Genomics of Psychrophilic Bacteria and Archaea

Bowman, John P.

doi:10.1007/978-3-319-57057-0_15

Cited by 33 publications

(26 citation statements)

References 163 publications

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“…Because data on isolation environment is not typically included with genome metadata it is difficult to determine how many complete genomes of Antarctic bacteria and archaea have been sequenced. However, Bowman (2017) recently identified only 32 completely sequenced psychrophile genomes, suggesting that bacteria and archaea from the perennially cold Antarctic are not well represented.…”

Section: Discussionmentioning

confidence: 99%

Identification of Microbial Dark Matter in Antarctic Environments

Bowman

2018

Front. Microbiol.

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Numerous studies have applied molecular techniques to understand the diversity, evolution, and ecological function of Antarctic bacteria and archaea. One common technique is sequencing of the 16S rRNA gene, which produces a nearly quantitative profile of community membership. However, the utility of this and similar approaches is limited by what is known about the evolution, physiology, and ecology of surveyed taxa. When representative genomes are available in public databases some of this information can be gleaned from genomic studies, and automated pipelines exist to carry out this task. Here the paprica metabolic inference pipeline was used to assess how well Antarctic microbial communities are represented by the available completed genomes. The NCBI’s Sequence Read Archive (SRA) was searched for Antarctic datasets that used one of the Illumina platforms to sequence the 16S rRNA gene. These data were quality controlled and denoised to identify unique reads, then analyzed with paprica to determine the degree of overlap with the closest phylogenetic neighbor with a completely sequenced genome. While some unique reads had perfect mapping to 16S rRNA genes from completed genomes, the mean percent overlap for all mapped reads was 86.6%. When samples were grouped by environment, some environments appeared more or less well represented by the available genomes. For the domain Bacteria, seawater was particularly poorly represented with a mean overlap of 80.2%, while for the domain Archaea glacial ice was particularly poorly represented with an overlap of only 48.0% for a single sample. These findings suggest that a considerable effort is needed to improve the representation of Antarctic microbes in genome sequence databases.

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Section: Discussionmentioning

confidence: 99%

Identification of Microbial Dark Matter in Antarctic Environments

Bowman

2018

Front. Microbiol.

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“…DUF3494s are typically found in psychrophilic organisms, prevalently bacteria belonging to the phyla of Flavobacterium and Bacteroidetes . In some cases, the DUF3494 fold is associated with an N‐terminal signal peptide and with the secretion domain T9SS typical of Bacteroidetes extracellular proteins .…”

Section: The Duf3494 Protein Familymentioning

confidence: 99%

Ice‐binding proteins and the ‘domain of unknown function’ 3494 family

et al. 2019

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Ice‐binding proteins (IBPs) control the growth and shape of ice crystals to cope with subzero temperatures in psychrophilic and freeze‐tolerant organisms. Recently, numerous proteins containing the domain of unknown function (DUF) 3494 were found to bind ice crystals and, hence, are classified as IBPs. DUF3494 IBPs constitute today the most widespread of the known IBP families. They can be found in different organisms including bacteria, yeasts and microalgae, supporting the hypothesis of horizontal transfer of its gene. Although the 3D structure is always a discontinuous β‐solenoid with a triangular cross‐section and an adjacent alpha‐helix, DUF3494 IBPs present very diverse activities in terms of the magnitude of their thermal hysteresis and inhibition of ice recrystallization. The proteins are secreted into the environments around the host cells or are anchored on their cell membranes. This review covers several aspects of this new class of IBPs, which promise to leave their mark on several research fields including structural biology, protein biochemistry and cryobiology.

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“…Nowadays, many genomes are available for a wide range of psychrophilic bacteria and archaea. As of early 2017, approximately 130 cold-adapted species have genome sequences [19]. Trait surveys, limited to the perspective of gene gain, reveal prevalence of genes demonstratively providing better growth at low temperature including compatible solute uptake and synthesis, antifreeze proteins and polyunsaturated fatty acids.…”

Section: Cold Environmentsmentioning

confidence: 99%

“…Trait surveys, limited to the perspective of gene gain, reveal prevalence of genes demonstratively providing better growth at low temperature including compatible solute uptake and synthesis, antifreeze proteins and polyunsaturated fatty acids. This includes the presence of anti-freeze DUF3494-type proteins that occur in all domains of life but is limited to cold-adapted taxa and is absent in higher-temperature adapted life [19]. Among these adaptations, the factors responsible for the adjustment of membrane fluidity are of prime importance, whereas the large diversity of factors contributing to limit the toxicity of highly concentrated dissolved oxygen has been already investigated.…”

Section: Cold Environmentsmentioning

confidence: 99%

“…Nevertheless, further genome sequences are needed to detect whether there are some general trends in cold-adaptation or, if on the contrary, each microorganism has its own specific strategy. Proteomic analyses are also progressing and are required to establish the relationships that should exist between the expression of regulatory proteins and the environmental temperature [19].…”

Section: Cold Environmentsmentioning

confidence: 99%

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Exploring Marine Environments for the Identification of Extremophiles and Their Enzymes for Sustainable and Green Bioprocesses

et al. 2018

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Sea environments harbor a wide variety of life forms that have adapted to live in hard and sometimes extreme conditions. Among the marine living organisms, extremophiles represent a group of microorganisms that attract increasing interest in relation to their ability to produce an array of molecules that enable them to thrive in almost every marine environment. Extremophiles can be found in virtually every extreme environment on Earth, since they can tolerate very harsh environmental conditions in terms of temperature, pH, pressure, radiation, etc. Marine extremophiles are the focus of growing interest in relation to their ability to produce biotechnologically useful enzymes, the so-called extremozymes. Thanks to their resistance to temperature, pH, salt, and pollutants, marine extremozymes are promising biocatalysts for new and sustainable industrial processes, thus representing an opportunity for several biotechnological applications. Since the marine microbioma, i.e., the complex of microorganisms living in sea environments, is still largely unexplored finding new species is a central issue for green biotechnology. Here we described the main marine environments where extremophiles can be found, some existing or potential biotechnological applications of marine extremozymes for biofuels production and bioremediation, and some possible approaches for the search of new biotechnologically useful species from marine environments.

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Genomics of Psychrophilic Bacteria and Archaea

Cited by 33 publications

References 163 publications

Identification of Microbial Dark Matter in Antarctic Environments

Identification of Microbial Dark Matter in Antarctic Environments

Ice‐binding proteins and the ‘domain of unknown function’ 3494 family

Exploring Marine Environments for the Identification of Extremophiles and Their Enzymes for Sustainable and Green Bioprocesses

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