Genetic potential for exopolysaccharide synthesis in activated sludge bacteria uncovered by genome-resolved metagenomics

Dueholm, Morten Kam Dahl; Besteman, Maaike; Zeuner, Emil Juel; Riisgaard-Jensen, Marie; Nielsen, Morten Eneberg; Vestergaard, Sofie Zacho; Heidelbach, Søren; Bekker, Nicolai Sundgaard; Nielsen, Per Halkjær

doi:10.1016/j.watres.2022.119485

Cited by 32 publications

(18 citation statements)

References 79 publications

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“…Microorganisms can form biofilm with diversified exopolysaccharide (EPS) production in bacteria involved through three pathways such as Wzx/Wzy‐dependent, synthase‐dependent, and ABC transporter‐dependent pathway 68 . The dose‐dependent antibiofilm activity of AgNPs, CuONPs, and Ag‐CuO NCs was shown in Figure 10.…”

Section: Resultsmentioning

confidence: 99%

Green synthesized AgNPs, CuONPs, and Ag‐CuO NCs to effective antibiofilm activities and their potential application in aquaculture

Manikandan,

Arumugam,

Abdul

et al. 2023

Applied Organom Chemis

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The expanded emergence of drug‐resistant microbes remains a concern to the scientific community in developing effective therapeutics. Approach of green chemistry based nanomaterials fabrication is in high demand, due to biocompatibility, non‐toxic, and high surface area that adheres more biomolecules on surface. Green fabricated silver nanoparticles (AgNPs), copper oxide nanoparticles (CuONPs), and silver–copper oxide nanocomposites (Ag‐CuO NCs) were characterized by fluorescence and Raman spectroscopy, field emission scanning electron microscopy (FE‐SEM) with energy‐dispersive X‐ray spectroscopy (EDX), and thermogravimetric (TG)/differential scanning calorimetry (DSC) analysis. Antibiofilm potential of green fabricated AgNPs, CuONPs, and Ag‐CuO NCs was tested against aquatic pathogenic microorganisms such as Aeromonas hydrophila, Pseudomonas aeruginosa, and Staphylococcus aureus. This present study deals with bacterial growth rate, biofilm inhibition, and antibiofilm architecture of AgNPs, CuONPs, and Ag‐CuO NCs under the visualization of confocal laser scanning electron microscopy (CLSM). The FE‐SEM technique was used to observe dense and compact structure (control without NPs treatment) with treatment of NPs that showed reduced amount of cell population in A. hydrophila, P. aeruginosa, and S. aureus. The effective antibiofilm inhibition of Ag‐CuO NCs was achieved by reducing micro‐colonies compared with AgNPs and CuONPs. The AgNPs, CuONPs, and Ag‐CuO NCs demonstrated antibiofilm properties against Gram‐negative and Gram‐positive bacteria, indicating a combinatorial effect of green fabricated NPs in combination with plant metabolites against pathogenic bacteria. As a result, aforementioned nano‐product merits further investigation in order to be used as a potent adjuvant therapy as antagonistic toward various bacterial diseases in aquaculture.

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Section: Resultsmentioning

confidence: 99%

Green synthesized AgNPs, CuONPs, and Ag‐CuO NCs to effective antibiofilm activities and their potential application in aquaculture

Manikandan,

Arumugam,

Abdul

et al. 2023

Applied Organom Chemis

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“…The lack of a comprehensive database of highly annotated EPS genes in wastewater microorganisms has been reported as one main limitation (Albertsen et al, 2013b; Barr et al, 2015; Dueholm et al, 2023). Databases of high-quality MAGs from sludge metagenomes (Singleton et al, 2021) developed using genome-centric metagenomics (Albertsen et al, 2013a) now allow for elucidating at higher resolution the genetic potential of wastewater microorganisms for EPS biosynthesis, like exopolysaccharides (Dueholm et al, 2023). Still only 11% of the 1000 HQ MAGs examined by the authors encoded homologs to known exopolysaccharide gene clusters, highlighting the pressing need to further resolve this EPS and their genetic dark matter.…”

Section: Discussionmentioning

confidence: 99%

“…The task of elucidating EPS biosynthetic pathways is not as simple as for the investigation of, e.g., catabolic pathways within the nitrogen or phosphorus cycle of wastewater microorganisms (Gao et al, 2019;Rubio-Rincon et al, 2019). The lack of a comprehensive database of highly annotated EPS genes in wastewater microorganisms has been reported as one main limitation (Albertsen et al, 2013b;Barr et al, 2015;Dueholm et al, 2023). Databases of high-quality MAGs from sludge metagenomes (Singleton et al, 2021) developed using genome-centric metagenomics (Albertsen et al, 2013a) now allow for elucidating at higher resolution the genetic potential of wastewater microorganisms for EPS biosynthesis, like exopolysaccharides (Dueholm et al, 2023).…”

Section: Genomic and Functional Determinants Of Eps Biosynthesis In C...mentioning

confidence: 99%

“…Competibacter" and other representative genera of wastewater ecosystems clustered relatively closely at functional genetic groups. More detailed, targeted analyses of EPS biosynthetic gene clusters can reveal the fine-scale genetic differentiations, following the recent developments by Dueholm et al (2023).…”

Section: Chemical and Monomeric Variability Of Structural Eps In Gran...mentioning

confidence: 99%

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Production of extracellular polymeric substances in granular sludge under selection forAccumulibacterandCompetibacter

Guimarães

Gubser

Lin

et al. 2023

Preprint

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Granular sludge intensifies the removal of nutrients from wastewater. Granules structured by extracellular polymeric substances (EPS) can be recovered as biomaterial. Links between microbial selection and EPS formation during granulation need to get uncovered. We inoculated anaerobic-aerobic sequencing batch reactors with either flocs or granules to study the relationships between microbial selection, bioaggregation, exopolymer formation, and EPS composition. Selection for slow-growing organisms like the model polyphosphate-accumulating organism "Candidatus Accumulibacter" (max. 83% vs. amplicon sequencing read counts) and glycogen-accumulating organism "Ca. Competibacter" (max. 45%) sustained granulation. Gel-forming exopolymers were produced as high as above 40% of the volatile solids of the biomass by stepwise increase of the organic loading rate (0.3 to 2.0 g CODAc d-1 LR-1). Confocal laser scanning microscopy, FT-IR spectroscopy, and HPAE-PAD chromatography revealed the complex and dynamic chemical compositions of the structural EPS in relation to microbial population shifts along reactor regimes. The analysis of 20 representative genomes of "Ca. Accumulibacter" and "Ca. Competibacter" recovered from public databases revealed their functional potential to produce EPS among other representative wastewater microorganisms. The more than 40 functional gene categories annotated highlight the complexity of EPS metabolic networks from monomers processing to assembly, export, and epimerizations. The combination of ecological engineering principles and systems microbiology will help unravel and direct the production of EPS from wastewater, valorizing residual granular sludge into beneficial biomaterials for the circular economy.

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“…xanthus secretes extracellular polysaccharides during migration and colonization (Zhou and Nan, 2017). A recent study also identified pel genes in the MAG of Myxococcota in activated sludge systems (Dueholm et al, 2023). Pel is widely conserved in gram-positive and gram-negative bacteria, contributes to biofilm and pellicle formation, and mediates cellcell interactions (Jennings et al, 2015).…”

Section: Biofilm Formationmentioning

confidence: 99%

Comparative metagenomic analysis provides novel insights into the ecophysiology of Myxococcota in activated sludge systems

Kurashita,

Hatamoto,

Tomita

et al. 2024

Preprint

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Myxobacteria, belonging to the phylum Myxococcota, are ubiquitous in soil, marine, and other environments. Recent metagenomic sequencing analysis has shown that Myxococcota are predominant in activated sludge systems; however, their ecophysiological traits remain unclear. In this study, we evaluated the potential biological functions of 46 metagenomic bins of Myxococcota reconstructed from activated sludge samples from four municipal sewage treatment plants. The results showed that most Myxococcota bins had an almost complete set of genes associated with glycolysis and the TCA cycle. Palsa-1104 and Polyangiales bins contain glycoside hydrolase GH13 and peptidase M23, which are presumably involved in the lysis of the cell wall and cellular cytoplasm, indicating that part of the Myxococcota from activated sludge can prey on other microorganisms. The previously known cell contact-dependent predatory functions of Myxococcus xanthus are conserved in the family Myxococcaceae, though not in other families. Two bins belonging to Palsa-1104 had phototrophic gene clusters, suggesting that these bins may have both heterotrophic and autotrophic metabolisms. Assessment of the social behavior of the activated sludge Myxococcota, a FruA gene, and a C-signal gene involved in the regulation of fruiting body formation were lacking in Myxococcota bins, suggesting that they are incapable of fruiting body formation. In addition, multiple bins of Myxococcota had novel secondary metabolite biosynthesis gene clusters that may be used for the predation of other bacteria in the activated sludge. Our metagenome-based analyses provide novel insights into the microbial interactions associated with Myxococcota in activated sludge ecosystems.

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Genetic potential for exopolysaccharide synthesis in activated sludge bacteria uncovered by genome-resolved metagenomics

Cited by 32 publications

References 79 publications

Green synthesized AgNPs, CuONPs, and Ag‐CuO NCs to effective antibiofilm activities and their potential application in aquaculture

Green synthesized AgNPs, CuONPs, and Ag‐CuO NCs to effective antibiofilm activities and their potential application in aquaculture

Production of extracellular polymeric substances in granular sludge under selection forAccumulibacterandCompetibacter

Comparative metagenomic analysis provides novel insights into the ecophysiology of Myxococcota in activated sludge systems

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