Mutual Impacts and Interactions of Antibiotic Resistance Genes, Microcystin Synthetase Genes, Graphene Oxide, and Microcystis Aeruginosa in Synthetic Wastewater

Abstract The physiological impacts and interactions of ARGs abundance, microcystin synthetase genes expression, GO, and M. aeruginosa in synthetic wastewater were investigated. The results demonstrated that the absolute abundance of sul1, sul2, tetW, and tetM in synthetic wastewater dramatically increased to 365.2%, 427.1%, 375.2%, and 231.7%, respectively, when the GO concentration was 0.01 mg/L. Even more interesting is that the sum gene copy numbers of mcyA-J also increased to 243.2%. The appearance of GO made the significant correlation exist between ARGs abundance and mcyA-J expression. Furthermore, M. aeruginosa displayed better photosynthetic performance and more MCs production at 0.01 mg/L GO. There were 65 pairs of positive correlations between the intracellular differential metabolites of M. aeruginosa and the abundance of sul1, sul2, tetM, and tetW with various GO concentrations. The GO will impact the metabolites and metabolic pathway in M. aeruginosa. The metabolic changes impacted the ARGs, microcystin synthetase genes, and physiological characters in algal cells. Furthermore, there were complex correlations among sul1, sul2, tetM, tetW, mcyA-J, MCs, photosynthetic performance parameters, and ROS. The different concentration of GO will aggravate the hazards of M. aeruginosa by promoting the expression of mcyA-J, producing more MCs, simultaneously, it may cause the spread of ARGs.

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Quantitative Real-Time PCR for Determination of Microcystin Synthetase E Copy Numbers for Microcystis and Anabaena in Lakes

Applied and Environmental Microbiology ◽

10.1128/aem.69.12.7289-7297.2003 ◽

2003 ◽

Vol 69 (12) ◽

pp. 7289-7297 ◽

Cited By ~ 209

Author(s):

Jaana Vaitomaa ◽

Anne Rantala ◽

Katrianna Halinen ◽

Leo Rouhiainen ◽

Petra Tallberg ◽

...

Keyword(s):

Real Time ◽

Real Time Pcr ◽

Quantitative Methods ◽

Gene Copy ◽

Quantitative Real Time Pcr ◽

Microcystin Synthetase ◽

Copy Numbers ◽

Restoration Strategies ◽

Cell Densities ◽

Gene Copy Numbers

ABSTRACT Cyanobacterial mass occurrences in freshwater lakes are generally formed by Anabaena, Microcystis, and Planktothrix, which may produce cyclic heptapeptide hepatotoxins, microcystins. Thus far, identification of the most potent microcystin producer in a lake has not been possible due to a lack of quantitative methods. The aim of this study was to identify the microcystin-producing genera and to determine the copy numbers of microcystin synthetase gene E (mcyE) in Lake Tuusulanjärvi and Lake Hiidenvesi in Finland by quantitative real-time PCR. The microcystin concentrations and cyanobacterial cell densities of these lakes were also determined. The microcystin concentrations correlated positively with the sum of Microcystis and Anabaena mcyE copy numbers from both Lake Tuusulanjärvi and Lake Hiidenvesi, indicating that mcyE gene copy numbers can be used as surrogates for hepatotoxic Microcystis and Anabaena. The main microcystin producer in Lake Tuusulanjärvi was Microcystis spp., since average Microcystis mcyE copy numbers were >30 times more abundant than those of Anabaena. Lake Hiidenvesi seemed to contain both nontoxic and toxic Anabaena as well as toxic Microcystis strains. Identifying the most potent microcystin producer in a lake could be valuable for designing lake restoration strategies, among other uses.

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Faculty Opinions recommendation of Fewer genes than organelles: extremely low and variable gene copy numbers in mitochondria of somatic plant cells.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.7497956.7792054 ◽

2011 ◽

Author(s):

Wataru Sakamoto

Keyword(s):

Plant Cells ◽

Gene Copy ◽

Copy Numbers ◽

Variable Gene ◽

Gene Copy Numbers

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Predominance of ammonia-oxidizing archaea andnirK-gene-bearing denitrifiers among ammonia-oxidizing and denitrifying populations in sediments of a large urban eutrophic lake (Lake Donghu)

Canadian Journal of Microbiology ◽

10.1139/cjm-2013-0083 ◽

2013 ◽

Vol 59 (7) ◽

pp. 456-464 ◽

Cited By ~ 20

Author(s):

Jie Hou ◽

Xiuyun Cao ◽

Chunlei Song ◽

Yiyong Zhou

Keyword(s):

Amoa Gene ◽

Eutrophic Lake ◽

Gene Copy ◽

Nirs Gene ◽

Bacterial Amoa Gene ◽

Archaeal Amoa Gene ◽

Copy Numbers ◽

Significant Difference ◽

Nirk Gene ◽

Gene Copy Numbers

The coupled nitrification–denitrification process plays a pivotal role in cycling and removal of nitrogen in aquatic ecosystems. In the present study, the communities of ammonia oxidizers and denitrifiers in the sediments of 2 basins (Guozhenghu Basin and Tuanhu Basin) of a large urban eutrophic lake (Lake Donghu) were determined using the ammonia monooxygenase subunit A (amoA) gene and the nitrite reductase gene. At all sites of this study, the archaeal amoA gene predominated over the bacterial amoA gene, whereas the functional gene for denitrification nirK gene far outnumbered the nirS gene. Spatially, compared with the Tuanhu Basin, the Guozhenghu Basin showed a significantly greater abundance of the archaeal amoA gene but less abundance of the nirK and nirS genes, while there was no significant difference of bacterial amoA gene copy numbers between the 2 basins. Unlike the archaeal amoA gene, the nirK gene showed a significant difference in community structure between the 2 basins. Archaeal amoA diversity was limited to the water–sediment cluster of Crenarchaeota, in sharp contrast with nirK for which 22 distinct operational taxonomic units were found. Accumulation of organic substances were found to be positively related to nirK and nirS gene copy numbers but negatively related to archaeal amoA gene copy numbers, whereas the abundance of the bacterial amoA gene was related to ammonia concentration.

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Evolution of dosage compensation does not depend on genomic background

10.1101/2020.08.14.251801 ◽

2020 ◽

Author(s):

Michail Rovatsos ◽

Lukáš Kratochvíl

Keyword(s):

Dosage Compensation ◽

Sex Chromosomes ◽

Sex Chromosome ◽

Genomic Region ◽

Gene Copy ◽

Gene Dose ◽

Copy Numbers ◽

Compensation Mechanisms ◽

Gene Copy Numbers ◽

Softshell Turtles

AbstractOrganisms evolved various mechanisms to cope with the differences in the gene copy numbers between sexes caused by degeneration of Y and W sex chromosomes. Complete dosage compensation or at least expression balance between sexes was reported predominantly in XX/XY, but rarely in ZZ/ZW systems. However, this often-reported pattern is based on comparisons of lineages where sex chromosomes evolved from non-homologous genomic regions, potentially differing in sensitivity to differences in gene copy numbers. Here we document that two reptilian lineages (XX/XY iguanas and ZZ/ZW softshell turtles), which independently co-opted the same ancestral genomic region for the function of sex chromosomes, evolved different gene dose regulatory mechanisms. The independent co-option of the same genomic region for the role of sex chromosome as in the iguanas and the softshell turtles offers a great opportunity for testing evolutionary scenarios on the sex chromosome evolution under the explicit control for the genomic background and for gene identity. We showed that the parallel loss of functional genes from the Y chromosome of the green anole and the W chromosome of the Florida softshell turtle led to different dosage compensation mechanisms. Our approach controlling for genetic background thus does not support that the variability in the regulation of the gene dose differences is a consequence of ancestral autosomal gene content.

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Expanding an expanded genome: long-read sequencing ofTrypanosoma cruzi

10.1101/279174 ◽

2018 ◽

Cited By ~ 3

Author(s):

Luisa Berná ◽

Matías Rodríguez ◽

María Laura Chiribao ◽

Adriana Parodi-Talice ◽

Sebastián Pita ◽

...

Keyword(s):

Repetitive Sequences ◽

Gc Content ◽

Gene Copy ◽

Accurate Estimation ◽

Sequencing Technologies ◽

Copy Numbers ◽

Long Reads ◽

Long Read ◽

Large Clusters ◽

Gene Copy Numbers

Although the genome ofTrypanosoma cruzi, the causative agent of Chagas disease, was first made available in 2005, with additional strains reported later, the intrinsic genome complexity of this parasite (abundance of repetitive sequences and genes organized in tandem) has traditionally hindered high-quality genome assembly and annotation. This also limits diverse types of analyses that require high degree of precision. Long reads generated by third-generation sequencing technologies are particularly suitable to address the challenges associated withT. cruzi´sgenome since they permit directly determining the full sequence of large clusters of repetitive sequences without collapsing them. This, in turn, allows not only accurate estimation of gene copy numbers but also circumvents assembly fragmentation. Here, we present the analysis of the genome sequences of twoT. cruziclones: the hybrid TCC (DTU TcVI) and the non-hybrid Dm28c (DTU TcI), determined by PacBio SMRT technology. The improved assemblies herein obtained permitted us to accurately estimate gene copy numbers, abundance and distribution of repetitive sequences (including satellites and retroelements). We found that the genome ofT. cruziis composed of a "core compartment" and a "disruptive compartment" which exhibit opposite gene and GC content composition. New tandem and disperse repetitive sequences were identified, including some located inside coding sequences. Additionally, homologous chromosomes were separately assembled, allowing us to retrieve haplotypes as separate contigs instead of a unique mosaic sequence. Finally, manual annotation of surface multigene families MUC and trans-sialidases allows now a better overview of these complex groups of genes.

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Growth of sedimentaryBathyarchaeotaon lignin as an energy source

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1718854115 ◽

2018 ◽

Vol 115 (23) ◽

pp. 6022-6027 ◽

Cited By ~ 60

Author(s):

Tiantian Yu ◽

Weichao Wu ◽

Wenyue Liang ◽

Mark Alexander Lever ◽

Kai-Uwe Hinrichs ◽

...

Keyword(s):

Energy Source ◽

Estuarine Sediments ◽

Gene Copy ◽

Organic Substrates ◽

Metabolic Functions ◽

Copy Numbers ◽

Tetraether Lipids ◽

Archaeal Lipids ◽

Gene Copy Numbers ◽

Direct Confirmation

Members of the archaeal phylumBathyarchaeotaare among the most abundant microorganisms on Earth. Although versatile metabolic capabilities such as acetogenesis, methanogenesis, and fermentation have been suggested for bathyarchaeotal members, no direct confirmation of these metabolic functions has been achieved through growth ofBathyarchaeotain the laboratory. Here we demonstrate, on the basis of gene-copy numbers and probing of archaeal lipids, the growth ofBathyarchaeotasubgroup Bathy-8 in enrichments of estuarine sediments with the biopolymer lignin. Other organic substrates (casein, oleic acid, cellulose, and phenol) did not significantly stimulate growth ofBathyarchaeota. Meanwhile, putative bathyarchaeotal tetraether lipids incorporated13C from13C-bicarbonate only when added in concert with lignin. Our results are consistent with organoautotrophic growth of a bathyarchaeotal group with lignin as an energy source and bicarbonate as a carbon source and shed light into the cycling of one of Earth’s most abundant biopolymers in anoxic marine sediment.

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