Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes

mSystems, Journal Year: 2018, Volume and Issue: 3(5)

Published: Sept. 24, 2018

To describe a microbe's physiology, including its metabolism, environmental roles, and growth characteristics, it must be grown in laboratory culture. Unfortunately, many phylogenetically novel groups have never been cultured, so their physiologies only inferred from genomics characteristics. Although the diversity, or number of different taxonomic groups, uncultured clades has studied well, global abundances, numbers cells any given environment, not assessed. We quantified degree similarity 16S rRNA gene sequences diverse environments publicly available metagenome metatranscriptome databases, which we show far less culture bias present primer-amplified surveys, to those nearest cultured relatives. Whether normalized scaffold read depths not, highest abundances metagenomic belong seawater, freshwater, terrestrial subsurface, soil, hypersaline environments, marine sediment, hot springs, hydrothermal vents, nonhuman hosts, snow, bioreactors (22% 87% genera classes 0% 64% phyla). The exceptions were human human-associated dominated by (45% 97%). estimate that phyla could comprise 7.3 × 10

Language: Английский

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SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter

mBio, Journal Year: 2017, Volume and Issue: 8(2)

Published: April 19, 2017

ABSTRACT Deep-ocean regions beyond the reach of sunlight contain an estimated 615 Pg dissolved organic matter (DOM), much which persists for thousands years. It is thought that bacteria oxidize DOM until it too dilute or refractory to support microbial activity. We analyzed five single-amplified genomes (SAGs) from abundant SAR202 clade dark-ocean bacterioplankton and found they encode multiple families paralogous enzymes involved in carbon catabolism, including several oxidative we hypothesize participate degradation cyclic alkanes. The partial encoded 152 flavin mononucleotide/F420-dependent monooxygenases (FMNOs), many are predicted be type II Baeyer-Villiger (BVMOs) catalyze oxygen insertion into semilabile alicyclic large number enzymes, as well other appear play complementary roles catabolic pathways, suggests might final steps biological oxidation relatively recalcitrant compounds persist. IMPORTANCE Carbon ocean massively sequestered a complex mixture biologically molecules accumulate chemical end member diagenetic change. However, few details known about biochemical machinery sequestration deep ocean. Reconstruction metabolism deep-ocean clade, SAR202, led postulation new pathways may penultimate stages forms These tied proliferation enzymes. This research illuminates biochemistry broadly consequential reconstructing global cycle.

Language: Английский

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Cultivation and genomics of the first freshwater SAR11 (LD12) isolate

The ISME Journal, Journal Year: 2018, Volume and Issue: 12(7), P. 1846 - 1860

Published: March 29, 2018

Abstract Evolutionary transitions between fresh and salt water happen infrequently among bacterioplankton. Within the ubiquitous highly abundant heterotrophic Alphaproteobacteria order Pelagibacterales (SAR11), most members live in marine habitats, but LD12 subclade has evolved as a unique freshwater lineage. cells occur some of dominant bacterioplankton, yet this group remained elusive to cultivation, hampering more thorough understanding its biology. Here, we report first successful isolation an representative, strain LSUCC0530, using high-throughput dilution-to-extinction cultivation methods, complete genome sequence. Growth experiments corroborate ecological data suggesting active populations brackish up salinities ~5. LSUCC0530 smallest closed thus far reported for SAR11 (1.16 Mbp). The affirms many previous metabolic predictions from cultivation-independent analyses, like Embden–Meyerhof–Parnas glycolysis pathway, also provides novel insights, such isocitrate dehydrogenase LD12, likely homologous recombination malate synthase outside clade, analogous substitutions ion transporters with others that throughout rest clade. support metagenomic recruitment results temperature-based ecotype diversification within LD12. Key gene losses osmolyte uptake provide succinct hypothesis evolutionary transition freshwater. For propose provisional nomenclature Candidatus fonsibacter ubiquis.

Language: Английский

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Planktonic Marine Archaea

Annual Review of Marine Science, Journal Year: 2018, Volume and Issue: 11(1), P. 131 - 158

Published: Sept. 13, 2018

Archaea are ubiquitous and abundant members of the marine plankton. Once thought as rare organisms found in exotic extremes temperature, pressure, or salinity, archaea now known nearly every environment. Though frequently referred to collectively, planktonic actually comprise four major phylogenetic groups, each with its own distinct physiology ecology. Only one group—the Thaumarchaeota—has cultivated representatives, making an attractive focus point for latest developments cultivation-independent molecular methods. Here, we review ecology, physiology, biogeochemical impact archaeal groups using recent insights from cultures large-scale environmental sequencing studies. We highlight key gaps our knowledge about ecological roles carbon flow food web interactions. emphasize incredible uncultivated diversity within suggesting there is much more be done.

Language: Английский

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Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes

The ISME Journal, Journal Year: 2018, Volume and Issue: 13(3), P. 618 - 631

Published: Oct. 12, 2018

Language: Английский

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Microbial niches in marine oxygen minimum zones

Nature Reviews Microbiology, Journal Year: 2018, Volume and Issue: 16(12), P. 723 - 729

Published: Sept. 24, 2018

Language: Английский

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Genomic evidence for the degradation of terrestrial organic matter by pelagic Arctic Ocean Chloroflexi bacteria

Communications Biology, Journal Year: 2018, Volume and Issue: 1(1)

Published: June 29, 2018

The Arctic Ocean currently receives a large supply of global river discharge and terrestrial dissolved organic matter. Moreover, an increase in freshwater runoff riverine transport matter to the is predicted consequence thawing permafrost increased precipitation. fate humic-rich material its impact on marine carbon cycle are largely unknown. Here, metagenomic survey Canada Basin Western showed that pelagic Chloroflexi from replete with aromatic compound degradation genes, acquired part by lateral transfer bacteria. Our results imply have capacity use their role may changing hydrological cycle.

Language: Английский

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Marine Sponges as Chloroflexi Hot Spots: Genomic Insights and High-Resolution Visualization of an Abundant and Diverse Symbiotic Clade

mSystems, Journal Year: 2018, Volume and Issue: 3(6)

Published: Oct. 30, 2018

Members of the widespread bacterial phylum Chloroflexi can dominate high-microbial-abundance (HMA) sponge microbiomes. In Sponge Microbiome Project, sequences amounted to 20 30% total microbiome certain HMA genera with classes/clades SAR202, Caldilineae, and Anaerolineae being most prominent. We performed metagenomic single-cell genomic analyses elucidate functional gene repertoire symbionts Aplysina aerophoba. Eighteen draft genomes were reconstructed placed into phylogenetic context which six investigated in detail. Common features related central energy carbon converting pathways, amino acid fatty metabolism, respiration. Clade-specific metabolic included a massively expanded for carbohydrate degradation Caldilineae genomes, but only utilization by SAR202. While import cofactors vitamins, SAR202 harbor genes encoding components involved cofactor biosynthesis. A number relevant symbiosis further identified, including CRISPR-Cas systems, eukaryote-like repeat proteins, secondary metabolite clusters. visualized extracellular matrix at ultrastructural resolution fluorescence situ hybridization-correlative light electron microscopy (FISH-CLEM) method. Carbohydrate potential was reported previously "Candidatus Poribacteria" SAUL, typical sponges, we propose here that collectively engage dissolved organic matter, both labile recalcitrant. Thus, microbes may not provide nutrients host, they also contribute matter (DOM) recycling primary productivity reef ecosystems via pathway termed loop. IMPORTANCEChloroflexi represent widespread, yet enigmatic few cultivated members. used approaches characterize marine sponges. The results this study suggest clade-specific specialization have from seawater. Considering abundance dominance sponges many benthic environments, predict role biogeochemical cycles is larger than thought.

Language: Английский

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Metabolic diversity within the globally abundant Marine Group II Euryarchaea offers insight into ecological patterns

Nature Communications, Journal Year: 2019, Volume and Issue: 10(1)

Published: Jan. 11, 2019

Abstract Despite their discovery over 25 years ago, the Marine Group II Euryarchaea (MGII) remain a difficult group of organisms to study, lacking cultured isolates and genome references. The MGII have been identified in marine samples from around world, evidence supports photoheterotrophic lifestyle combining phototrophy via proteorhodopsins with remineralization high molecular weight organic matter. Divided between two clades, distinct ecological patterns that are not understood based on limited number available genomes. Here, I present comparative genomic analysis 250 genomes, providing comprehensive investigation these mesophilic archaea. This identifies 17 subclades including nine previously lacked reference metabolic potential distribution genera reveals roles environment, identifying algal-saccharide-degrading coastal subclades, protein-degrading oligotrophic surface ocean mesopelagic proteorhodopsins, common all other subclades.

Language: Английский

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Benchmarking microbial growth rate predictions from metagenomes

The ISME Journal, Journal Year: 2020, Volume and Issue: 15(1), P. 183 - 195

Published: Sept. 16, 2020

Growth rates are central to understanding microbial interactions and community dynamics. Metagenomic growth estimators have been developed, specifically codon usage bias (CUB) for maximum "peak-to-trough ratio" (PTR) in situ rates. Both were originally tested with pure cultures, but natural populations more heterogeneous, especially individual cell histories pertinent PTR. To test these methods, we compared predictors observed of freshly collected marine prokaryotes unamended seawater. We prefiltered diluted samples remove grazers greatly reduce virus infection, so net approximated gross growth. sampled over 44 h abundances metagenomes, generating 101 metagenome-assembled genomes (MAGs), including Actinobacteria, Verrucomicrobia, SAR406, MGII archaea, etc. tracked each MAG population by cell-abundance-normalized read recruitment, finding 0 5.99 per day, the first reported several groups, used as benchmarks. PTR, calculated three rarely correlated (r ~-0.26-0.08), except rapidly growing γ-Proteobacteria ~0.63-0.92), while CUB moderately well = 0.57). This suggests that current PTR approaches poorly predict actual most bacterial populations, can be from genomic characteristics.

Language: Английский

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