Biodegradation of sulfamethoxazole by a bacterial consortium of Achromobacter denitrificans PR1 and Leucobacter sp. GP

Reis, Ana C.; Čvančarová, Monika; Liu, Ying; Lenz, Markus; Hettich, Timm; Kolvenbach, Boris A.; Corvini, Philippe F.-X.; Nunes, Olga C.

doi:10.1007/s00253-018-9411-9

Cited by 44 publications

(42 citation statements)

References 84 publications

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“…As reported previously, strain GP shares the highest 16S rRNA gene sequence similarity with members of the genus Leucobacter, 94.6–96.9% (see Additional file 2 Table S3), below the 98.7% threshold currently used to define a new species [26, 46] and close to the 97% threshold used to define a new genus [47]. The phylogenetic analysis inferred from the alignment of the near-complete 16S rRNA gene between all fully sequenced Leucobacter spp.…”

Section: Resultsmentioning

confidence: 80%

“…Contig 5, with 74 kb, was found to contain various integrative and conjugative elements (Table 2) [44]. Besides, this contig contained all antimicrobial resistance genes found in the genome of strain GP ( sul 1, tet (33), aad A1, qac E), as well as two copies of the sad A gene encoding for the previously described sulfonamide monooxygenase [26]. Table 2 Homology searches for contig 5 against the NCBI database [45] revealed residual homology to Enterobacter cloacae strain EclC2185’s genomic island (accession number MH545561.1, 5187 bp alignment with 99% identity to the genomic island of this strain) containing a class I integron with multi-drug resistance genes ( aad A1, sul 1, and qac E).…”

Section: Resultsmentioning

confidence: 99%

“…Furthermore, the evolution of this abundant group of Alphaproteobacteria and their ecological importance has been further elucidated using comparative genomic approaches [25]. In a previous study, we have described a microbial consortium between Achromobacter denitrificans strain PR1 and strain GP that depends on strain PR1’s presence for growth [26]. Strain GP showed the highest pairwise similarity of its 16S rRNA gene sequence to members of the genus Leucobacter .…”

Section: Introductionmentioning

confidence: 99%

“…Strain GP showed the highest pairwise similarity of its 16S rRNA gene sequence to members of the genus Leucobacter . Independently of the tested culture media, cofactors and culture conditions no pure cultures were obtained for strain GP [26]. To characterize strain GP, we have sequenced the two-member consortium and reconstructed its draft genome.…”

Section: Introductionmentioning

confidence: 99%

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Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader ‘Candidatus Leucobacter sulfamidivorax’ strain GP

et al. 2019

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BackgroundMicrobial communities recurrently establish metabolic associations resulting in increased fitness and ability to perform complex tasks, such as xenobiotic degradation. In a previous study, we have described a sulfonamide-degrading consortium consisting of a novel low-abundant actinobacterium, named strain GP, and Achromobacter denitrificans PR1. However, we found that strain GP was unable to grow independently and could not be further purified.ResultsPrevious studies suggested that strain GP might represent a new putative species within the Leucobacter genus (16S rRNA gene similarity < 97%). In this study, we found that average nucleotide identity (ANI) with other Leucobacter spp. ranged between 76.8 and 82.1%, further corroborating the affiliation of strain GP to a new provisional species. The average amino acid identity (AAI) and percentage of conserved genes (POCP) values were near the lower edge of the genus delimitation thresholds (65 and 55%, respectively). Phylogenetic analysis of core genes between strain GP and Leucobacter spp. corroborated these findings. Comparative genomic analysis indicates that strain GP may have lost genes related to tetrapyrrole biosynthesis and thiol transporters, both crucial for the correct assembly of cytochromes and aerobic growth. However, supplying exogenous heme and catalase was insufficient to abolish the dependent phenotype. The actinobacterium harbors at least two copies of a novel genetic element containing a sulfonamide monooxygenase (sadA) flanked by a single IS1380 family transposase. Additionally, two homologs of sadB (4-aminophenol monooxygenase) were identified in the metagenome-assembled draft genome of strain GP, but these were not located in the vicinity of sadA nor of mobile or integrative elements.ConclusionsComparative genomics of the genus Leucobacter suggested the absence of some genes encoding for important metabolic traits in strain GP. Nevertheless, although media and culture conditions were tailored to supply its potential metabolic needs, these conditions were insufficient to isolate the PR1-dependent actinobacterium further. This study gives important insights regarding strain GP metabolism; however, gene expression and functional studies are necessary to characterize and further isolate strain GP. Based on our data, we propose to classify strain GP in a provisional new species within the genus Leucobacter, ‘Candidatus Leucobacter sulfamidivorax‘.

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Section: Resultsmentioning

confidence: 80%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader ‘Candidatus Leucobacter sulfamidivorax’ strain GP

et al. 2019

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“…GP. 11 A. denitrificans efficiently utilizes 16 phthalate diesters and their downstream products through the protocatechuate 3,4-cleavage pathway, which makes A. denitrificans SP1 a very attractive candidate to be employed as an efficient biofactory in waste water treatment processes. 12 A. denitrificans strain SP1 efficiently remediates di(2-ethylhexyl) phthalate.…”

Section: Ftir Spectramentioning

confidence: 99%

Oxidized humic acids from the soil of heat power plant

Miletić

Avdalović

Milić

et al. 2020

JSCS

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Humic acids isolated from the soil of a heat power plant (HA-E) contaminated with oil were analyzed by Fourier transform infrared spectroscopy (FTIR). In comparison with a humic acids standard (HA-S), a lack of an intense broad band of the stretching vibrations of hydrogen-bonded hydroxyl groups (3600-3200 cm-1) is evident. The HA-E spectra have a peak at 1649 cm-1 , which could belong to carbonyl groups. HA-E are heavily oxidized and among the isolated microorganisms, Achromobacter denitrificans may be responsible for such intensive oxidation of HA-E. To the phylogenetically diverse nitrate-reducing microorganisms that have the capacity to utilize reduced HA as electron donors in soils, A. denitrificans can be added.

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Substrate availability and toxicity shape the structure of microbial communities engaged in metabolic division of labor

Fang

Chen

Tang

et al. 2022

mLife

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Metabolic division of labor (MDOL) represents a widespread natural phenomenon, whereby a complex metabolic pathway is shared between different strains within a community in a mutually beneficial manner. However, little is known about how the composition of such a microbial community is regulated. We hypothesized that when degradation of an organic compound is carried out via MDOL, the concentration and toxicity of the substrate modulate the benefit allocation between the two microbial populations, thus affecting the structure of this community. We tested this hypothesis by combining modeling with experiments using a synthetic consortium. Our modeling analysis suggests that the proportion of the population executing the first metabolic step can be simply estimated by Monod‐like formulas governed by substrate concentration and toxicity. Our model and the proposed formula were able to quantitatively predict the structure of our synthetic consortium. Further analysis demonstrates that our rule is also applicable in estimating community structures in spatially structured environments. Together, our work clearly demonstrates that the structure of MDOL communities can be quantitatively predicted using available information on environmental factors, thus providing novel insights into how to manage artificial microbial systems for the wide application of the bioindustry.

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Biodegradation of sulfamethoxazole by a bacterial consortium of Achromobacter denitrificans PR1 and Leucobacter sp. GP

Cited by 44 publications

References 84 publications

Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader ‘Candidatus Leucobacter sulfamidivorax’ strain GP

Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader ‘Candidatus Leucobacter sulfamidivorax’ strain GP

Oxidized humic acids from the soil of heat power plant

Substrate availability and toxicity shape the structure of microbial communities engaged in metabolic division of labor

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