High-throughput single-cell cultivation reveals the underexplored rare biosphere in deep-sea sediments along the Southwest Indian Ridge

Hu, Beiyu; Xu, Bingxue; Yun, Juanli; Wang, Jian; Xie, Bingliang; Li, Caiming; Yu, Yanghuan; Lan, Ying; Zhu, Yaxin; Dai, Xin; Huang, Ying; Huang, Li; Pan, Jian-Zhang; Du, Wei

doi:10.1039/c9lc00761j

Cited by 33 publications

(20 citation statements)

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“…3e). Later, Zhou et al (2018) used the MSP platform under anaerobic conditions to separate several potentially new species and genera from the gut of Reticulitermes chinensis The MSP platform was further improved for long-term cultivation to tackle the problem of rare marine microbe isolation (Hu et al 2020). The improved MSP platform increased the recovery of slow-growing microbes and enabled longterm cultivation of up to five months.…”

Section: High-throughput Single-cell Cultivation For Uncultured Microbesmentioning

confidence: 99%

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One cell at a time: droplet-based microbial cultivation, screening and sequencing

et al. 2021

Mar Life Sci Technol

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Microbes thrive and, in turn, influence the earth's environment, but most are poorly understood because of our limited capacity to reveal their natural diversity and function. Developing novel tools and effective strategies are critical to ease this dilemma and will help to understand their roles in ecology and human health. Recently, droplet microfluidics is emerging as a promising technology for microbial studies with value in microbial cultivating, screening, and sequencing. This review aims to provide an overview of droplet microfluidics techniques for microbial research. First, some critical points or steps in the microfluidic system are introduced, such as droplet stabilization, manipulation, and detection. We then highlight the recent progress of droplet-based methods for microbiological applications, from high-throughput single-cell cultivation, screening to the targeted or whole-genome sequencing of single cells.

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Section: High-throughput Single-cell Cultivation For Uncultured Microbesmentioning

confidence: 99%

“…Copyright (2019) Elsevier). d Schematic of semi-automated droplet picker (Fig.3D, and 3F reprinted with permission fromHu et al 2020. Lab Chip 20: 363-372.…”

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confidence: 99%

One cell at a time: droplet-based microbial cultivation, screening and sequencing

et al. 2021

Mar Life Sci Technol

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“…An improved high-throughput microfluidic streak plate (MSP) platform could be used to accelerate the isolation of micro-organisms from deep-sea environments. Based on the characteristics of slow growth of deep-sea species, a semi-automatic droplet picker was used to improve the isolation efficiency of MSP, whereas improved humidity control enabled long-term cultivation in low-nutrient medium (Hu et al 2020). The results showed that > 90% of the OTUs detected in the MSP pool belonged to the rare biosphere, including 15 potential new species (Hu et al 2020).…”

Section: Perspective Cultivation Strategiesmentioning

confidence: 99%

“…Based on the characteristics of slow growth of deep-sea species, a semi-automatic droplet picker was used to improve the isolation efficiency of MSP, whereas improved humidity control enabled long-term cultivation in low-nutrient medium (Hu et al 2020). The results showed that > 90% of the OTUs detected in the MSP pool belonged to the rare biosphere, including 15 potential new species (Hu et al 2020). Furthermore, I-tip and encapsulation technology based in situ and electrical retrieval approaches of micro-organisms from marine animals are valuable technologies for thraustochytrid isolation (Ben-Dov et al 2009;Jung et al 2014;Koyama et al 2015).…”

Section: Perspective Cultivation Strategiesmentioning

confidence: 99%

Cultivation and diversity analysis of novel marine thraustochytrids

Liu

Wang

2020

Mar Life Sci Technol

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Thraustochytrids are a group of unicellular marine heterotrophic protists, and have long been known for their biotechnological potentials in producing squalene, polyunsaturated fatty acids (PUFAs) and other bioactive products. There are less than a hundred known strains from diverse marine habitats. Therefore, the discovery of new strains from natural environments is still one of the major limitations for fully exploring this interesting group of marine protists. At present, numerous attempts have been made to study thraustochytrids, mainly focusing on isolating new strains, analyzing the diversity in specific marine habitats, and increasing the yield of bioactive substances. There is a lack of a systematic study of the culturable diversity, and cultivation strategies. This paper reviews the distribution and diversity of culturable thraustochytrids from a range of marine environments, and describes in detail the most commonly used isolation methods and the control of culture parameters. Furthermore, the perspective approaches of isolation and cultivation for the discovery of new strains are discussed. Finally, the future directions of novel marine thraustochytrid research are proposed. The ultimate goal is to promote the awareness of biotechnological potentials of culturable thraustochytrid strains in industrial and biomedical applications.

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“…Various culture-based and culture-independent approaches have attempted to describe both the microbial diversity and the array of metabolic capabilities present in these singular ecosystems, but with more effort devoted to omics-based studies in recent years at the expense of time-consuming culture-based approaches ( Connon and Giovannoni, 2002 ; DeSantis et al, 2007 ; Rinke et al, 2013 ; Chen et al, 2021 ). The cutting-edge approaches for isolation and cultivation of prokaryotes such as microencapsulation, single-cell and droplet-based cultivation, and cell sorting based cultivation (e.g., reverse genomics; Zengler et al, 2005 ; Nichols et al, 2010 ; Boitard et al, 2015 ; Jiang et al, 2016 ; Berdy et al, 2017 ; Terekhov et al, 2018 ; Hu et al, 2020 ; Lewis et al, 2021 ) are very promising but cannot be applied to all microbial taxa as they do not mimic all environmental conditions, and in particular high temperature and pressure. Despite these significant achievements, the vast majority of the genera and phyla of bacteria and archaea on Earth, including those from the deep biosphere, do not have cultured representatives ( Whitman et al, 1998 ; Lloyd et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

High-Pressure Microfluidics for Ultra-Fast Microbial Phenotyping

et al. 2022

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Here, we present a novel methodology based on high-pressure microfluidics to rapidly perform temperature-based phenotyping of microbial strains from deep-sea environments. The main advantage concerns the multiple on-chip temperature conditions that can be achieved in a single experiment at pressures representative of the deep-sea, overcoming the conventional limitations of large-scale batch metal reactors to conduct fast screening investigations. We monitored the growth of the model strain Thermococcus barophilus over 40 temperature and pressure conditions, without any decompression, in only 1 week, whereas it takes weeks or months with conventional approaches. The results are later compared with data from the literature. An additional example is also shown for a hydrogenotrophic methanogen strain (Methanothermococcus thermolithotrophicus), demonstrating the robustness of the methodology. These microfluidic tools can be used in laboratories to accelerate characterizations of new isolated species, changing the widely accepted paradigm that high-pressure microbiology experiments are time-consuming.

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High-throughput single-cell cultivation reveals the underexplored rare biosphere in deep-sea sediments along the Southwest Indian Ridge

Abstract: An improved microfluidic streak plate technique relying on droplet microfluidics can advance the exploration of deep-sea rare microbes.

Cited by 33 publications

References 48 publications

One cell at a time: droplet-based microbial cultivation, screening and sequencing

One cell at a time: droplet-based microbial cultivation, screening and sequencing

Cultivation and diversity analysis of novel marine thraustochytrids

High-Pressure Microfluidics for Ultra-Fast Microbial Phenotyping

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