The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Cognizing and characterizing the organic phosphorus in lake sediments: Advances and challenges.

Combined amendment and capping of sediment with ferrihydrite and magnetite to control internal phosphorus release.

Regime shifts between nitrogen (N) and phosphorus (P) limitation, which trigger cyanobacterial succession, occur in shallow eutrophic lakes seasonally. However, the underlying mechanism is not yet fully illustrated. We provide a novel insight to address this from interactions between sediment P and nitrification through monthly field investigations including 204 samples and microcosm experiments in Lake Chaohu. Total N to P mass ratios (TN/TP) varied significantly across seasons especially during algal bloom in summer, with the average value being 26.1 in June and descending to 7.8 in September gradually, triggering dominant cyanobacterial succession from Microcystis to Dolichospermum. The regulation effect of sediment N/P on water column TN/TP was stronger in summer than in other seasons. Iron-bound P and alkaline phosphatase activity in sediment, rather than ammonium, contributed to the higher part of nitrification. Furthermore, our microcosm experiments confirmed that soluble active P and enzymatic hydrolysis of organic P, accumulating during algal bloom, fueled nitrifiers and nitrification in sediments. These processes promoted lake N removal and led to relative N deficiency in turn. Our results highlight that N and P cycles do not exist independently but rather interact with each other during lake eutrophication, supporting the dual N and P reduction program to mitigate eutrophication in shallow eutrophic lakes.

Interactions between Phosphorus Enrichment and Nitrification Accelerate Relative Nitrogen Deficiency during Cyanobacterial Blooms in a Large Shallow Eutrophic Lake.

Carbapenemase gene-positive (CP) Gram-negative bacilli are of significant clinical and public health concern. Their rapid detection and containment are critical to preventing their spread and additional infections they can cause. To this end, CDC developed the Antibiotic Resistance Laboratory Network (AR Lab Network), in which public health laboratories across all 50 states, several cities, and Puerto Rico characterize clinical isolates of carbapenem-resistant Enterobacterales (CRE), Pseudomonas aeruginosa (CRPA), and Acinetobacter baumannii (CRAB) and conduct colonization screens to detect the presence of mobile carbapenemase genes. In its first 3 years, the AR Lab Network tested 76,887 isolates and 31,001 rectal swab colonization screens. Targeted carbapenemase genes (blaKPC, blaNDM, blaOXA-48-like, blaVIM, or blaIMP) were detected by PCR in 35% of CRE, 2% of CRPA, and <1% of CRAB isolates and 8% of colonization screens tested, respectively. blaKPC and blaVIM were the most common genes in CP-CRE and CP-CRPA isolates, respectively, but regional differences in the frequency of carbapenemase genes detected were apparent. In CRE and CRPA isolates tested for carbapenemase production and the presence of the targeted genes, 97% had concordant results; 3% of CRE and 2% of CRPA isolates were carbapenemase production positive but PCR negative for those genes. Isolates harboring blaNDM showed the highest frequency of resistance across the carbapenems tested, and those harboring blaIMP and blaOXA-48-like genes showed the lowest frequency of carbapenem resistance. The AR Lab Network provides a national snapshot of rare and emerging carbapenemase genes, delivering data to inform public health actions to limit the spread of these antibiotic resistance threats.

Detection and Characterization of Targeted Carbapenem-Resistant Health Care-Associated Threats: Findings from the Antibiotic Resistance Laboratory Network, 2017 to 2019.

High-resolution characteristics and mechanisms of endogenous phosphorus migration and transformation impacted by algal blooms decomposition.

The variations of labile arsenic diffusion driven by algal bloom decomposition in eutrophic lake ecosystems.

Effect of light and nutrients on interspecific interactions between submerged macrophytes: implications for restoration of multispecies aquatic vegetation in eutrophic lakes

Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae have become widespread in hospitals and the environment. Here, we describe a blaKPC-2-carrying plasmid called pCRE3-KPC, which was recovered from a clinical multidrug-resistant Citrobacter braakii CRE3 strain in China. The complete nucleotide sequence of pCRE3-KPC was determined by combining MiSeq and MinION sequencing and then compared with those of three related plasmids. Plasmid conjugal transfer and electroporation tests, modified carbapenem inactivation method, and bacterial antimicrobial susceptibility test were carried out. We compared this plasmid with three related plasmids to verify that the backbone of pCRE3-KPC was composed of the backbones of the IncR plasmid and IncP6 plasmid. Further bioinformatics analysis showed that pCRE3-KPC carried two resistance-related regions (the blaKPC-2 gene cluster and the aacC2-tmrB-related region). The aacC2-tmrB-related region included two novel insertion sequences (ISCfr28 and ISCfr16). IMPORTANCE Reports of human-pathogenic C. braakii strains, especially of strains showing resistance to carbapenems, are rare. To the best of our knowledge, our results represent the first detection of carbapenemase gene blaKPC-2 in C. braakii strains. In addition, we have studied detailed genetic characteristics of the novel IncR/IncP6 hybrid plasmid pCRE3-KPC, which was isolated from a clinical multidrug-resistant Citrobacter braakii CRE3 strain. Our results may provide further insight into the horizontal transfer of multidrug resistance genes in bacteria and into the genomic diversity and molecular evolution of plasmids.

Novel IncR/IncP6 Hybrid Plasmid pCRE3-KPC Recovered from a Clinical KPC-2-Producing Citrobacter braakii Isolate.

The extremely serious urban runoff eutrophication and black odorous phenomenon pose a significant threat to the lake aquatic ecosystem, resulting in a significantly increased frequency, magnitude, and duration of algal blooms in lakes. However, few investigations focus on small tributaries of the lakes, despite the ubiquity and potential local importance of these runoffs. Thus, the labile sediments NH4+-N, NO3−-N, PO43−, Fe2+, and S2− in black odorous runoff at Wuxi were overall analyzed at high resolution using diffusive gradients in thin films (DGT). The variations in labile N, P, Fe, and S distribution profiles at different sampling sites indicated high heterogeneity in sediments. The concentrations of labile P, Fe, and S showed synchronous variation from the sediment-water interface (SWI) up to −20 mm along sediment profiles. Moreover, there existed a significant positive correlation among labile P, Fe, and S concentrations (p < 0.05), which might represent typical odor compounds’ FeS and H2S synchronous release process in urban runoff. Furthermore, the apparent diffusion fluxes of labile P, Fe, and S across the SWI were all released upward, while fluxes of NH4+-N and NO3−-N release downward, indicating the sediments act as source and sink of P and N, respectively. Sediments’ potential for endogenous P and N fractions release results in the black−odorous water, and sediment finally abouchement the Taihu, which intensifies further lake eutrophication phenomenon.

https://www.mdpi.com/1660-4601/19/20/13240/pdf?version=1665742939

In Situ Simultaneous Analysis of Nitrogen and Phosphorus Migration in Urban Black Odorous Runoff

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