Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes

Lloyd, Karen G.; Steen, Andrew D.; Ladau, Joshua; Yin, Junqi; Crosby, Lonnie D.

doi:10.1128/msystems.00055-18

Cited by 305 publications

(283 citation statements)

References 52 publications

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“…As environmental microbiologists, we are typically confronted with communities of catabolically diverse organisms in complex chemical systems. Some of these organisms may be well characterized, with isolates in culture collections and genomes fully sequenced, but many may be largely unknown, including and perhaps dominated by clades that have no cultured representatives (microbial dark matter) (Lloyd et al, 2018). The systems of interest may be natural and pristine, contaminated or engineered.…”

Section: Resultsmentioning

confidence: 99%

Minireview: demystifying microbial reaction energetics

Amend

LaRowe

2019

Environmental Microbiology

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SummaryThe biology literature is rife with misleading information on how to quantify catabolic reaction energetics. The principal misconception is that the sign and value of the standard Gibbs energy (ΔGr0) define the direction and energy yield of a reaction; they do not. ΔGr0 is one part of the actual Gibbs energy of a reaction (ΔGr), with a second part accounting for deviations from the standard composition. It is also frequently assumed that ΔGr0 applies only to 25 °C and 1 bar; it does not. ΔGr0 is a function of temperature and pressure. Here, we review how to determine ΔGr as a function of temperature, pressure and chemical composition for microbial catabolic reactions, including a discussion of the effects of ionic strength on ΔGr and highlighting the large effects when multi‐valent ions are part of the reaction. We also calculate ΔGr for five example catabolisms at specific environmental conditions: aerobic respiration of glucose in freshwater, anaerobic respiration of acetate in marine sediment, hydrogenotrophic methanogenesis in a laboratory batch reactor, anaerobic ammonia oxidation in a wastewater reactor and aerobic pyrite oxidation in acid mine drainage. These examples serve as templates to determine the energy yields of other catabolic reactions at environmentally relevant conditions.

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Section: Resultsmentioning

confidence: 99%

Minireview: demystifying microbial reaction energetics

Amend

LaRowe

2019

Environmental Microbiology

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“…The definition of the cultured and uncultured myxobacteria was according to user-provided metadata or literature retrieval. Meantime, the isolation sources of all sequences were retrieved from the original annotations, published studies, or documents of culture collections, and then manually assigned to multiple defined environmental categories referring to the previously described schema (42) (48). To simplify categorizations, sequences from marine animals, marine plants, marine biofilms, and others were classified as sequences from marine organisms, whereas those from terrestrial animals, terrestrial plants, terrestrial biofilms, and others as sequences from terrestrial organisms.…”

Section: Methodsmentioning

confidence: 99%

Meta-16S rRNA gene phylogenetic reconstruction reveals astonishing diversity of the cosmopolitan myxobacteria

Liu

Yao

Zhu

2019

Preprint

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23Numerous ecological studies for myxobacteria have been conducted well, but their 24 true diversity hidden in plain sight remains to be explored. To bridge this gap, we here 25 implemented a comprehensive survey of diversity and distribution of myxobacteria by 26 using 4997 publicly available 16S rRNA gene sequences (≥1200 bp) collected from 27 several hundreds of sites across multiple countries and regions. In the study, the 28 meta-16S rRNA gene phylogenetic reconstruction clearly revealed that these 29 sequences were classified to 998 species, 445 genera, 58 families, and 20 suborders, 30 highlighting a considerable taxonomic diversity of myxobacteria, the great majority of 31 which belonged to new taxa. Most cultured myxobacteria including the 32 well-described type strains were strongly inclined to locate on the shallow branches of 33 the phylogenetic tree; on the contrary, the majority of uncultured myxobacteria the 34 deep branches. The geographical analysis of sequences based on their environmental 35 categories clearly demonstrated that myxobacteria showed a nearly cosmopolitan 36 distribution, despite the presence of some habitat-specific taxa, especially at genus 37 and species levels. Among all abundant suborders, members of Suborder_4, 38 Suborder_15, and Suborder_17 were more widely distributed in marine environments, 39 the remaining suborders preferred to reside in terrestrial ecosystems, particularly in 40 soils, indicating a potential selectivity of geographical distribution. In conclusion, this 41 study profiles a clear framework of diversity and distribution of the cosmopolitan 42 myxobacteria and sheds light on the isolation of the uncultured myxobacteria. 43 44 48thousands of publicly available and high-quality 16S rRNA gene sequences of 49 myxobacteria by using the phylogenetic reconstruction. The study presented an 50 astonishing diversity than that expected from the previous studies. This study further 51 demonstrated that the culturability of myxobacteria was perfectly comparable to its 52 phylogeny in the phylogenetic tree. The geographical analysis clearly indicated that 53 myxobacteria showed a nearly cosmopolitan distribution, while some taxa exhibited 54 obvious preferences for specific environmental conditions. Together, our study 55 provides novel insights into the diversity, distributions, and ecological preferences of 56 of myxobacteria from diverse environments and lays the foundation for innovation of 57 isolation techniques and the discovery of new secondary metabolites. 58 59 KRYWORDS: myxobacteria; phylogenetic diversity; geographical distribution; 60 environments 61 62 63 64 65 66 67 Myxobacteria are a large group of organisms, which taxonomically belong to the 68 order Myxococcales within the class Deltaproteobacteria (1). They are one of nature's 69 "endowed" and extensively dispersed in natural environments, preferentially in places 70 that are rich in microbes and organic matter. Myxobacteria are one of the fascinating 71 and unique bacteria by virtue of thei...

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“…However, the lack of comprehensive sets of reference genomes and low cultivation rates hinder the study of these communities. On average, a quarter of freshwater community members detected by 16S rRNA gene or metagenomic surveys belong to yet-uncultured phyla, with an additional two thirds belonging to uncultured genera, families, or classes [4]. In fact, only a tenth of freshwater microbial cells belong to cultivated species or genera, the smallest cultivated fraction among all major environments on Earth ( i.e.…”

Section: Introductionmentioning

confidence: 99%

“…In fact, only a tenth of freshwater microbial cells belong to cultivated species or genera, the smallest cultivated fraction among all major environments on Earth ( i.e. , environments with over 10 25 microbial cells estimated worldwide [4]; but see also [5]). Recent efforts to recover metagenome-assembled genomes (MAGs) from freshwater environments have largely targeted specific taxa [6–10].…”

Section: Introductionmentioning

confidence: 99%