Whole genome sequencing of Microbacterium sp. AISO3 from polluted San Jacinto River sediment reveals high bacterial mobility, metabolic versatility and heavy metal resistance

Abstract Background Neonatal listeriosis is a rare but severe disease manifesting as septicemia and central nervous system (CNS) infections with a high fatality rate of around 20 to 30%. Whole genome sequencing (WGS) is a promising technique for pathogen identification and infection source tracing with its high resolution. Case presentation A case of neonatal sepsis with listeriosis was reported with positive blood culture for Listeria monocytogenes. The case was investigated to confirm the vertical transmission of the infection and identify the potential food source of the maternal L. monocytogenes infection using WGS. L. monocytogenes was isolated from the neonate’s blood sample the day after caesarean delivery and from the mother’s genital and pudenda swab samples 5 days and 13 days after caesarean delivery. WGS showed that the isolate from the neonate was identical to the genome type of the isolates from the mother, with only one of the 4 isolates from the mother differing by one single nucleotide polymorphism (SNP). By WGS, one L. monocytogenes isolate from a ready-to-eat (RTE) meat sample in the patients’ community market shared the same sequence type but was ruled out as the cause of infection, with 57 SNP differences to the strain causing the maternal-neonatal infection. The food isolate also carried a novel plasmid pLM1686 that harbored heavy metal resistance genes. After caesarean section, the mother was treated with a third generation cephalosporin which L. monocytogenes is naturally resistant to, which may explain why genital and pudenda swabs were still culture-positive for L. monocytogenes 13 days after delivery. Conclusions Genital swab culture for L. monocytogenes had been informative in the diagnosis of maternal listeriosis in this case. The high resolution of WGS confirmed the maternal-neonatal transmission of L. monocytogenes infection and ruled out the L. monocytogenes contaminated RTE meat from the local market as the direct source of the mother’s infection.

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Whole Genome Sequencing and Comparative Genomic Analyses of Lysinibacillus pakistanensis LZH-9, a Halotolerant Strain with Excellent COD Removal Capability

Microorganisms ◽

10.3390/microorganisms8050716 ◽

2020 ◽

Vol 8 (5) ◽

pp. 716

Author(s):

Xueling Wu ◽

Han Zhou ◽

Liangzhi Li ◽

Enhui Wang ◽

Xiangyu Zhou ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Industrial Wastewater ◽

Treatment Plant ◽

Cod Removal ◽

Comparative Genomic ◽

Whole Genome ◽

Toxic Compound ◽

Adaptive Mutations ◽

Metabolic Versatility

Halotolerant microorganisms are promising in bio-treatment of hypersaline industrial wastewater. Four halotolerant bacteria strains were isolated from wastewater treatment plant, of which a strain LZH-9 could grow in the presence of up to 14% (w/v) NaCl, and it removed 81.9% chemical oxygen demand (COD) at 96 h after optimization. Whole genome sequencing of Lysinibacillus pakistanensis LZH-9 and comparative genomic analysis revealed metabolic versatility of different species of Lysinibacillus, and abundant genes involved in xenobiotics biodegradation, resistance to toxic compound, and salinity were found in all tested species of Lysinibacillus, in which Horizontal Gene Transfer (HGT) contributed to the acquisition of many important properties of Lysinibacillus spp. such as toxic compound resistance and osmotic stress resistance as revealed by phylogenetic analyses. Besides, genome wide positive selection analyses revealed seven genes that contained adaptive mutations in Lysinibacillus spp., most of which were multifunctional. Further expression assessment with Codon Adaption Index (CAI) also reflected the high metabolic rate of L. pakistanensis to digest potential carbon or nitrogen sources in organic contaminants, which was closely linked with efficient COD removal ability of strain LZH-9. The high COD removal efficiency and halotolerance as well as genomic evidences suggested that L. pakistanensis LZH-9 was promising in treating hypersaline industrial wastewater.

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Whole genome sequencing and metabolomics analyses reveal the biosynthesis of nerol in a multi-stress-tolerant Meyerozyma guilliermondii GXDK6

10.21203/rs.3.rs-91176/v1 ◽

2020 ◽

Author(s):

Xueyan Mo ◽

Xinghua Cai ◽

Qinyan Hui ◽

Huijie Sun ◽

Ran Yu ◽

...

Keyword(s):

Heavy Metal ◽

Carbon Source ◽

Chemical Synthesis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Large Scale ◽

Gas Chromatography Mass Spectrometry ◽

Whole Genome ◽

Scale Production ◽

Meyerozyma Guilliermondii

Abstract BackgroundNerol (C10H18O), an acyclic monoterpene, naturally presents in plant essential oils, and is used widely in food, cosmetics and pharmaceuticals as the valuable fragrance. Meanwhile, chemical synthesis is the only strategy for large-scale production of nerol, and the disadvantages of chemical synthesis greatly limited the production and its application. These defects drive the interests of researchers shift to the production of nerol by eco-friendly methods known as biosynthesis methods. However, the main technical bottleneck restricting the biosynthesis of nerol is the lacking of corresponding natural aroma-producing microorganisms.ResultsIn this study, a novel multi-stress-tolerant probiotics Meyerozyma guilliermondii GXDK6 with aroma-producing properties was identified by whole genome sequencing and metabolomics technology. GXDK6 showed a broad pH tolerance in the range of 2.5–10.0. The species also showed salt tolerance with up to 12% NaCl and up to 18% of KCl or MgCl2. GXDK6 exhibited heavy-metal Mn2+ tolerance of up to 5494 ppm. GXDK6 could also ferment with a total of 21 kinds of single organic matter as the carbon source, and produce abundant aromatic metabolites. Results from the gas chromatography–mass spectrometry indicated the production of 8–14 types of aromatic metabolites (isopentanol, nerol, geraniol, phenylethanol, isobutanol, etc.) when GXDK6 was fermented up to 72 h with glucose, sucrose, fructose, or xylose as the single carbon source. Among of them, nerol was found as a novel aromatic metabolite from GXDK6 fermentation, and its biosynthesis mechanism had also been further revealed.ConclusionA novel aroma-producing M. guilliermondii GXDK6 was identified successfully by whole genome sequencing and metabolomics technology. GXDK6 showed high multi-stress-tolerant properties with acid–base, salty, and heavy-metal environments. The aroma-producing mechanism of nerol in GXDK6 had also been revealed. These findings indicated the aroma-producing M. guilliermondii GXDK6 with multi-stress-tolerant properties has great potential value in the fermentation industry.

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Whole genome sequencing and metabolomics analyses reveal the biosynthesis of nerol in a multi-stress-tolerant Meyerozyma guilliermondii GXDK6

Microbial Cell Factories ◽

10.1186/s12934-020-01490-2 ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Xueyan Mo ◽

Xinghua Cai ◽

Qinyan Hui ◽

Huijie Sun ◽

Ran Yu ◽

...

Keyword(s):

Heavy Metal ◽

Carbon Source ◽

Chemical Synthesis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Large Scale ◽

Gas Chromatography Mass Spectrometry ◽

Whole Genome ◽

Scale Production ◽

Plant Essential Oils

Abstract Background Nerol (C10H18O), an acyclic monoterpene, naturally presents in plant essential oils, and is used widely in food, cosmetics and pharmaceuticals as the valuable fragrance. Meanwhile, chemical synthesis is the only strategy for large-scale production of nerol, and the disadvantages of chemical synthesis greatly limit the production and its application. These defects drive the interests of researchers shift to the production of nerol by eco-friendly methods known as biosynthesis methods. However, the main technical bottleneck restricting the biosynthesis of nerol is the lacking of corresponding natural aroma-producing microorganisms. Results In this study, a novel multi-stress-tolerant probiotics Meyerozymaguilliermondii GXDK6 with aroma-producing properties was identified by whole genome sequencing and metabolomics technology. GXDK6 showed a broad pH tolerance in the range of 2.5–10.0. The species also showed salt tolerance with up to 12% NaCl and up to 18% of KCl or MgCl2. GXDK6 exhibited heavy-metal Mn2+ tolerance of up to 5494 ppm. GXDK6 could also ferment with a total of 21 kinds of single organic matter as the carbon source, and produce abundant aromatic metabolites. Results from the gas chromatography–mass spectrometry indicated the production of 8–14 types of aromatic metabolites (isopentanol, nerol, geraniol, phenylethanol, isobutanol, etc.) when GXDK6 was fermented up to 72 h with glucose, sucrose, fructose, or xylose as the single carbon source. Among them, nerol was found to be a novel aromatic metabolite from GXDK6 fermentation, and its biosynthesis mechanism had also been further revealed. Conclusion A novel aroma-producing M. guilliermondii GXDK6 was identified successfully by whole genome sequencing and metabolomics technology. GXDK6 showed high multi-stress-tolerant properties with acid–base, salty, and heavy-metal environments. The aroma-producing mechanism of nerol in GXDK6 had also been revealed. These findings indicated the aroma-producing M. guilliermondii GXDK6 with multi-stress-tolerant properties has great potential value in the fermentation industry.

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Genome sequencing reveals mechanisms for heavy metal resistance and polycyclic aromatic hydrocarbon degradation in Delftia lacustris strain LZ-C

Ecotoxicology ◽

10.1007/s10646-015-1583-9 ◽

2015 ◽

Vol 25 (1) ◽

pp. 234-247 ◽

Cited By ~ 26

Author(s):

Wenyang Wu ◽

Haiying Huang ◽

Zhenmin Ling ◽

Zhengsheng Yu ◽

Yiming Jiang ◽

...

Keyword(s):

Heavy Metal ◽

Polycyclic Aromatic Hydrocarbon ◽

Aromatic Hydrocarbon ◽

Genome Sequencing ◽

Heavy Metal Resistance ◽

Metal Resistance ◽

Hydrocarbon Degradation ◽

Polycyclic Aromatic ◽

Polycyclic Aromatic Hydrocarbon Degradation

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Whole genome sequencing of a multidrug-resistant Bacillus thuringiensis HM-311 obtained from the Radiation and Heavy metal-polluted soil

Journal of Global Antimicrobial Resistance ◽

10.1016/j.jgar.2020.04.022 ◽

2020 ◽

Vol 21 ◽

pp. 275-277

Author(s):

Wenlu Zuo ◽

Jingchen Li ◽

Jie Zheng ◽

Lei Zhang ◽

Qi Yang ◽

...

Keyword(s):

Heavy Metal ◽

Bacillus Thuringiensis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Multidrug Resistant ◽

Polluted Soil ◽

Whole Genome

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Genome Sequencing Revealed Chromium and Other Heavy Metal Resistance Genes in E. cloacae B2-Dha

Journal of Microbial & Biochemical Technology ◽

10.4172/1948-5948.1000365 ◽

2017 ◽

Vol 9 (5) ◽

Author(s):

Neelu NN ◽

Sibdas G ◽

Aminur R ◽

Abul M ◽

Bjorn O ◽

...

Keyword(s):

Heavy Metal ◽

Genome Sequencing ◽

Resistance Genes ◽

Heavy Metal Resistance ◽

Metal Resistance

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Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics

Microbiome ◽

10.1186/s40168-021-01016-x ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Yuan Lin ◽

Liye Wang ◽

Ke Xu ◽

Kan Li ◽

Hongqiang Ren

Keyword(s):

Heavy Metals ◽

Heavy Metal ◽

Phosphorus Removal ◽

Heavy Metal Resistance ◽

Resistance Mechanisms ◽

Metal Resistance ◽

Energy Utilization ◽

Nitrogen And Phosphorus ◽

Denitrifying Phosphorus Removal ◽

Metabolic Versatility

Abstract Background Denitrifying phosphorus removal sludge (DPRS) is widely adopted for nitrogen and phosphorus removal in wastewater treatment but faces threats from heavy metals. However, a lack of understanding of the taxon-specific heavy metal-resistance mechanisms hinders the targeted optimization of DPRS’s robustness in nutrient removal. Results We obtained 403 high- or medium-quality metagenome-assembled genomes from DPRS treated by elevating cadmium, nickel, and chromium pressure. Then, the proteomic responses of individual taxa under heavy metal pressures were characterized, with an emphasis on functions involving heavy metal resistance and maintenance of nutrient metabolism. When oxygen availability was constrained by high-concentration heavy metals, comammox Nitrospira overproduced highly oxygen-affinitive hemoglobin and electron-transporting cytochrome c-like proteins, underpinning its ability to enhance oxygen acquisition and utilization. In contrast, Nitrosomonas overexpressed ammonia monooxygenase and nitrite reductase to facilitate the partial nitrification and denitrification process for maintaining nitrogen removal. Comparisons between phosphorus-accumulating organisms (PAOs) demonstrated different heavy metal-resistance mechanisms adopted by Dechloromonas and Candidatus Accumulibacter, despite their high genomic similarities. In particular, Dechloromonas outcompeted the canonical PAO Candidatus Accumulibacter in synthesizing polyphosphate, a potential public good for heavy metal detoxification. The superiority of Dechloromonas in energy utilization, radical elimination, and damaged cell component repair also contributed to its dominance under heavy metal pressures. Moreover, the enrichment analysis revealed that functions involved in extracellular polymeric substance formation, siderophore activity, and heavy metal efflux were significantly overexpressed due to the related activities of specific taxa. Conclusions Our study demonstrates that heavy metal-resistance mechanisms within a multipartite community are highly heterogeneous between different taxa. These findings provide a fundamental understanding of how the heterogeneity of individual microorganisms contributes to the metabolic versatility and robustness of microbiomes inhabiting dynamic environments, which is vital for manipulating the adaptation of microbial assemblages under adverse environmental stimuli.

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