Uncultivated microbes in need of their own taxonomy

The ISME Journal, Год журнала: 2017, Номер 11(11), С. 2399 - 2406

Опубликована: Июль 21, 2017

Abstract The great majority of microbial species remains uncultured, severely limiting their taxonomic characterization and thus communication among scientists. Although Candidatus was devised as a provisional category to classify uncultured taxa, it has not been widely accepted owing technical limitations lack priority names in the official nomenclature. High-throughput sequencing provides potential for data-rich descriptions uncultivated microbes, comparable quality those cultured organisms. In order fully realize this potential, standards guidelines on how perform these are needed. Here we aimed outline draw roadmap new genome-based taxonomy that, at least initially, would be parallel but highly convergent one existence isolates. particular, recommend use DNA genome sequences, recovered by population binning or single-cell techniques, basis (i) identification phylogenetic placement, (ii) bioinformatics-based functional phenotypic predictions, well (iii) type material. We also implementation an independent nomenclatural system following same nomenclature rules Bacteria Archaea with its own list validly published names. If adopted, will only facilitate comprehensive ‘uncultivated majority’, provide unified catalogue names, thereby avoiding synonyms confusion. suggest that committee experts, supported international microbiological society, should formed govern classification system.

Язык: Английский

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Global Organization and Proposed Megataxonomy of the Virus World

Microbiology and Molecular Biology Reviews, Год журнала: 2020, Номер 84(2)

Опубликована: Март 3, 2020

Viruses and mobile genetic elements are molecular parasites or symbionts that coevolve with nearly all forms of cellular life. The route virus replication protein expression is determined by the viral genome type. Comparison these routes led to classification viruses into seven “Baltimore classes” (BCs) define major features reproduction. However, recent phylogenomic studies identified multiple evolutionary connections among within each BCs as well between different classes.

Язык: Английский

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Biophysical processes supporting the diversity of microbial life in soil

FEMS Microbiology Reviews, Год журнала: 2017, Номер 41(5), С. 599 - 623

Опубликована: Июль 10, 2017

Soil, the living terrestrial skin of Earth, plays a central role in supporting life and is home to an unimaginable diversity microorganisms. This review explores key drivers for microbial soils under different climates land-use practices at scales ranging from soil pores landscapes. We delineate special features as habitat (focusing on bacteria) consequences communities. covers recent modeling advances that link physical processes with (termed biophysical processes). Readers are introduced concepts governing water organization associated transport properties dispersion ranges often determined by spatial highly dynamic aqueous phase. The narrow hydrological windows wetting phase connectedness crucial resource distribution longer range Feedbacks between activity their immediate environment responsible emergence stabilization structure-the scaffolding ecological functioning. synthesize insights historical contemporary studies provide outlook challenges opportunities developing quantitative framework predict component

Язык: Английский

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Rare microbial taxa as the major drivers of ecosystem multifunctionality in long-term fertilized soils

Soil Biology and Biochemistry, Год журнала: 2019, Номер 141, С. 107686 - 107686

Опубликована: Ноя. 22, 2019

Язык: Английский

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Innovations to culturing the uncultured microbial majority

Nature Reviews Microbiology, Год журнала: 2020, Номер 19(4), С. 225 - 240

Опубликована: Окт. 22, 2020

Язык: Английский

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The biomass and biodiversity of the continental subsurface

Nature Geoscience, Год журнала: 2018, Номер 11(10), С. 707 - 717

Опубликована: Сен. 21, 2018

Язык: Английский

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Soil microbial communities drive the resistance of ecosystem multifunctionality to global change in drylands across the globe

Ecology Letters, Год журнала: 2017, Номер 20(10), С. 1295 - 1305

Опубликована: Сен. 17, 2017

The relationship between soil microbial communities and the resistance of multiple ecosystem functions linked to C, N P cycling (multifunctionality resistance) global change has never been assessed globally in natural ecosystems. We collected soils from 59 dryland ecosystems worldwide investigate importance as predictor multifunctionality climate nitrogen fertilisation. Multifunctionality had a lower wetting-drying cycles than warming or deposition. was regulated by changes composition (relative abundance phylotypes) but not richness, total fungi bacteria fungal: bacterial ratio. Our results suggest that positive effects particular taxa on could potentially be controlled altering pH. Together, our work demonstrates strong links community six continents, provides insights into for buffering drylands worldwide.

Язык: Английский

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Diversity is the question, not the answer

The ISME Journal, Год журнала: 2016, Номер 11(1), С. 1 - 6

Опубликована: Сен. 16, 2016

Local diversity (within-sample or alpha diversity) is often implicated as a cause of success failure microbial community. However, the relationships between and emergent properties community, such its stability, productivity invasibility, are much more nuanced. I argue that without context provides limited insights into mechanisms underpinning community patterns. provide examples from traditional ecology to discuss common complications assumptions about within-sample may prevent us digging deeper specific outcomes. suggest measurement should serve starting point for further inquiry ecological rather than an 'answer'

Язык: Английский

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OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units

mSphere, Год журнала: 2017, Номер 2(2)

Опубликована: Март 10, 2017

Assignment of 16S rRNA gene sequences to operational taxonomic units (OTUs) is a computational bottleneck in the process analyzing microbial communities. Although this has been an active area research, it difficult overcome time and memory demands while improving quality OTU assignments. Here, we developed new assignment algorithm that iteratively reassigns OTUs optimize Matthews correlation coefficient (MCC), measure To assess algorithm, OptiClust, compared 10 other algorithms using from two simulated four natural Using OptiClust MCC values averaged 15.2 16.5% higher than generated when used average neighbor distance-based greedy clustering with VSEARCH, respectively. Furthermore, on average, was 94.6 times faster just as fast VSEARCH. An empirical analysis efficiency showed required perform scaled quadratically number unique data set. The significant improvement assignments over previously existing methods will significantly enhance downstream by limiting splitting similar into separate merging dissimilar same OTU. development represents advance likely have numerous applications. IMPORTANCE communities diverse environments sequencing expanded our knowledge biogeography microorganisms. important step groups based their similarity database or each other, irrespective database. In study, present for latter approach. seeks metric shuffling between groups. We found produces more robust does so rapid memory-efficient manner. This allow factors shape them.

Язык: Английский

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Diversity-triggered deterministic bacterial assembly constrains community functions

Nature Communications, Год журнала: 2019, Номер 10(1)

Опубликована: Авг. 23, 2019

Abstract A growing body of evidence suggests that microbial α-diversity (local species richness) may have positive effects on ecosystem function. However, less attention has been paid to β-diversity (the variation among local assemblages). Here we studied the impact stochastic/deterministic community assembly processes, which are related β-diversity, and consequences for Bacterial communities differing in were generated their structures potential functional traits inferred from DNA sequencing. Phylogenetic null modeling analysis stochastic processes dominant high-diversity communities. low-diversity communities, deterministic dominant, associating with reduction specialized functions correlated specific bacterial taxa. Overall, suggest low-diversity-induced constrain functions, highlighting roles generating sustaining function soil ecosystems.

Язык: Английский

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