Whole genome sequencing of cyanobacterium Nostoc sp. CCCryo 231-06 using microfluidic single cell technology

Liu, Yuguang; Jeraldo, Patricio; Herbert, William G.; McDonough, Samantha J.; Eckloff, Bruce W.; Schulze‐Makuch, Dirk; Vera, Jean‐Pierre de; Cockell, Charles S.; Leya, Thomas; Baqué, Mickaël; Jen, Jin

doi:10.1016/j.isci.2022.104291

Cited by 9 publications

(3 citation statements)

References 61 publications

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“…However, with sufficient number of single cells (regardless of different experimental conditions), it is possible to co-assemble a consensus Nostoc genome to near completion. Therefore, in this work, we co-assembled using all 48 samples targeting the Nostoc isolate 14 . We emphasize the “consensus” aspect of this recovered reference sequence, and consequently this sequence will not completely match the genotypes of samples from each single exposure condition.…”

Section: Methodsmentioning

confidence: 99%

Non-random genetic alterations in the cyanobacterium Nostoc sp. exposed to space conditions

Liu

Jeraldo

Herbert

et al. 2022

Sci Rep

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Understanding the impact of long-term exposure of microorganisms to space is critical in understanding how these exposures impact the evolution and adaptation of microbial life under space conditions. In this work we subjected Nostoc sp. CCCryo 231-06, a cyanobacterium capable of living under many different ecological conditions, and also surviving in extreme ones, to a 23-month stay at the International Space Station (the Biology and Mars Experiment, BIOMEX, on the EXPOSE-R2 platform) and returned it to Earth for single-cell genome analysis. We used microfluidic technology and single cell sequencing to identify the changes that occurred in the whole genome of single Nostoc cells. The variant profile showed that biofilm and photosystem associated loci were the most altered, with an increased variant rate of synonymous base pair substitutions. The cause(s) of these non-random alterations and their implications to the evolutionary potential of single bacterial cells under long-term cosmic exposure warrants further investigation.

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Section: Methodsmentioning

confidence: 99%

Non-random genetic alterations in the cyanobacterium Nostoc sp. exposed to space conditions

Liu

Jeraldo

Herbert

et al. 2022

Sci Rep

Self Cite

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“…Each cell was checked for contaminants using the microscope before lysis, amplification, and full genome sequencing. This technique is applicable to other filamentous cyanobacteria and can be used to study extremophiles of interest in astrobiology [53].…”

Section: Single-cell Genome Sequencingmentioning

confidence: 99%

Emerging Technologies for the Discovery of Novel Diversity in Cyanobacteria and Algae and the Elucidation of Their Valuable Metabolites

Zammit,

Buttigieg

2023

Diversity

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Until recently, the study of cyanobacteria and microalgae has been hampered by the need to cultivate these organisms to gain insight into their cytomorphology, life cycle and molecular biology. However, various microbial species characterized by thick sheaths of exopolymeric substances were difficult to isolate in culture due to their associated symbiotic bacteria. Other microbes evaded culture. Such challenges have now been overcome by the development of metagenomic techniques that allow direct DNA sequencing from environmental samples, as well as high resolution microscopy techniques that permit direct imaging of environmental samples. The sampling of understudied taxa from extreme environments and of toxic species has been facilitated by specialized robotic equipment. Single-cell sequencing has allowed for the proper characterization of microalgal species and their response to environmental changes. Various strains of cyanobacteria, microalgae and macroalgae have gained renewed interest for their high-value metabolites. This paper provides an overview of the emerging technologies and explains how they are being used to identify such strains and their products for industrial application. Advances in genetic engineering and CRISPR technology have facilitated the production of strains that are more amenable to culture, metabolite extraction, scale-up and application in biorefinery approaches. Emerging analytical techniques are discussed, with the advent of multiomics and its application in this field.

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“…Isolation of desired individual cells from a population or consortium is a key step in single‐cell analysis 1 , 2 . This process can be generally achieved via fluorescence‐activated cell sorting (FACS) and shows great potential for in‐depth analysis of the structure and function of the microbiome when it links downstream single‐cell sequencing directly from an in situ sample 3 , 4 , 5 . However, it's usually complex in operation and cost demanding when we sort bacteria cells (10‐fold smaller in size than a typical human cell) using a FACS system at single‐cell precision.…”

Section: Introductionmentioning

confidence: 99%

Artificial intelligence‐assisted automatic and index‐based microbial single‐cell sorting system for One‐Cell‐One‐Tube

Diao

Kan

Zhao

et al. 2022

mLife

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Identification, sorting, and sequencing of individual cells directly from in situ samples have great potential for in-depth analysis of the structure and function of microbiomes. In this work, based on an artificial intelligence (AI)-assisted object detection model for cell phenotype screening and a cross-interface contact method for single-cell exporting, we developed an automatic and index-based system called EasySort AUTO, where individual microbial cells are sorted and then packaged in a microdroplet and automatically exported in a precisely indexed, "One-Cell-One-Tube" manner. The target cell is automatically identified based on an AI-assisted object detection model and then mobilized via an optical tweezer for sorting. Then, a crossinterface contact microfluidic printing method that we developed enables the automated transfer of cells from the chip to the tube, which leads to coupling with subsequent single-cell culture or sequencing. The efficiency of the system for single-cell printing is >93%. The throughput of the system for single-cell printing is ~120 cells/h. Moreover, >80% of single cells of both yeast and Escherichia coli are culturable, suggesting the superior preservation of cell viability during sorting. Finally, AI-assisted object detection supports automated sorting of target cells with high accuracy from mixed yeast samples, which was validated by downstream single-cell proliferation assays. The automation, index maintenance, and vitality preservation of EasySort AUTO suggest its excellent application potential for single-cell sorting.

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Whole genome sequencing of cyanobacterium Nostoc sp. CCCryo 231-06 using microfluidic single cell technology

Cited by 9 publications

References 61 publications

Non-random genetic alterations in the cyanobacterium Nostoc sp. exposed to space conditions

Non-random genetic alterations in the cyanobacterium Nostoc sp. exposed to space conditions

Emerging Technologies for the Discovery of Novel Diversity in Cyanobacteria and Algae and the Elucidation of Their Valuable Metabolites

Artificial intelligence‐assisted automatic and index‐based microbial single‐cell sorting system for One‐Cell‐One‐Tube

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