Innovations to culturing the uncultured microbial majority

Lewis, William H.; Tahon, Guillaume; Geesink, Patricia; Sousa, Diana Z.; Ettema, Thijs J. G.

doi:10.1038/s41579-020-00458-8

Cited by 364 publications

(298 citation statements)

References 146 publications

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“…Meanwhile, it should be noted that the taxonomic assignment of these phylogenetically distinct CODH-OTUs is difficult because CODHech genes are considered to be often horizontally transferred and taxonomically remote species are found in FirmiCOD-Hech subclades. Further studies like targeted metagenomics (Grieb et al 2020) or isolation (Batani et al 2019;Lewis et al 2020) methods which have been recently developed are needed to obtain more genomic information for taxonomic assignment of these CODH-OTUs. Most of the CODH-OTUs found in CO-enriched samples were not detected in the JI sample before enrichment (Fig.…”

Section: Discussionmentioning

confidence: 99%

Diversity analysis of thermophilic hydrogenogenic carboxydotrophs by carbon monoxide dehydrogenase amplicon sequencing using new primers

et al. 2021

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The microbial H2-producing (hydrogenogenic) carbon monoxide (CO)-oxidizing activity by the membrane-associated CO dehydrogenase (CODH)/energy-converting hydrogenase (ECH) complex is an important metabolic process in the microbial community. However, the studies on hydrogenogenic carboxydotrophs had to rely on inherently cultivation and isolation methods due to their rare abundance, which was a bottleneck in ecological study. Here, we provided gene-targeted sequencing method for the diversity estimation of thermophilic hydrogenogenic carboxydotrophs. We designed six new degenerate primer pairs which effectively amplified the coding regions of CODH genes forming gene clusters with ECH genes (CODHech genes) in Firmicutes which includes major thermophilic hydrogenogenic carboxydotrophs in terrestrial thermal habitats. Amplicon sequencing by these primers using DNAs from terrestrial hydrothermal sediments and CO-gas-incubated samples specifically detected multiple CODH genes which were identical or phylogenetically related to the CODHech genes in Firmictes. Furthermore, we found that phylogenetically distinct CODHech genes were enriched in CO-gas-incubated samples, suggesting that our primers detected uncultured hydrogenogenic carboxydotrophs as well. The new CODH-targeted primers provided us with a fine-grained (~ 97.9% in nucleotide sequence identity) diversity analysis of thermophilic hydrogenogenic carboxydotrophs by amplicon sequencing and will bolster the ecological study of these microorganisms.

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Section: Discussionmentioning

confidence: 99%

Diversity analysis of thermophilic hydrogenogenic carboxydotrophs by carbon monoxide dehydrogenase amplicon sequencing using new primers

et al. 2021

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“…Therefore, it is crucial to increase our capability for bringing microorganisms from the environment into culture [60], which will advance our understanding of their global biogeochemical cycles [48]. Among the uncultured majorities, the phylum Chloroflexi is ubiquitous and often abundant in sediments, soils and wastewater treatment systems, as well as in deep-sea extreme environments [64].…”

Section: Discussionmentioning

confidence: 99%

“…Microorganisms in the deep marine subsurface sediments represent a large unexplored biosphere, exploring and resolving their metabolisms are essential to understand the global biogeochemical cycles [59][60][61]. Despite the global importance of these microorganisms, deep-sea sediments are among the least understood environments, partly due to the difficulty of sampling as well as the complexity of inhabiting communities [59].…”

Section: Discussionmentioning

confidence: 99%

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Cultivation and characterization of a novel clade of deep-sea Chloroflexi: providing a glimpse of the phylum Chloroflexi involved in sulfur cycling

Zheng

Cai

Liu

et al. 2021

Preprint

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Chloroflexi bacteria are abundant and globally distributed in various unexplored biospheres on Earth. However, only few Chloroflexi members have been cultivated, hampering further understanding of this important group. In the current study, we firstly clarify the high abundance of the phylum Chloroflexi in deep-sea sediments via the operational taxonomic units analysis. We further successfully isolate a novel Chloroflexi strain ZRK33 from cold seep sediments by using an enrichment medium constantly supplemented with rifampicin. Phylogenetic analyses based on 16S rRNA gene, genome, RpoB and EF-tu proteins indicate that strain ZRK33 represents a novel class, and the class is designated as Sulfochloroflexia because whole set of genes encoding key enzymes responsible for assimilatory sulfate reduction are identified in the genome of strain ZRK33. Indeed, assimilation of sulfate or thiosulfate by strain ZRK33 evidently benefits its growth and morphogenesis. Proteomic results suggest that metabolization of sulfate or thiosulfate significantly promotes the transport and degradation of various macromolecules and thereby stimulating the energy production. Notably, the putative genes associated with assimilatory and dissimilatory sulfate reduction ubiquitously distribute in the metagenome-assembled genomes of 27 Chloroflexi members derived from deep-sea sediments, strongly suggesting that Chloroflexi bacteria play undocumented key roles in deep-sea sulfur cycling.

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“…The introduction of novel methods to increase microbial cultivability presents a huge potential to expand the isolation of plant beneficial organisms (Sarhan et al, 2019). Different methods based on in situ and high throughput cultivation have been proposed, such as diffusion chambers, microfluidic streak plate (MSP), hollow-fiber membrane chamber (HFMC), double encapsulation technique, soil substrate membrane system (SSMS), and isolation chip (Ichip) (Sarhan et al, 2019;Lewis et al, 2020). Other approaches include improved growth conditions and development of alternative culture media, especially considering oligotrophs requirements (Vartoukian et al, 2010), once this condition is more effective for the enrichment of rock-weathering bacteria (Hirsch et al, 1995).…”

Section: Concomitant Use Of Rocks and Weathering Bacteria As Fertilizmentioning

confidence: 99%

Use of Mineral Weathering Bacteria to Enhance Nutrient Availability in Crops: A Review

et al. 2020

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Rock powders are low-cost potential sources of most of the nutrients required by higher plants for growth and development. However, slow dissolution rates of minerals represent an obstacle to the widespread use of rock powders in agriculture. Rhizosphere processes and biological weathering may further enhance mineral dissolution since the interaction between minerals, plants, and bacteria results in the release of macro- and micronutrients into the soil solution. Plants are important agents in this process acting directly in the mineral dissolution or sustaining a wide diversity of weathering microorganisms in the root environment. Meanwhile, root microorganisms promote mineral dissolution by producing complexing ligands (siderophores and organic acids), affecting the pH (via organic or inorganic acid production), or performing redox reactions. Besides that, a wide variety of rhizosphere bacteria and fungi could also promote plant development directly, synergistically contributing to the weathering activity performed by plants. The inoculation of weathering bacteria in soil or plants, especially combined with the use of crushed rocks, can increase soil fertility and improve crop production. This approach is more sustainable than conventional fertilization practices, which may contribute to reducing climate change linked to agricultural activity. Besides, it could decrease the dependency of developing countries on imported fertilizers, thus improving local development.

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Innovations to culturing the uncultured microbial majority

Cited by 364 publications

References 146 publications

Diversity analysis of thermophilic hydrogenogenic carboxydotrophs by carbon monoxide dehydrogenase amplicon sequencing using new primers

Diversity analysis of thermophilic hydrogenogenic carboxydotrophs by carbon monoxide dehydrogenase amplicon sequencing using new primers

Cultivation and characterization of a novel clade of deep-sea Chloroflexi: providing a glimpse of the phylum Chloroflexi involved in sulfur cycling

Use of Mineral Weathering Bacteria to Enhance Nutrient Availability in Crops: A Review

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