulfide) in deeper sediment to the reduction of an electron acceptor (oxygen or nitrate) near the surface. While this electric metabolism is prevalent in both marine and freshwater sediments, detailed electronic measurements of the conductivity previously focused on the marine cable bacteria (Candidatus Electrothrix), rather than freshwater cable bacteria, which form a separate genus (Candidatus Electronema) and contribute essential geochemical roles in freshwater sediments. Here, we characterize the electron transport characteristics of Ca. Electronema cable bacteria from Southern California freshwater sediments. Current-voltage measurements of intact cable filaments bridging interdigitated electrodes confirmed their persistent conductivity under a controlled atmosphere and the variable sensitivity of this conduction to air exposure. Electrostatic and conductive atomic force microscopies mapped out the characteristics of the cell envelope's nanofiber network, implicating it as the conductive pathway in a manner consistent with previous findings in marine cable bacteria. Four-probe measurements of microelectrodes addressing intact cables demonstrated nanoampere currents up to 200 μm lengths at modest driving voltages, allowing us to quantify the nanofiber conductivity at 0.1 S/cm for freshwater cable bacteria filaments under our measurement conditions. Such a high conductivity can support the remarkable sulfide-to-oxygen electrical currents mediated by cable bacteria in sediments. These measurements expand the knowledgebase of long-distance electron transport to the freshwater niche while shedding light on the underlying conductive network of cable bacteria.

An S-methyltransferase that produces the climate-active gas dimethylsulfide is widespread across diverse marine bacteria.

Hydrogen sulfide (H2S), methanethiol (MeSH) and dimethylsulfide (DMS) are abundant sulfur gases with roles in biogeochemical cycling, chemotaxis and/or climate regulation. Catabolism of the marine osmolyte dimethylsulfoniopropionate (DMSP) is a major source of DMS and MeSH, but both also result from S-methylation of H2S via MddA, an H2S and MeSH S-methyltransferase whose gene is abundant in soil but scarce in marine environments. Here we identify the S-adenosine methionine (SAM)-dependent MeSH and H2S S-methyltransferase 'MddH', which is widespread in diverse marine bacteria and some freshwater and soil bacteria. mddH is predicted in up to ~5% and ~15% of seawater and coastal sediment bacteria, respectively, which is considerably higher than mddA. Furthermore, marine mddH transcript levels are similar to those for the most abundant DMSP lyase gene dddP. This study implies that the importance of H2S and MeSH S-methylation pathways in marine environments is significantly underestimated.

Effects of cable bacteria on vertical redox profile formation and phenanthrene biodegradation in intertidal sediment responded to tide

Periodic oxygen permeation is critical for pollutant removal within intertidal sediments. However, tidal effects on the vertical redox profile associated with cable bacterial activity is not well understood. In this study, we simulated and quantified the effects of tidal flooding, exposing, and their periodic alternation on vertical redox reactions and phenanthrene removal driven by cable bacteria in the riverbank sediment. Results show that electrogenic sulfur oxidation (e-SOx) mediated by cable bacteria during exposing process drove the vertical permeation of oxidation potential characterized by a decrease in Fe(II) and sulfide concentrations. The sulfate produced was observed in deep sediment (5–10 mm) and served as an electron acceptor for anaerobic oxidation, thereby triggering the functional succession of microbial community. About 78.2 % and 80.8 % of phenanthrene was degraded in deep sediment where cable bacteria grew well under exposing and tidal conditions. Anaerobic processes during tidal flood were also found to be important for the survival of cable bacteria. Higher cable bacteria abundance (up to 1.5 %) was observed under tidal conditions compared to that under continuous exposing conditions and flooding conditions. This might be attributed to lower oxidation stress and sulfide replenishment via sulfate reduction while flooding. Under tidal conditions, the cable bacteria interacted with sulfate reduction bacteria (e.g. Desulfobacca spp. and Desulfatiglans spp.) and maintained the dynamic balance of HS− and SO42− in sediment profiles. This HS−-SO42− cycle could serve as a “redox connector” that continuously delivers oxidation potential to deep sediments, resulting in the removal of organic pollutants. The findings provide preliminary evidence of the self-purification mechanisms within intertidal sediments and suggest a potential strategy for sediment remediation.

Impacts of hydrodynamic disturbance on black blooms: An in-situ study in Lake Taihu

The occurrence of black blooms, a kind of black water phenomenon, mostly formed by the decomposition of cyanobacterial blooms poses a threat to both drinking water supplies and the survival of aquatic organisms. Meteorological and hydrological conditions play a crucial role in their formation, while the specific impact of hydrodynamic disturbances on the black blooms remains unclear. The aim of this study is to investigate in depth the impact of hydrodynamic disturbances on the formation and development of black blooms, as well as their effects on the microbiota in surface sediments during the process. During the occurrence of black blooms in Lake Taihu, in-situ water and surface sediment samples were collected. By combining studies of the changes in water quality and microbial communities, the potential driving mechanisms of hydrodynamic disturbances were analyzed. The results indicate that during the outbreak stage (MS), hydrodynamic disturbances drove the release of anaerobic byproducts in sediments (NH4+-N ≥ 0.5 mg/L, TN ≥ 2.03 mg/L, TP ≥ 0.15 mg/L), and varying levels of hydrodynamic disturbance led to significant differences in microbial communities (ANOSIM, R = 0.477, p < 0.05). This influenced the abundance of microorganisms with carbon and sulfur cycling functions in sediments, where stronger hydrodynamics promoted the coupling of carbon mineralization and fermentation processes, while weaker hydrodynamic disturbances facilitated the coupling of carbon mineralization and sulfate reduction processes. Additionally, hydrodynamic disturbances influenced the potential functions of sulfate-reducing bacteria (SRB) in sediments, altering the interactions between SRB and other microorganisms. This study, for the first time, investigated the impact of hydrodynamics on the formation of black blooms from the perspective of their interaction with microorganisms. These findings broaden our understanding of the significance of hydrodynamic disturbances during black bloom occurrences and contribute to our ability to predict the formation of black blooms through modeling.

Comparing Sediment Bacterial Communities of Volcanic Lakes and Surrounding Rivers in Inner Mongolia Autonomous Region, Northeastern China.

Volcanic lakes originate from a volcanic crater or caldera, and were a crucial component of aquatic ecosystems. Sediment bacteria play an important role in the nutrient cycling of aquatic ecosystems; however, their patterns distribution in volcanic lakes and the surrounding river habitats are unknown. In this study, we compare the sediment bacterial communities and their co-occurrence networks between these two habitats in the Inner Mongolia Autonomous Region, Northeastern China (the Arxan UNESCO Global Geopark), using 16S rRNA gene amplicon sequencing. The results revealed that there were significant variations in the physicochemical parameters of the sediment between these two habitats. The bacterial α-diversity, β-diversity, and community composition of the sediment also significantly differed between these two habitats. Network analysis showed that the co-occurrence patterns and keystone taxa in the sediment differed between these two habitats. The sediment bacterial communities in the river habitats were more stable than those in the lake habitats in the face of environmental change. Canonical correspondence analysis demonstrated that both physical (pH and MC) and nutrition-related factors (TN, TP, LOI, and TOC) were the most important environmental factors shaping the variations of bacterial community composition (BCC) in the sediment between these two habitats. This work could greatly improve our understanding of the sediment BCC of the sediment from aquatic ecosystems in the UNESCO Global Geopark.

Deterministic processes dominate microbial assembly mechanisms in the gut microbiota of cold-water fish between summer and winter.

Exploring the effects of seasonal variation on the gut microbiota of cold-water fish plays an important role in understanding the relationship between seasonal variation and cold-water fish. Gut samples of cold-water fish and environmental samples were collected during summer and winter from the lower reaches of the Yalong River. The results of the 16S rRNA sequencing showed that significant differences were identified in the composition and diversity of gut bacteria of cold-water fish. Co-occurrence network complexity of the gut bacteria of cold-water fish was higher in summer compared to winter (Sum: nodes: 256; edges: 20,450; Win: nodes: 580; edges: 16,725). Furthermore, from summer to winter, the contribution of sediment bacteria (Sum: 5.3%; Win: 23.7%) decreased in the gut bacteria of cold-water fish, while the contribution of water bacteria (Sum: 0%; Win: 27.7%) increased. The normalized stochastic ratio (NST) and infer community assembly mechanisms by phylogenetic bin-based null model analysis (iCAMP) showed that deterministic processes played a more important role than stochastic processes in the microbial assembly mechanism of gut bacteria of cold-water fish. From summer to winter, the contribution of deterministic processes to gut bacteria community assembly mechanisms decreased, while the contribution of stochastic processes increased. Overall, these results demonstrated that seasonal variation influenced the gut bacteria of cold-water fish and served as a potential reference for future research to understand the adaptation of fish to varying environments.

Culture-dependent identification of rare marine sediment bacteria from the Gulf of Mexico and Antarctica.

Laboratory-viable cultivars of previously uncultured bacteria further taxonomic understanding. Despite many years of modern microbiological investigations, the vast majority of bacterial taxonomy remains uncharacterized. While many attempts have been made to decrease this knowledge gap, culture-based approaches parse away at the unknown and are critical for improvement of both culturing techniques and computational prediction efficacy. To this end of providing culture-based approaches, we present a multi-faceted approach to recovering marine environmental bacteria. We employ combinations of nutritional availability, inoculation techniques, and incubation parameters in our recovery of marine sediment-associated bacteria from the Gulf of Mexico and Antarctica. The recovered biodiversity spans several taxa, with 16S-ITS-23S rRNA gene-based identification of multiple isolates belonging to rarer genera increasingly undergoing phylogenetic rearrangements. Our modifications to traditional culturing techniques have not only recovered rarer taxa, but also resulted in the recovery of biotechnologically promising bacteria. Together, we propose our stepwise combinations of recovery parameters as a viable approach to decreasing the bacterial knowledge gap.

The Antibacterial Efficacy of a Compound Extracted from Marine Sediment Bacterium Enterococcus Lactis (S-2): A Comparative Analysis Through In-Vitro and In-Silico Assessments.

Marine sediment bacteria have been generating considerable attention lately due to their potential as valuable reservoirs of novel antimicrobial agents. In vitro and in silico antibacterial activities of antibacterial compounds isolated from the marine sediment bacterium Enterococcus Lactis (S-2). Coastal sediment samples were collected from Rameswaram, Ramnathapuram District, Tamil Nadu, India. Bacteria were isolated using the crowded plate method, and their phenotypic and genotypic characteristics were studied. Purified bacteria were cultured in large volumes, secondary metabolites were extracted, and novel antibacterial agents were isolated from the aqueous extract. Novel compound antibacterial activity was studied through in-silico and invitro. The mechanism activity of antibacterial activity was confirmed by a high-resolution transmission electron microscope. Genotypic analysis confirmed that the isolated S-2 bacteria were Enterococcus lactis, and the aqueous extract showed antibacterial activity against Staphylococcus aureus (17 mm zone of inhibition) and Proteus mirabilis (12 mm zone of inhibition). A bioactive molecule, 13- hydroxy-9-(1-hydroxyethyl)-11-methoxy-2,4dioxapentacyclo[10.7.1.0³,⁴.0⁵,²¹.0¹³,¹⁶]icosa- 1(20),5,7,12,14(19), 16-hexane-18-one, was isolated from aqueous extracts of the S-2 bacterium. Chromatography and spectroscopic analysis confirmed the identity of the isolated compound. Novel compound potential antibacterial activity showing against S. aureus (18 mm zone of inhibition) and MIC 250 μg/mL, which was confirmed by tetrazolium staining. The antibacterial activity mechanism was confirmed by transmission electron microscopy. Molecular docking studies show good binding (-9.9 kcal/mol) of the compound with 3U2D, while molecular dynamic simulation studies confirm the conformationally stable structure of the complex between 3U2D and 13-hydroxy-9-(1-hydroxyethyl)-11-methoxy-2,4-dioxapentacyclo [10.7.1.0³,⁴.0⁵,²¹.0¹³,¹⁶]icosa-1(20),5,7,12,14(19), 16-hexane-18-one. It has been observed from the docking study of 3U2D with standard drug ciprofloxacin that the lower affinity is compared to the test ligand, which has a docking score of 7.3 kcal/mol. Out of interacting residues of protein 3U2D residue, Thr173 and Ile86 formed conventional hydrogen bonds. Marine bacterium E. lactis produces a novel antibacterial compound (13-hydroxy- 9-(1-hydroxyethyl)-11-methoxy-2,4-dioxapentacyclo[10.7.1.0³,⁴.0⁵,²¹.0¹³,¹⁶]icosa- 1(20),5,7,12,14(19),16-hexane-18-one), which shows antibacterial activity against clinical S. aureus, confirmed by in vitro and in silico analysis. This molecule can used as a lead molecule for antibacterial activity.

Biological activities and metabolomic profiles of extracts from the marine sediment bacterium Nocardiopsis alba DP1B cultivated in different media

The soil bacterium DP1B was isolated from a marine sediment collected off the coast of Randayan Island, Kalimantan Barat, Indonesia and identified based on 16S rDNA as Nocardiopsis alba. The bacterium was cultivated in seven different media (A1, ISP1, ISP2, ISP4, PDB, PC-1, and SCB) with three different solvents [distilled water, 5 % NaCl solution, artificial seawater (ASW)] combinations, shaken at 200 rpm, 30 °C, for 7 days. The culture broths were extracted with ethyl acetate and each extract was tested for its antimicrobial activity and brine shrimp lethality, and the chemical diversity was assessed using thin-layer chromatography (TLC), gas chromatography (GC), and liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). The result showed that almost all extracts showed antibacterial but not antifungal activity, whereas their brine shrimp toxicity levels vary from high to low. The best medium/solvent combinations for antibacterial activity and toxicity were PC-1 (in either distilled water, 5% NaCl solution, or ASW) and SCB in ASW. Different chemical diversity profiles were observed on TLC, GC-MS, and LC-MS/MS. Extracts from the PC-1 cultures seem to contain a significant number of cyclic dipeptides, whereas those from the SCB cultures contain sesquiterpenes, indicating that media and solvent compositions can affect the secondary metabolite profiles of DP1B. In addition, untargeted metabolomic analyses using LC-MS/MS showed many molecular ions that did not match with those in the Global Natural Products Social Molecular Networking (GNPS) database, suggesting that DP1B has great potential as a source of new natural products.

Occurrence and distribution of antibiotic pollution and antibiotic resistance genes in seagrass meadow sediments based on metagenomics

Seagrass meadows are one of the most important coastal ecosystems that provide essential ecological and economic services. The contamination levels of antibiotic and antibiotic resistance genes (ARGs) in coastal ecosystems are severely elevated owing to anthropogenic disturbances, such as terrestrial input, aquaculture effluent, and sewage discharge. However, few studies have focused on the occurrence and distribution of antibiotics and their corresponding ARGs in this habitat. Thus, we investigated the antibiotic and ARGs profiles, microbial communities, and ARG-carrying host bacteria in typical seagrass meadow sediments collected from Swan Lake, Caofeidian shoal harbor, Qingdao Bay, and Sishili Bay in the Bohai Sea and northern Yellow Sea. The total concentrations of 30 detected antibiotics ranged from 99.35 to 478.02 μg/kg, tetracyclines were more prevalent than other antibiotics. Metagenomic analyses showed that 342 ARG subtypes associated with 22 ARG types were identified in the seagrass meadow sediments. Multidrug resistance genes and RanA were the most dominant ARG types and subtypes, respectively. Co-occurrence network analysis revealed that Halioglobus, Zeaxanthinibacter, and Aureitalea may be potential hosts at the genus level, and the relative abundances of these bacteria were higher in Sishili Bay than those in other areas. This study provided important insights into the pollution status of antibiotics and ARGs in typical seagrass meadow sediments. Effective management should be performed to control the potential ecological health risks in seagrass meadow ecosystems.

Millennial changes and cooling trends in land surface warm-season temperatures during the Holocene

The scarcity of proxies and calibration models for quantitatively reconstructing millennial timescale seasonal temperature tremendously constraints our understanding of the Holocene thermal variation and its driven mechanisms. Here, we established two global warm-season temperature models by applying deep learning neural network analysis to the branched tetraether membrane lipids originating from surface soil and lacustrine sediment bacteria. We utilized these optimal models in global well-dated lacustrine, peatland, and loess profiles covering the Holocene. All reconstructions of warm-season temperatures, consistent with climate model simulations, indicate cooling trends since the early Holocene, primarily induced by decreased solar radiation in the Northern Hemisphere due to the precession peak at the early. We further demonstrated that the membrane lipids can effectively enhance the future millennial seasonal temperature research, including winter temperatures, without being restricted by geographical location and sedimentary carrier.

The Source of Thermophilic Bacteria in Lake Baikal Cold Sediments—Coastal Hydrotherms or Deep Fluids?

The Source of Thermophilic Bacteria in Lake Baikal Cold Sediments—Coastal Hydrotherms or Deep Fluids?