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Philosophical Transactions of the Royal... Nov 2006The number of species of Bacteria and Archaea (ca 5000) is surprisingly small considering their early evolution, genetic diversity and residence in all ecosystems. The... (Review)
Review
The number of species of Bacteria and Archaea (ca 5000) is surprisingly small considering their early evolution, genetic diversity and residence in all ecosystems. The bacterial species definition accounts in part for the small number of named species. The primary procedures required to identify new species of Bacteria and Archaea are DNA-DNA hybridization and phenotypic characterization. Recently, 16S rRNA gene sequencing and phylogenetic analysis have been applied to bacterial taxonomy. Although 16S phylogeny is arguably excellent for classification of Bacteria and Archaea from the Domain level down to the family or genus, it lacks resolution below that level. Newer approaches, including multilocus sequence analysis, and genome sequence and microarray analyses, promise to provide necessary information to better understand bacterial speciation. Indeed, recent data using these approaches, while meagre, support the view that speciation processes may occur at the subspecies level within ecological niches (ecovars) and owing to biogeography (geovars). A major dilemma for bacterial taxonomists is how to incorporate this new information into the present hierarchical system for classification of Bacteria and Archaea without causing undesirable confusion and contention. This author proposes the genomic-phylogenetic species concept (GPSC) for the taxonomy of prokaryotes. The aim is twofold. First, the GPSC would provide a conceptual and testable framework for bacterial taxonomy. Second, the GPSC would replace the burdensome requirement for DNA hybridization presently needed to describe new species. Furthermore, the GPSC is consistent with the present treatment at higher taxonomic levels.
Topics: Archaea; Bacteria; Classification; Genetic Speciation; Genetic Techniques; Phylogeny; Species Specificity
PubMed: 17062409
DOI: 10.1098/rstb.2006.1914 -
The ISME Journal Nov 2017The Archaea occupy a key position in the Tree of Life, and are a major fraction of microbial diversity. Abundant in soils, ocean sediments and the water column, they... (Review)
Review
The Archaea occupy a key position in the Tree of Life, and are a major fraction of microbial diversity. Abundant in soils, ocean sediments and the water column, they have crucial roles in processes mediating global carbon and nutrient fluxes. Moreover, they represent an important component of the human microbiome, where their role in health and disease is still unclear. The development of culture-independent sequencing techniques has provided unprecedented access to genomic data from a large number of so far inaccessible archaeal lineages. This is revolutionizing our view of the diversity and metabolic potential of the Archaea in a wide variety of environments, an important step toward understanding their ecological role. The archaeal tree is being rapidly filled up with new branches constituting phyla, classes and orders, generating novel challenges for high-rank systematics, and providing key information for dissecting the origin of this domain, the evolutionary trajectories that have shaped its current diversity, and its relationships with Bacteria and Eukarya. The present picture is that of a huge diversity of the Archaea, which we are only starting to explore.
Topics: Archaea; Biodiversity; Ecology; Genome, Archaeal; Phylogeny
PubMed: 28777382
DOI: 10.1038/ismej.2017.122 -
Molecular Microbiology May 2003The recently discovered structural similarities between the archaeal Orc1/Cdc6 and bacterial DnaA initiator proteins for chromosome replication have exciting... (Review)
Review
The recently discovered structural similarities between the archaeal Orc1/Cdc6 and bacterial DnaA initiator proteins for chromosome replication have exciting implications for cell cycle regulation. Together with current attempts to identify archaeal chromosome replication origins, the information is likely to yield fundamental insights into replication control in both archaea and eukaryotes within the near future. Several proteins that affect, or are likely to affect, chromatin structure and genome segregation in archaea have been described recently, including Sph1 and 2, ScpA and B, Sir2, Alba and Rio1p. Important insights into the properties of the MinD and FtsZ cell division proteins, and of putative cytoskeletal elements, have recently been gained in bacteria. As these proteins also are present among archaea, it is likely that the new information will also be essential for understanding archaeal genome segregation and cell division. A series of interesting cell cycle issues has been brought to light through the discovery of the novel Nanoarchaeota phylum, and these are outlined briefly. Exciting areas for extended cell cycle investigations of archaea are identified, including termination of chromosome replication, application of in situ cytological techniques for localization of cell cycle proteins and the regulatory roles of GTP-binding proteins and small RNAs.
Topics: Archaea; Archaeal Proteins; Cell Cycle; Cell Cycle Proteins; Cytoskeletal Proteins; DNA Replication; Genome, Archaeal
PubMed: 12694607
DOI: 10.1046/j.1365-2958.2003.03414.x -
Journal of Biosciences Oct 2019The International Space Station (ISS) is a confined and closed habitat with unique conditions such as cosmic radiation, and microgravity. These conditions have a strong... (Review)
Review
The International Space Station (ISS) is a confined and closed habitat with unique conditions such as cosmic radiation, and microgravity. These conditions have a strong effect on the human and spacecraft microflora. They can affect the immune response of the crew-members, thus posing a threat to their health. Microbial diversity and abundance of microorganisms from surfaces, air filters and air samples on the ISS have been studied. Enterobacteriaceae, Bacillus spp., Propionibacterium spp., Corynebacterium spp., and Staphylococcus spp. were among the most frequently isolated bacteria. Microbial growth, biofilm formation, stress response, and pathogenicity are affected by microgravity. Increased resistance to antibiotics in bacteria isolated from the ISS has often been reported. Enterococcus faecalis and Staphylococcus spp. isolates from the ISS have been shown to harbor plasmid-encoded transfer genes. These genes facilitate the dissemination of antibiotic resistances. These features of ISS-pathogens call for novel approaches including highly effective antimicrobials which can be easily used on the ISS. A promising material is the antimicrobial surface coating AGXX, a self-recycling material consisting of two noble metals. It drastically reduced microbial growth of multi-resistant human pathogens, such as staphylococci and enterococci. Further novel approaches include the application of cold atmospheric plasma for the sterilization of spacecrafts.
Topics: Archaea; Bacteria; Biofilms; Spacecraft; Species Specificity
PubMed: 31719234
DOI: No ID Found -
Proceedings of the National Academy of... Jun 1996
Review
Topics: Adaptation, Physiological; Archaea; Phylogeny; RNA, Ribosomal
PubMed: 8692796
DOI: 10.1073/pnas.93.13.6228 -
Cell Mar 2018The recent recovery of genomes for organisms from phyla with no isolated representative (candidate phyla) via cultivation-independent genomics enabled delineation of... (Review)
Review
The recent recovery of genomes for organisms from phyla with no isolated representative (candidate phyla) via cultivation-independent genomics enabled delineation of major new microbial lineages, namely the bacterial candidate phyla radiation (CPR), DPANN archaea, and Asgard archaea. CPR and DPANN organisms are inferred to be mostly symbionts, and some are episymbionts of other microbial community members. Asgard genomes encode typically eukaryotic systems, and their inclusion in phylogenetic analyses results in placement of eukaryotes as a branch within Archaea. Here, we illustrate how new genomes have changed the structure of the tree of life and altered our understanding of biology, evolution, and metabolic roles in biogeochemical processes.
Topics: Archaea; Bacteria; Genetic Variation; Metagenome; Metagenomics; Phylogeny; RNA, Ribosomal, 16S; Species Specificity
PubMed: 29522741
DOI: 10.1016/j.cell.2018.02.016 -
FEMS Microbiology Reviews Jul 2011The tree of life is split into three main branches: eukaryotes, bacteria, and archaea. Our knowledge of eukaryotic and bacteria cell biology has been built on a... (Review)
Review
The tree of life is split into three main branches: eukaryotes, bacteria, and archaea. Our knowledge of eukaryotic and bacteria cell biology has been built on a foundation of studies in model organisms, using the complementary approaches of genetics and biochemistry. Archaea have led to some exciting discoveries in the field of biochemistry, but archaeal genetics has been slow to get off the ground, not least because these organisms inhabit some of the more inhospitable places on earth and are therefore believed to be difficult to culture. In fact, many species can be cultivated with relative ease and there has been tremendous progress in the development of genetic tools for both major archaeal phyla, the Euryarchaeota and the Crenarchaeota. There are several model organisms available for methanogens, halophiles, and thermophiles; in the latter group, there are genetic systems for Sulfolobales and Thermococcales. In this review, we present the advantages and disadvantages of working with each archaeal group, give an overview of their different genetic systems, and direct the neophyte archaeologist to the most appropriate model organism.
Topics: Archaea; Biochemistry; Crenarchaeota; Euryarchaeota; Gene Expression Regulation, Archaeal; Genetic Techniques; Genetics, Microbial; Models, Genetic; Phylogeny
PubMed: 21265868
DOI: 10.1111/j.1574-6976.2011.00265.x -
Current Issues in Molecular Biology 2019Methanotrophic microorganisms utilize methane as an electron donor and a carbon source. To date, the capacity to oxidize methane is restricted to microorganisms from... (Review)
Review
Methanotrophic microorganisms utilize methane as an electron donor and a carbon source. To date, the capacity to oxidize methane is restricted to microorganisms from three bacterial and one archaeal phyla. Most of our knowledge of methanotrophic metabolism has been obtained using highly enriched or pure cultures grown in the laboratory. However, many methanotrophs currently evade cultivation, thus metagenomics provides a complementary approach for gaining insight into currently unisolated microorganisms. Here we synthesize the studies using metagenomics to glean information about methanotrophs. We complement this summary with an analysis of methanotroph marker genes from 235 publically available metagenomic datasets. We analyze the phylogenetic and environmental distribution of methanotrophs sampled by metagenomics. We also highlight metabolic insights that methanotroph genomes assembled from metagenomes are illuminating. In summary, metagenomics has increased methanotrophic foliage within the tree of life, as well as provided new insights into methanotroph metabolism, which collectively can guide new cultivation efforts. Lastly, given the importance of methanotrophs for biotechnological applications and their capacity to filter greenhouse gases from a variety of ecosystems, metagenomics will continue to be an important component in the arsenal of tools needed for understanding methanotroph diversity and metabolism in both engineered and natural systems.
Topics: Archaea; Biodiversity; Energy Metabolism; Metagenome; Metagenomics; Methane; Methanobacteriales; Microbiota; Phylogeny; Soil Microbiology
PubMed: 31166185
DOI: 10.21775/cimb.033.057 -
The ISME Journal Apr 2023D-glutamate (D-Glu) is an essential component of bacterial peptidoglycans, representing an important, yet overlooked, pool of organic matter in global oceans. However,...
D-glutamate (D-Glu) is an essential component of bacterial peptidoglycans, representing an important, yet overlooked, pool of organic matter in global oceans. However, little is known on D-Glu catabolism by marine microorganisms. Here, a novel catabolic pathway for D-Glu was identified using the marine bacterium Pseudoalteromonas sp. CF6-2 as the model. Two novel enzymes (DgcN, DgcA), together with a transcriptional regulator DgcR, are crucial for D-Glu catabolism in strain CF6-2. Genetic and biochemical data confirm that DgcN is a N-acetyltransferase which catalyzes the formation of N-acetyl-D-Glu from D-Glu. DgcA is a racemase that converts N-acetyl-D-Glu to N-acetyl-L-Glu, which is further hydrolyzed to L-Glu. DgcR positively regulates the transcription of dgcN and dgcA. Structural and biochemical analyses suggested that DgcN and its homologs, which use D-Glu as the acyl receptor, represent a new group of the general control non-repressible 5 (GCN5)-related N-acetyltransferases (GNAT) superfamily. DgcA and DgcN occur widely in marine bacteria (particularly Rhodobacterales) and halophilic archaea (Halobacteria) and are abundant in marine and hypersaline metagenome datasets. Thus, this study reveals a novel D-Glu catabolic pathway in ecologically important marine bacteria and halophilic archaea and helps better understand the catabolism and recycling of D-Glu in these ecosystems.
Topics: Glutamic Acid; Proteobacteria; Ecosystem; Bacteria; Archaea
PubMed: 36690779
DOI: 10.1038/s41396-023-01364-6 -
FEMS Microbiology Ecology Jul 2010We are becoming increasingly aware of the role played by archaea in the biogeochemical cycling of the elements. Metabolism of metals is linked to fundamental metabolic... (Review)
Review
We are becoming increasingly aware of the role played by archaea in the biogeochemical cycling of the elements. Metabolism of metals is linked to fundamental metabolic functions, including nitrogen fixation, energy production, and cellular processes based on oxidoreductions. Comparative genomic analyses have shown that genes for metabolism, resistance, and detoxification of metals are widespread throughout the archaeal domain. Archaea share with other organisms strategies allowing them to utilize essential metals and maintain metal ions within a physiological range, although comparative proteomics show, in a few cases, preferences for specific genetic traits related to metals. A more in-depth understanding of the physiology of acidophilic archaea might lead to the development of new strategies for the bioremediation of metal-polluted sites and other applications, such as biomining.
Topics: Archaea; Biodegradation, Environmental; Biological Transport, Active; Comparative Genomic Hybridization; Environmental Microbiology; Metals; Proteome
PubMed: 20455933
DOI: 10.1111/j.1574-6941.2010.00876.x