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Wiretapping into microbial interactions by single cell genomics.

Stepanauskas R - Front Microbiol (2015)

View Article: PubMed Central - PubMed

Affiliation: Bigelow Laboratory for Ocean Sciences East Boothbay, ME, USA.

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Over the past decade, single cell genomics (SCG) made a swift transition from science fiction to a handy new tool in the biologist's toolset... The power of this technology lies in its ability to retrieve information-rich genomic blueprints from the most fundamental units of biological organization—individual cells... This is particularly significant in the case of bacteria, archaea, and protists, where single cells constitute complete organisms... Such interactions are thought to be of paramount importance to the functioning of oceans, soils, macroorganismal (including human) biomes and other microbially-dominated ecosystems, although their in situ studies have been severely hampered by methodological difficulties... In one of the first applications of SCG on eukaryotes, multiple cells of the candidate phylum Picozoa (formerly Picobilliphyta) were found to contain fragments of bacterial and viral DNA, while no genes involved in photosynthesis were identified (Yoon et al., )... The same SCG study also retrieved a complete genome of a novel nanovirus from an infected Picozoa cell... Subsequent studies confirmed that substantial genome content variation among individuals, indicative of extensive horizontal gene exchange, is the rule rather than the exception in natural microbial populations (Ochman et al., ; Papke et al., ; Shapiro et al., ), with likely major implications to their resilience and adaptability to new conditions, such as climate change or exposure to antibiotics... In the past 5 years, the scale of SCG projects grew from single genomes (Marcy et al., ; Woyke et al., ) to 10 s and 100 s of genomes (Rinke et al., ; Swan et al., ; Kashtan et al., ), and further technology improvements are well-underway... Increasingly sophisticated research applications will also drive improvements in SCG data quality, such as better genome recovery and reduced frequency of assembly errors... Like any technology, SCG is at its best when combined with other research tools, in order to most effectively address transformative science questions... There is little doubt that SCG will be increasingly utilized in diverse microbial studies, complementing cultivation-based, community omics, biogeochemical, and other research approaches.

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Schematic representation of the various types of DNA molecules (in red) and their occurrence inside and outside of eukaryotic (top) and bacterial (bottom) cells.
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Figure 1: Schematic representation of the various types of DNA molecules (in red) and their occurrence inside and outside of eukaryotic (top) and bacterial (bottom) cells.

Mentions: An exciting feature that sets SCG apart from other cultivation-independent technologies is the retrieval of sequences of all the DNA molecules in a cell, in this way providing evidence for their physical co-occurrence (or absence) in the analyzed cell or consortia of multiple cells. Such molecules may include multiple chromosomes and plasmids of the host organism; genomes of organelles, symbionts, viruses, and other infecting agents and prey items; and naturally transformed DNA (Figure 1). The ability to collect this type of information offers a major, but still underutilized opportunity to microbiology. Infections, symbioses, phagotrophy, horizontal gene transfer, formation of consortia, and other interactions among unicellular, uncultured organisms and extracellular genetic elements can now be analyzed directly, in their natural environment. Such interactions are thought to be of paramount importance to the functioning of oceans, soils, macroorganismal (including human) biomes and other microbially-dominated ecosystems, although their in situ studies have been severely hampered by methodological difficulties.


Wiretapping into microbial interactions by single cell genomics.

Stepanauskas R - Front Microbiol (2015)

Schematic representation of the various types of DNA molecules (in red) and their occurrence inside and outside of eukaryotic (top) and bacterial (bottom) cells.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4389542&req=5

Figure 1: Schematic representation of the various types of DNA molecules (in red) and their occurrence inside and outside of eukaryotic (top) and bacterial (bottom) cells.
Mentions: An exciting feature that sets SCG apart from other cultivation-independent technologies is the retrieval of sequences of all the DNA molecules in a cell, in this way providing evidence for their physical co-occurrence (or absence) in the analyzed cell or consortia of multiple cells. Such molecules may include multiple chromosomes and plasmids of the host organism; genomes of organelles, symbionts, viruses, and other infecting agents and prey items; and naturally transformed DNA (Figure 1). The ability to collect this type of information offers a major, but still underutilized opportunity to microbiology. Infections, symbioses, phagotrophy, horizontal gene transfer, formation of consortia, and other interactions among unicellular, uncultured organisms and extracellular genetic elements can now be analyzed directly, in their natural environment. Such interactions are thought to be of paramount importance to the functioning of oceans, soils, macroorganismal (including human) biomes and other microbially-dominated ecosystems, although their in situ studies have been severely hampered by methodological difficulties.

View Article: PubMed Central - PubMed

Affiliation: Bigelow Laboratory for Ocean Sciences East Boothbay, ME, USA.

AUTOMATICALLY GENERATED EXCERPT
Please rate it.

Over the past decade, single cell genomics (SCG) made a swift transition from science fiction to a handy new tool in the biologist's toolset... The power of this technology lies in its ability to retrieve information-rich genomic blueprints from the most fundamental units of biological organization—individual cells... This is particularly significant in the case of bacteria, archaea, and protists, where single cells constitute complete organisms... Such interactions are thought to be of paramount importance to the functioning of oceans, soils, macroorganismal (including human) biomes and other microbially-dominated ecosystems, although their in situ studies have been severely hampered by methodological difficulties... In one of the first applications of SCG on eukaryotes, multiple cells of the candidate phylum Picozoa (formerly Picobilliphyta) were found to contain fragments of bacterial and viral DNA, while no genes involved in photosynthesis were identified (Yoon et al., )... The same SCG study also retrieved a complete genome of a novel nanovirus from an infected Picozoa cell... Subsequent studies confirmed that substantial genome content variation among individuals, indicative of extensive horizontal gene exchange, is the rule rather than the exception in natural microbial populations (Ochman et al., ; Papke et al., ; Shapiro et al., ), with likely major implications to their resilience and adaptability to new conditions, such as climate change or exposure to antibiotics... In the past 5 years, the scale of SCG projects grew from single genomes (Marcy et al., ; Woyke et al., ) to 10 s and 100 s of genomes (Rinke et al., ; Swan et al., ; Kashtan et al., ), and further technology improvements are well-underway... Increasingly sophisticated research applications will also drive improvements in SCG data quality, such as better genome recovery and reduced frequency of assembly errors... Like any technology, SCG is at its best when combined with other research tools, in order to most effectively address transformative science questions... There is little doubt that SCG will be increasingly utilized in diverse microbial studies, complementing cultivation-based, community omics, biogeochemical, and other research approaches.

No MeSH data available.