Unraveling bacteria-mediated degradation of lignin-derived aromatic compounds in a freshwater environment

Li, Jialing; Wang, Pandeng; Salam, Nimaichand; Li, Xin; Ahmad, Manzoor; Tian, Yongsheng; Duan, Li; Huang, Li-Nan; Xiao, Min; Mou, Xiaozhen; Li, Wenjun

doi:10.1016/j.scitotenv.2020.141236

Cited by 29 publications

(19 citation statements)

References 60 publications

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“…We also included in our growth profile assays marine-isolated Rhodococcus strains MS13 and H-CA8f as control [ 48 , 49 ], since they apparently do not harbor VanOD-encoded genes, even though they carry the classical PCA pathway [ 50 ], as revealed by BLAST searches and confirmed by growth on PCA as a sole carbon and energy source ( Figure 4 ). Accordingly, both Rhodococcus strains of marine origin were unable to grow on VA ( Figure 4 ), confirming the previous bioinformatic survey that revealed the absence of VanOD encoded genes, and suggesting that VA degradation activity could be linked to Rhodococcus species found mainly in soil or freshwater environments, probably correlated to lignin depolymerization [ 51 , 52 , 53 ].…”

Section: Resultssupporting

confidence: 85%

Identification of a Phylogenetically Divergent Vanillate O-Demethylase from Rhodococcus ruber R1 Supporting Growth on Meta-Methoxylated Aromatic Acids

et al. 2022

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Rieske-type two-component vanillate O-demethylases (VanODs) catalyze conversion of the lignin-derived monomer vanillate into protocatechuate in several bacterial species. Currently, VanODs have received attention because of the demand of effective lignin valorization technologies, since these enzymes own the potential to catalyze methoxy group demethylation of distinct lignin monomers. In this work, we identified a phylogenetically divergent VanOD from Rhodococcus ruber R1, only distantly related to previously described homologues and whose presence, along with a 3-hydroxybenzoate/gentisate pathway, correlated with the ability to grow on other meta-methoxylated aromatics, such as 3-methoxybenzoate and 5-methoxysalicylate. The complementation of catabolic abilities by heterologous expression in a host strain unable to grow on vanillate, and subsequent resting cell assays, suggest that the vanAB genes of R1 strain encode a proficient VanOD acting on different vanillate-like substrates; and also revealed that a methoxy group in the meta position and a carboxylic acid moiety in the aromatic ring are key for substrate recognition. Phylogenetic analysis of the oxygenase subunit of bacterial VanODs revealed three divergent groups constituted by homologues found in Proteobacteria (Type I), Actinobacteria (Type II), or Proteobacteria/Actinobacteria (Type III) in which the R1 VanOD is placed. These results suggest that VanOD from R1 strain, and its type III homologues, expand the range of methoxylated aromatics used as substrates by bacteria.

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Section: Resultssupporting

confidence: 85%

Identification of a Phylogenetically Divergent Vanillate O-Demethylase from Rhodococcus ruber R1 Supporting Growth on Meta-Methoxylated Aromatic Acids

et al. 2022

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“…The present investigation was consistent with such observations—in TLW, higher relative abundances of cyanobacteria were detected in the stratified lakes (Big Turkey and Little Turkey Lakes) compared to the shallow, well-mixed lake (Wishart Lake) (Figure 3; Table 1). Picocyanobacteria have previously been observed to reach peak abundances prior to the onset of thermal stratification, (Callieri & Stockner, 2000; Fahnenstiel et al, 1991; Li et al, 2020), but herein Synechococcales sequences were found to be predominant in lakes year-round independent of the onset of thermal stratification. Highly variable vertical distribution of populations within thermally stratified lakes has previously been reported (Hall & Vincent, 1994; Stockner et al, 2006) and samples collected at different depths within the metalimnion of Big Turkey and Little Turkey Lake also showed variability in picocyanobacterial 16S rRNA gene ASVs suggesting heterogeneity in water column distribution.…”

Section: Discussion Conclusion and Implicationsmentioning

confidence: 84%

Early Seasonal Increases and Persistence in Relative Abundance of Potentially Toxic Cyanobacteria: Concerning Impacts of Extended Ice-Free Periods in Northern Temperate Lakes

Cameron¹,

Müller²,

Stone

et al. 2022

Preprint

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Cyanobacteria threaten public and ecosystem health globally through the production of secondary metabolites including potent toxins, and disruption of water treatment processes. Warmer water temperatures and high nutrient availability are key characteristics associated with the occurrence of cyanobacteria. There is typically concern of cyanobacteria blooms (e.g., visible biomass accumulations) occurring in the summer season of eutrophic systems. However, in this study, the proliferation of cyanobacteria in lakes across all seasons and in absence of visual biomass indicators of bloom condition was observed in three oligotrophic lakes of the Turkey Lakes Watershed (TLW) in Ontario, located within a sugar maple dominated forest on the Canadian Shield. Almost 40 years of ice phenology data showed that rising temperatures have led to significantly longer ice-free periods and aquatic growing seasons in TLW. Warming is especially evident in the autumn, with the onset of ice-on periods commencing significantly later in the year. Cyanobacterial communities in three interconnected temperate, oligotrophic lakes were characterized over an 18-month period from July 2018 to January 2020 (across 10 synoptic sampling events) using amplicon sequencing of the V4 region of the 16S rRNA gene. During the winter, there was low abundance or occasional absence of cyanobacteria; however, a non-photosynthetic basal lineage of cyanobacteria (Melainabacteria) was present during periods of ice cover. Notably, photosynthetic populations reappeared in the water column immediately following the loss of ice-cover-they were especially abundant in lakes with surficial geology and lake morphometry that favor greater availability of fine sediment and associated nutrients. Thus, this collective analysis demonstrates that the convergence of key abiotic and biotic factors-climate forcing of hydrological and biogeochemical processes, and intrinsic landscape features-enable increases in the relative abundance of potentially toxic cyanobacteria within the temperate forest biome of Canada over increasingly longer periods of time.

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“…The carbon cycle of aromatic compounds in the ocean is an essential part of the global geochemical cycle. , R. nubinhibens can degrade aromatic compounds through the protocatechuate branch of the β-ketoadipate pathway (Figure A). , Based on sequencing analysis of the strains and heterogeneous expressions of two key genes in the nonmarine bacterium E. coli, previous studies showed that R. nubinhibens possess the ring-cleaving β-ketoadipate pathway encoded by the pca gene cluster containing pobA , pcaD , pcaC , pcaH , and pcaG (Figure B).…”

Section: Resultsmentioning

confidence: 99%

Developing a Base Editing System for Marine Roseobacter Clade Bacteria

et al. 2023

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The Roseobacter clade bacteria are of great significance in marine ecology and biogeochemical cycles, and they are potential microbial chassis for marine synthetic biology due to their versatile metabolic capabilities. Here, we adapted a CRISPR-Cas-based system, base editing, with the combination of nuclease-deactivated Cas9 and deaminase for Roseobacter clade bacteria. Taking the model roseobacter Roseovarius nubinhibens as an example, we achieved precise and efficient genome editing at single-nucleotide resolution without generating double-strand breaks or requesting donor DNAs. Since R. nubinhibens can metabolize aromatic compounds, we interrogated the key genes in the β-ketoadipate pathway with our base editing system via the introduction of premature STOP codons. The essentiality of these genes was demonstrated, and for the first time, we determined PcaQ as a transcription activator experimentally. This is the first report of CRISPR-Cas-based genome editing in the entire clade of Roseobacter bacteria. We believe that our work provides a paradigm for interrogating marine ecology and biogeochemistry with direct genotype-and-phenotype linkages and potentially opens a new avenue for the synthetic biology of marine Roseobacter bacteria.

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Unraveling bacteria-mediated degradation of lignin-derived aromatic compounds in a freshwater environment

Cited by 29 publications

References 60 publications

Identification of a Phylogenetically Divergent Vanillate O-Demethylase from Rhodococcus ruber R1 Supporting Growth on Meta-Methoxylated Aromatic Acids

Identification of a Phylogenetically Divergent Vanillate O-Demethylase from Rhodococcus ruber R1 Supporting Growth on Meta-Methoxylated Aromatic Acids

Early Seasonal Increases and Persistence in Relative Abundance of Potentially Toxic Cyanobacteria: Concerning Impacts of Extended Ice-Free Periods in Northern Temperate Lakes

Developing a Base Editing System for Marine Roseobacter Clade Bacteria

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