Insights into the phylogeny and coding potential of microbial dark matter

Nature, Год журнала: 2013, Номер 499(7459), С. 431 - 437

Опубликована: Июль 12, 2013

Genome sequencing enhances our understanding of the biological world by providing blueprints for evolutionary and functional diversity that shapes biosphere. However, microbial genomes are currently available limited phylogenetic breadth, owing to historical inability cultivate most microorganisms in laboratory. We apply single-cell genomics target sequence 201 uncultivated archaeal bacterial cells from nine diverse habitats belonging 29 major mostly uncharted branches tree life, so-called 'microbial dark matter'. With this additional genomic information, we able resolve many intra- inter-phylum-level relationships propose two new superphyla. uncover unexpected metabolic features extend biology challenge established boundaries between three domains life. These include a novel amino acid use opal stop codon, an archaeal-type purine synthesis Bacteria complete sigma factors Archaea similar those Bacteria. The also served phylogenetically anchor up 20% metagenomic reads some habitats, facilitating organism-level interpretation ecosystem function. This study greatly expands representation life provides systematic step towards better evolution on planet.

Язык: Английский

---

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

Nature Reviews Microbiology, Год журнала: 2014, Номер 12(9), С. 635 - 645

Опубликована: Авг. 14, 2014

Язык: Английский

---

A Guide to the Natural History of Freshwater Lake Bacteria

Microbiology and Molecular Biology Reviews, Год журнала: 2011, Номер 75(1), С. 14 - 49

Опубликована: Март 1, 2011

SUMMARY Freshwater bacteria are at the hub of biogeochemical cycles and control water quality in lakes. Despite this, little is known about identity ecology functionally significant lake bacteria. Molecular studies have identified many abundant bacteria, but there a large variation taxonomic or phylogenetic breadths among methods used for this exploration. Because an inconsistent overlapping naming structure has developed freshwater creating obstacle to identifying coherent ecological traits these groups. A discourse that unites field sorely needed. Here we present new phylogeny constructed from all published 16S rRNA gene sequences epilimnia propose unifying vocabulary discuss taxa. With place, review current information on ecology, ecophysiology, distribution highlight newly phylotypes. In second part our review, conduct meta-analyses compiled data, patterns bacterial phylotypes biomes across environmental gradients We conclude by emphasizing role can play providing framework future studies.

Язык: Английский

---

Sponge-Associated Microorganisms: Evolution, Ecology, and Biotechnological Potential

Microbiology and Molecular Biology Reviews, Год журнала: 2007, Номер 71(2), С. 295 - 347

Опубликована: Июнь 1, 2007

SUMMARY Marine sponges often contain diverse and abundant microbial communities, including bacteria, archaea, microalgae, fungi. In some cases, these associates comprise as much 40% of the sponge volume can contribute significantly to host metabolism (e.g., via photosynthesis or nitrogen fixation). We review in detail diversity microbes associated with sponges, extensive 16S rRNA-based phylogenetic analyses which support previously suggested existence a sponge-specific microbiota. These provide suitable vantage point from consider potential evolutionary ecological ramifications widespread, microorganisms. Subsequently, we examine ecology sponge-microbe associations, establishment maintenance sometimes intimate partnerships, varied nature interactions (ranging mutualism host-pathogen relationships), broad-scale patterns symbiont distribution. The importance associations is mirrored by their enormous biotechnological potential: marine are among animal kingdom's most prolific producers bioactive metabolites, at least compounds rather than origin. status this important field, outlining various approaches cultivation, cell separation, metagenomics) have been employed access chemical wealth associations.

Язык: Английский

---

Anammox bacteria: from discovery to application

Nature Reviews Microbiology, Год журнала: 2008, Номер 6(4), С. 320 - 326

Опубликована: Март 14, 2008

Язык: Английский

---

Methanotrophs and copper

FEMS Microbiology Reviews, Год журнала: 2010, Номер 34(4), С. 496 - 531

Опубликована: Янв. 30, 2010

Methanotrophs, cells that consume methane (CH4) as their sole source of carbon and energy, play key roles in the global cycle, including controlling anthropogenic natural emissions CH4, second-most important greenhouse gas after dioxide. These have also been widely used for bioremediation chlorinated solvents, help sustain diverse microbial communities well higher organisms through conversion CH4 to complex organic compounds (e.g. deep ocean subterranean environments with substantial fluxes). It has well-known over 30 years copper (Cu) plays a role physiology activity methanotrophs, but it is only recently we begun understand how these collect Cu, Cu oxidation by particulate monooxygenase, effect on proteome, affects ability methanotrophs oxidize different substrates. Here summarize current state knowledge phylogeny, environmental distribution, potential applications regional issues, regulating gene expression proteome cells, its effects enzymatic whole-cell activity, novel uptake system methanotrophs.

Язык: Английский

---

The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota

Clinical Microbiology Reviews, Год журнала: 2015, Номер 28(1), С. 237 - 264

Опубликована: Янв. 1, 2015

SUMMARY Bacterial culture was the first method used to describe human microbiota, but this is considered outdated by many researchers. Metagenomics studies have since been applied clinical microbiology; however, a “dark matter” of prokaryotes, which corresponds hole in our knowledge and includes minority bacterial populations, not elucidated these studies. By replicating natural environment, environmental microbiologists were reduce “great plate count anomaly,” difference between microscopic counts. The revolution identification also allowed rapid progress. 16S rRNA accurate new species. Mass spectrometry high-throughput rare species detection using methods increasing number conditions, culturomics extension known gut repertoire levels equivalent those pyrosequencing. Finally, taxonogenomics strategies became an emerging for describing species, associating genome sequence bacteria systematically. We provide comprehensive review on topics, demonstrating that both empirical hypothesis-driven approaches will enable increase prokaryote repertoire.

Язык: Английский

---

The under-recognized dominance of Verrucomicrobia in soil bacterial communities

Soil Biology and Biochemistry, Год журнала: 2011, Номер 43(7), С. 1450 - 1455

Опубликована: Апрель 15, 2011

Язык: Английский

---

How to make a living from anaerobic ammonium oxidation

FEMS Microbiology Reviews, Год журнала: 2012, Номер 37(3), С. 428 - 461

Опубликована: Дек. 4, 2012

Anaerobic ammonium-oxidizing (anammox) bacteria primarily grow by the oxidation of ammonium coupled to nitrite reduction, using CO2 as sole carbon source. Although they were neglected for a long time, anammox are encountered in an enormous species (micro)diversity virtually any anoxic environment that contains fixed nitrogen. It has even been estimated about 50% all nitrogen gas released into atmosphere is made these ‘impossible’ bacteria. Anammox catabolism most likely resides special cell organelle, anammoxosome, which surrounded highly unusual ladder-like (ladderane) lipids. Ammonium and reduction proceed cyclic electron flow through two intermediates, hydrazine nitric oxide, resulting generation proton-motive force ATP synthesis. Reduction reactions associated with fixation drain electrons from this cycle, replenished nitrate. Besides or nitrite, use broad range organic inorganic compounds donors. An analysis metabolic opportunities suggests alternative chemolithotrophic lifestyles independent compounds. We note current concepts still largely hypothetical put forward intriguing questions need experimental answers.

Язык: Английский

---

Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges

The ISME Journal, Год журнала: 2011, Номер 6(3), С. 564 - 576

Опубликована: Окт. 13, 2011

Язык: Английский

---