Sediment prokaryotic microbial community and potential biogeochemical cycle from saline lakes shaped by habitat

Changes in bacterial diversity of full-scale anaerobic digesters treating secondary sludge

Anaerobic digestion (AD) of secondary sludge (2S) presents challenges because of its high microbial content and complex cell wall structures. The purpose of this study was to investigate the effects of spatiotemporally-variable factors such as water temperature and dietary habits on the 2S bacterial community and its migration into digesters. Bacterial communities and functions were analyzed using high-throughput pyrosequencing. Spatiotemporal variations in bacterial populations were identified, with genera such as Zoogloea and Dechloromonas migrating into digesters and influencing organic degradation. Notably, Zoogloea was negatively correlated with VS removal, potentially due to cell floc formation, whereas Dechloromonas was positively correlated, suggesting its role in acetate metabolism anaerobically. This study emphasizes the importance of microbial migration from 2S to digesters, highlighting the need to monitor microbial communities along with conventional parameters to increase AD performance. These findings provide practical insights into optimizing sludge management and improving biogas production in AD plants.

Conductive materials enhance anaerobic membrane bioreactor (AnMBR) treating waste leachate at high organic loading rates

The treatment of landfill leachate using anaerobic membrane bioreactors (AnMBRs) often faces challenges such as poor removal efficiency, low methane yield and membrane fouling. This study applied AnMBRs with incrementally adding conductive materials to enhance the treatment of landfill leachate under high organic loading rates(35 kg COD/(m3∙d)). With 50 g/L activated carbon, COD removal percentages and methane yield increased to 81.03 ± 2.12% and 0.34 ± 0.01 m³ CH₄/kg COD, respectively. The addition of conductive materials dramatically increased EPS content of the sludge, which not only enhanced inter-microbial electron transmission but also increased the sludge's biological activity. The primary membrane fouling type for AnMBRs was cake layer, with Ca being the main inorganic foulant, and humic substances and proteins being the principal organic foulants. Combined cleaning methods effectively removed membrane foulants, resulting in total membrane flux recovery rates of higher than 96.5%. The conductive materials stimulated the enrichment and synergistic collaboration of acid-producing bacteria and methanogenic archaea.

A baroduric immobilized composite material promoting remediation of oil-polluted sediment at typical deep-sea condition: The performances and potential mechanisms

Contriving immobilized bioreagent is of great significance to enhance bioremediation of marine oil pollution. However, there remains a notable scarcity of correlational study conducted at deep sea condition. Herein, we first developed a baroduric microsphere encasing biotic and chemical materials to remediate oil-contaminated sediments at deep-sea microcosm. Total oil degradation efficiency of microsphere-treated group reached 71% within a month, representing an approximate 35% increase compared to natural remediation. Absorption and biodegradation by microsphere provided a comparable contribution to oil elimination. Together with scanning electron microscope observation, the physical mechanism was that the reticulate structure of microsphere surface facilitating oil adsorption and bacteria attachment. Via metabarcoding analysis for meta and metabolically-active microbes, we demonstrated the primary working center was located at the microsphere. Proteobacteria, Firmicutes, Bacteroidota and Desulfobacterota were the key activated bacteria. More importantly, we revealed the ecological mechanisms were associated with the following aspects: 1) the addition of microsphere significantly improved the metabolic activity of bacteria (particularly including several oil-degrading taxa); 2) the microspheres enhanced ecological stability and microbial functional diversification during bioremediation; 3) expressing activity of pathways involving oil component degradation, biosurfactant production, biofilm architecture, biogeochemical and energy cycling all were observed to be up-regulated in microsphere-treated samples. Altogether, our results provide important theoretical guidance and data support on application of immobilization technology in removing in-situ oil pollution of deep-sea sediment.

Bioavailability of dissolved organic matter (DOM) derived from seaweed Gracilaria lemaneiformis meditated by microorganisms

Seaweed Gracilaria lemaneiformis, a significant oceanic primary producer, releases substantial dissolved organic matter (DOM) during growth and decay, potentially impacting coastal organic carbon reservoirs and microbial communities. This study aimed to investigate the bioavailability of Gracilaria-derived DOM and its interactions with microbial communities. Laboratory experiments introduced Gracilaria-derived DOM into natural seawater, tracking variations in DOM composition, microbial structure, and eight extracellular enzyme activities over 168 h. The results indicated a rapid breakdown of dissolved organic carbon, nitrogen, and phosphorus, representing 48 % to 90 % of their total concentrations within 168 h, highlighting the high DOM bioavailability. Tryptophan substances were identified as the primary components of Gracilaria-derived DOM, being highly labile and utilized by microorganisms. Within the initial 0-12 h of DOM influx, Proteobacteria significantly increased and dominated in bacterial community, while after 48 h, as DOM decomposed, Desulfobacterota became the dominant group. The labile DOM stimulated bacteria, particularly Proteobacteria, to release substantial extracellular enzymes that peaked within the first 12 h. Subsequent substrate depletion led to decreased enzyme activities. Positive correlations were observed among bacterial abundance, enzyme activities, and tryptophan substances, emphasizing the intricate interplay among microbial communities, labile DOM, and extracellular enzymes. This study underscores the high bioavailability of Gracilaria-derived DOM and its interactions with microbial communities in nearshore environments.

Unveiling the role of emerging metagenomics for the examination of hypersaline environments

Hypersaline ecosystems are distributed all over the globe. They are subjected to poly-extreme stresses and are inhabited by halophilic microorganisms possessing multiple adaptations. The halophiles have many biotechnological applications such as nutrient supplements, antioxidant synthesis, salt tolerant enzyme production, osmolyte synthesis, biofuel production, electricity generation etc. However, halophiles are still underexplored in terms of complex ecological interactions and functions as compared to other niches. The advent of metagenomics and the recent advancement of next-generation sequencing tools have made it feasible to investigate the microflora of an ecosystem, its interactions and functions. Both target gene and shotgun metagenomic approaches are commonly employed for the taxonomic, phylogenetic, and functional analyses of the hypersaline microbial communities. This review discusses different types of hypersaline niches, their residential microflora, and an overview of the metagenomic approaches used to investigate them. Various applications, hurdles and the recent advancements in metagenomic approaches have also been focused on here for their better understanding and utilization in the study of hypersaline microbiome.

Aquibaculum sediminis sp. nov., a halotolerant bacteria isolated from salt lake sediment

An aerobic, Gram-stain negative bacterium was isolated from sediment samples of Barkol salt lake in Hami City, Xinjiang Uygur Autonomous Region, China, with the number EGI_FJ10229T. The strain is ellipse-shaped, oxidase-negative, catalase-positive, and has white, round, smooth, opaque colonies on marine 2216 E agar plate. Growth occurs at 4.0-37.0 ℃ (optimal:30.0 ℃), pH 7.0-9.0 (optimal: pH 8.0) and NaCl concentration of 0-8.0% (optimal: 3.0%). Phylogenetic analysis based on 16S rRNA gene and genome sequences indicated that the isolated strain should be assigned to the genus Aquibaculum and was most closely related to Aquibaculum arenosum CAU 1616 T. Average nucleotide identity (ANI) and Average amino-acid identity (AAI) values between the type species of the genus Aquibaculum and other related type species were lower than the threshold values recommended for bacterial species. The genomic DNA G + C content of EGI_FJ10229T was 65.41%. The major polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine, phosphatidylethanolamine and unidentified phospholipid. The major fatty acids (> 5%) were C19:0 cyclo ω8c (42.0%) and C18:1 ω7c (33.78%). The respiratory quinone identified was Q-10. Differential phenotypic and genotypic characteristics of this strain and species of genus Aquibaculum showed that the strain should be classified as representing a new species belonging to this genus, for which the name Aquibaculum sediminis sp. nov. is proposed. The type strain of the proposed novel species is EGI_FJ10229T (= KCTC 8570 T = GDMCC 1.4598 T).

Bioelectrochemically altering microbial ecology in upflow anaerobic sludge blanket to enhance methanogenesis fed with high-sulfate methanolic wastewater

A bioelectrochemical upflow anaerobic sludge blanket (BE-UASB) was constructed and compared with the traditional UASB to investigate the role of bioelectrocatalysis in modulating methanogenesis and sulfidogensis involved within anaerobic treatment of high-sulfate methanolic wastewater (COD/SO42- ratio ≤ 2). Methane production rate for BE-UASB was 1.4 times higher than that of the single UASB, while SO42- removal stabilized at 16.7%. Bioelectrocatalysis selectively enriched key functional anaerobes and stimulated the secretion of extracellular polymeric substances, especially humic acids favoring electron transfer, thereby accelerating the electroactive biofilms development of electrodes. Methanomethylovorans was the dominant genus (35%) to directly convert methanol to CH4. Methanobacterium as CO2 electroreduction methane-producing archaea appeared only on electrodes. Acetobacterium exhibited anode-dependence, which provided acetate for sulfate-reducing bacteria (norank Syntrophobacteraceae and Desulfomicrobium) through synergistic coexistence. This study confirmed that BE-UASB regulated the microbial ecology to achieve efficient removal and energy recovery of high-sulfate methanolic wastewater.

Unravelling biosynthesis and biodegradation potentials of microbial dark matters in hypersaline lakes

Biosynthesis and biodegradation of microorganisms critically underpin the development of biotechnology, new drugs and therapies, and environmental remediation. However, most uncultured microbial species along with their metabolic capacities in extreme environments, remain obscured. Here we unravel the metabolic potential of microbial dark matters (MDMs) in four deep-inland hypersaline lakes in Xinjiang, China. Utilizing metagenomic binning, we uncovered a rich diversity of 3030 metagenome-assembled genomes (MAGs) across 82 phyla, revealing a substantial portion, 2363 MAGs, as previously unclassified at the genus level. These unknown MAGs displayed unique distribution patterns across different lakes, indicating a strong correlation with varied physicochemical conditions. Our analysis revealed an extensive array of 9635 biosynthesis gene clusters (BGCs), with a remarkable 9403 being novel, suggesting untapped biotechnological potential. Notably, some MAGs from potentially new phyla exhibited a high density of these BGCs. Beyond biosynthesis, our study also identified novel biodegradation pathways, including dehalogenation, anaerobic ammonium oxidation (Anammox), and degradation of polycyclic aromatic hydrocarbons (PAHs) and plastics, in previously unknown microbial clades. These findings significantly enrich our understanding of biosynthesis and biodegradation processes and open new avenues for biotechnological innovation, emphasizing the untapped potential of microbial diversity in hypersaline environments.

Response of sediment microbial communities to the flow effect of the triangular artificial reef: A simulation-based experimental study

Artificial reefs (ARs), as an important tool for habitat restoration, play significant impacts on benthic microbial ecosystems. This study utilized 16S rRNA gene sequencing technology and computational fluid dynamics (CFD) flow simulation to investigate the effects of flow field distribution around ARs on microbial community structure. The results revealed distinct regional distribution patterns of microbial communities affected by different hydrodynamic conditions. Flow velocity and flow regime of water in sediment-water interface shaped the microbial community structure. The diversity and richness in R-HF were significantly decreased compared to other five regions (p < 0.05). At the phyla and OUT levels, most abundant taxa (1>%) showed an enrichment trend in R-HB. However, more than half of differentially abundant taxa were enriched in R-HB, which was significantly correlated with organic matter (OM). Bugbase phenotypic predictions indicated a low abundance of the anaerobic phenotype in R-HF and a high abundance of the biofilm-forming phenotype in R-HB.

Response of microbial diversity and function to the degradation of Barkol Saline Lake

Barkol Lake, a shrinking hypersaline lake situated in the northeast of Xinjiang, China, has experienced the exposure of its riverbed and the gradual drying up of its original sediment due to climate change and human activities, resulting in the formation of alkaline soils. These changes have correspondingly altered the physicochemical characteristics of the surrounding environment. Microorganisms play a crucial role, with special functioning involved in various nutrient cycling and energy transfer in saline lake environments. However, little is known about how the microbial community dynamics and metabolic functions in this shrinking saline lake relate to the degradation process. To address this knowledge gap, a cultivation-independent method of amplicon sequencing was used to identify and analyze the microbial community and its potential ecological functions in the sediment and degraded area. The microbial community diversity was found to be significantly lower in the degraded areas than in the sediment samples. The Pseudomonadota was dominant in Barkol Saline Lake. The abundance of Desulfobacterota and Bacillota in the degraded areas was lower than in the lake sediment, while Pseudomonadota, Acidobacteriota, and Actinobacteriota showed an opposite trend. The βNTI showed that microbial community assembly was primarily associated with deterministic processes in Barkol Saline Lake ecosystems and stochastic processes at the boundary between sediment and degraded areas. Functional predictions showed that sulfur metabolism, particularly sulfate respiration, was much higher in sediment samples than in the degraded areas. Overall, these findings provided a possible perspective for us to understand how microorganisms adapt to extreme environments and their role in saline lakes under environmental change.

Metagenomic assembled genomes indicated the potential application of hypersaline microbiome for plant growth promotion and stress alleviation in salinized soils

Climate change is causing unpredictable seasonal variations globally. Due to the continuously increasing earth's surface temperature, the rate of water evaporation is enhanced, conceiving a problem of soil salinization, especially in arid and semi-arid regions. The accumulation of salt degrades soil quality, impairs plant growth, and reduces agricultural yields. Salt-tolerant, plant-growth-promoting microorganisms may offer a solution, enhancing crop productivity and soil fertility in salinized areas. In the current study, genome-resolved metagenomic analysis has been performed to investigate the salt-tolerating and plant growth-promoting potential of two hypersaline ecosystems, Sambhar Lake and Drang Mine. The samples were co-assembled independently by Megahit, MetaSpades, and IDBA-UD tools. A total of 67 metagenomic assembled genomes (MAGs) were reconstructed following the binning process, including 15 from Megahit, 26 from MetaSpades, and 26 from IDBA_UD assembly tools. As compared to other assemblers, the MAGs obtained by MetaSpades were of superior quality, with a completeness range of 12.95%-96.56% and a contamination range of 0%-8.65%. The medium and high-quality MAGs from MetaSpades, upon functional annotation, revealed properties such as salt tolerance (91.3%), heavy metal tolerance (95.6%), exopolysaccharide (95.6%), and antioxidant (60.86%) biosynthesis. Several plant growth-promoting attributes, including phosphate solubilization and indole-3-acetic acid (IAA) production, were consistently identified across all obtained MAGs. Conversely, characteristics such as iron acquisition and potassium solubilization were observed in a substantial majority, specifically 91.3%, of the MAGs. The present study indicates that hypersaline microflora can be used as bio-fertilizing agents for agricultural practices in salinized areas by alleviating prevalent stresses.

IMPORTANCE

The strategic implementation of metagenomic assembled genomes (MAGs) in exploring the properties and harnessing microorganisms from ecosystems like hypersaline niches has transformative potential in agriculture. This approach promises to redefine our comprehension of microbial diversity and its ecosystem roles. Recovery and decoding of MAGs unlock genetic resources, enabling the development of new solutions for agricultural challenges. Enhanced understanding of these microbial communities can lead to more efficient nutrient cycling, pest control, and soil health maintenance. Consequently, traditional agricultural practices can be improved, resulting in increased yields, reduced environmental impacts, and heightened sustainability. MAGs offer a promising avenue for sustainable agriculture, bridging the gap between cutting-edge genomics and practical field applications.

Alterations in the composition and metabolite profiles of the saline-alkali soil microbial community through biochar application

Saline-alkali soil poses significant chanllenges to sustainable development of agriculture. Although biochar is commonly used as a soil organic amendment, its microbial remediation mechanism on saline-alkali soil requires further confirmation. To address this, we conducted a pot experiment using cotton seedlings to explore the potential remediation mechanism of rice straw biochar (BC) at three different levels on saline-alkaline soil. The results showed that adding of 2% biochar greatly improved the quality of saline-alkaline soil by reducing pH levels, electrical conductivity (EC), and water-soluble ions. Moreover, biochar increased the soil organic matter (SOM), nutrient availability and extracellular enzyme activity. Interestingly, it also reduced soil salinity and salt content in various cotton plant tissues. Additionally, biochar had a notable impact on the composition of the microbial community, causing changes in soil metabolic pathways. Notably, the addition of biochar promoted the growth and metabolism of dominant salt-tolerant bacteria, such as Proteobacteria, Bacteroidota, Acidobacteriota, and Actinobacteriota. By enhancing the positive correlation between microorganisms and metabolites, biochar alleviated the inhibitory effect of salt ions on microorganisms. In conclusion, the incorporation of biochar significantly improves the soil microenvironment, reduces soil salinity, and shows promise in ameliorating saline-alkaline soil conditions.

New insights into the sustainable use of co-pyrolyzed dredged sediment for the in situ remediation of Cd polluted sediments in coastal rivers

The remediation of Cd-polluted sediment in coastal rivers is essential because of its potential hazards to river and marine ecosystems. Herein, a co-pyrolysis product of contaminated dredged sediment (S@BC) was innovatively applied to cap and immobilize Cd-contaminated sediment in coastal rivers in situ, and their remediation efficiencies, mechanisms, and microbial responses were explored based on a 360 d incubation experiment. The results showed that although S@BC immobilization and capping restrained sediment Cd release to the overlying water, S@BC capping presented a high inhibitory efficiency (66.0% vs. 95.3% at 360 d). Fraction analysis indicated that labile Cd was partially transformed to stable fraction after remediation, with decreases of 0.5%- 32.7% in the acid-soluble fraction and increases of 5.0%- 182.8% in the residual fraction. S@BC immobilization and capping had minor influences on the sediment bacterial community structure compared to the control. S@BC could directly adsorb sediment mobile Cd (precipitation and complexation) to inhibit Cd release and change sediment properties (e.g., pH and cation exchange capacity) to indirectly reduce Cd release. Particularly, S@BC capping also promoted Cd stabilization by enhancing the sediment sulfate reduction process. Comparatively, S@BC capping was a priority approach for Cd-polluted sediment remediation. This study provides new insights into the remediation of Cd-contaminated sediments in coastal rivers.

Enhancement of anaerobic digestion of high salinity food waste by magnetite and potassium ions: Digestor performance, microbial and metabolomic analyses

The study investigated the effectiveness of magnetite and potassium ions (K+) in enhancing anaerobic digestion of high salinity food waste. Results indicated that both magnetite and K+ improved anaerobic digestion in high-salt environments, and their combination yielded even better results. The combination of magnetite and K+ promoted microorganism activity, and resulted in increased abundance of DMER64, Halobacteria and Methanosaeta. Metabolomic analysis revealed that magnetite mainly influenced quorum sensing, while K+ mainly stimulated the synthesis of compatible solutes, aiding in maintaining osmotic balance. The combined additives regulated pathways such as ATP binding cassette transport, methane metabolism, and inhibitory substance metabolism, enabling cells to resist environmental stress and maintain normal metabolic activity. Overall, this study demonstrated the potential of magnetite and K+ to enhance food waste anaerobic digestion in high salt conditions and provided valuable insights into the molecular mechanism.

The response mechanism of microorganisms to the organic carbon-driven formation of black and odorous water

The formation of black and odorous water is a complex process influenced by various factors such as organic matter and environmental conditions. However, there are limited studies on the role of microorganisms in water and sediment during the blackening and odorization process. In this study, we investigated the characteristics of black and odorous water formation by simulating organic carbon-driven black and odorous water through indoor experiments. The study revealed that the water turned black and odorous when DOC reached 50 mg/L and the microbial community structure in the water changed significantly during this process, with the relative abundance of Desulfobacterota increasing significantly and Desulfovibrio being the main dominant genus in Desulfobacterota. Additionally, we observed a notable decrease in the α-diversity of the microbial community in water and a considerable increase in microbial function of sulfur compounds respiration in water. In contrast, the sediment microbial community changed slightly, and the main functions of the sediment microbial community remained unchanged. The partial least squares path model (PLS-PM) suggested that organic carbon will drive the blackening and odorization process by affecting DO levels and microbial community structure and that the contribution of Desulfobacterota in water to the formation of black and odorous water was higher than that in sediment. Overall, our study provides insights into the characteristics of black and odorous water formation and suggests potential ways to prevent its formation by controlling DOC and inhibiting the growth of Desulfobacterota in water bodies.