Exploring Symbioses by Single-Cell Genomics

Kamke, Janine; Bayer, Kristina; Woyke, Tanja; Hentschel, Ute

doi:10.1086/bblv223n1p30

Cited by 19 publications

(9 citation statements)

References 94 publications

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“…While they have also been isolated from sea water and sediment, they are usually found in association with macroorganisms [3,72]. With this in mind, we investigated the genomes of our three deep sea sponge associated Pseudoalteromonas strains, together with two free-living isolates for the presence of potential symbiosis genes, such as genes mediating microbe–host interactions (genes containing eukaryotic-like domains, like ankyrin and tetratricopeptide repeats) or those that may be beneficial in the acquisition or production of nutrients such as proteases, sulfatases or peptidases for the host or the symbiont [61,73]. While the genomes of the sponge-associated and free-living Pseudoalteromonas sp.…”

Section: Discussionmentioning

confidence: 99%

Biotechnological Potential of Cold Adapted Pseudoalteromonas spp. Isolated from ‘Deep Sea’ Sponges

et al. 2017

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The marine genus Pseudoalteromonas is known for its versatile biotechnological potential with respect to the production of antimicrobials and enzymes of industrial interest. We have sequenced the genomes of three Pseudoalteromonas sp. strains isolated from different deep sea sponges on the Illumina MiSeq platform. The isolates have been screened for various industrially important enzymes and comparative genomics has been applied to investigate potential relationships between the isolates and their host organisms, while comparing them to free-living Pseudoalteromonas spp. from shallow and deep sea environments. The genomes of the sponge associated Pseudoalteromonas strains contained much lower levels of potential eukaryotic-like proteins which are known to be enriched in symbiotic sponge associated microorganisms, than might be expected for true sponge symbionts. While all the Pseudoalteromonas shared a large distinct subset of genes, nonetheless the number of unique and accessory genes is quite large and defines the pan-genome as open. Enzymatic screens indicate that a vast array of enzyme activities is expressed by the isolates, including β-galactosidase, β-glucosidase, and protease activities. A β-glucosidase gene from one of the Pseudoalteromonas isolates, strain EB27 was heterologously expressed in Escherichia coli and, following biochemical characterization, the recombinant enzyme was found to be cold-adapted, thermolabile, halotolerant, and alkaline active.

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Section: Discussionmentioning

confidence: 99%

Biotechnological Potential of Cold Adapted Pseudoalteromonas spp. Isolated from ‘Deep Sea’ Sponges

et al. 2017

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“…In general, large-insert paired-end libraries have been discouraged for MDA projects, because the prevalence of chimeric read pairs increases with the distance between the reads [43]. Even so, long insert libraries can be useful in the assembly process, as demonstrated by the assembly statistics from the two Wolbachia genomes.…”

Section: Discussionmentioning

confidence: 99%

Testing the Reproducibility of Multiple Displacement Amplification on Genomes of Clonal Endosymbiont Populations

2013

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The multiple displacement amplification method has revolutionized genomic studies of uncultured bacteria, where the extraction of pure DNA in sufficient quantity for next-generation sequencing is challenging. However, the method is problematic in that it amplifies the target DNA unevenly, induces the formation of chimeric reads and also amplifies contaminating DNA. Here, we have tested the reproducibility of the multiple displacement amplification method using serial dilutions of extracted genomic DNA and intact cells from the cultured endosymbiont Bartonella australis. The amplified DNA was sequenced with the Illumina sequencing technology, and the results were compared to sequence data obtained from unamplified DNA in this study as well as from a previously published genome project. We show that artifacts such as the extent of the amplification bias, the percentage of chimeric reads and the relative fraction of contaminating DNA increase dramatically for the smallest amounts of template DNA. The pattern of read coverage was reproducibly obtained for samples with higher amounts of template DNA, suggesting that the bias is non-random and genome-specific. A re-analysis of previously published sequence data obtained after amplification from clonal endosymbiont populations confirmed these predictions. We conclude that many of the artifacts associated with the use of the multiple displacement amplification method can be alleviated or much reduced by using multiple cells as the template for the amplification. These findings should be particularly useful for researchers studying the genomes of endosymbionts and other uncultured bacteria, for which a small clonal population of cells can be isolated.

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“…Single-cell genomics has become the most useful tool to investigate the genomic repertoire of distinct uncultivated microbial symbionts (Kamke et al, 2012) and other microorganisms (Woyke et al, 2009;Yoon et al, 2011;Stepanauskas, 2012). It also has previously been successfully applied to a poribacterial cell (Siegl et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges

et al. 2013

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Many marine sponges are hosts to dense and phylogenetically diverse microbial communities that are located in the extracellular matrix of the animal. The candidate phylum Poribacteria is a predominant member of the sponge microbiome and its representatives are nearly exclusively found in sponges. Here we used single-cell genomics to obtain comprehensive insights into the metabolic potential of individual poribacterial cells representing three distinct phylogenetic groups within Poribacteria. Genome sizes were up to 5.4 Mbp and genome coverage was as high as 98.5%. Common features of the poribacterial genomes indicated that heterotrophy is likely to be of importance for this bacterial candidate phylum. Carbohydrate-active enzyme database screening and further detailed analysis of carbohydrate metabolism suggested the ability to degrade diverse carbohydrate sources likely originating from seawater and from the host itself. The presence of uronic acid degradation pathways as well as several specific sulfatases provides strong support that Poribacteria degrade glycosaminoglycan chains of proteoglycans, which are important components of the sponge host matrix. Dominant glycoside hydrolase families further suggest degradation of other glycoproteins in the host matrix. We therefore propose that Poribacteria are well adapted to an existence in the sponge extracellular matrix. Poribacteria may be viewed as efficient scavengers and recyclers of a particular suite of carbon compounds that are unique to sponges as microbial ecosystems.

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Exploring Symbioses by Single-Cell Genomics

Cited by 19 publications

References 94 publications

Biotechnological Potential of Cold Adapted Pseudoalteromonas spp. Isolated from ‘Deep Sea’ Sponges

Biotechnological Potential of Cold Adapted Pseudoalteromonas spp. Isolated from ‘Deep Sea’ Sponges

Testing the Reproducibility of Multiple Displacement Amplification on Genomes of Clonal Endosymbiont Populations

Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges

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