Species- and site-specific genome editing in complex bacterial communities

Nature Microbiology, Journal Year: 2021, Volume and Issue: 7(1), P. 34 - 47

Published: Dec. 6, 2021

Language: Английский

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Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation

Nature Methods, Journal Year: 2022, Volume and Issue: 19(11), P. 1438 - 1448

Published: Oct. 17, 2022

Abstract Advances in microscopy hold great promise for allowing quantitative and precise measurement of morphological molecular phenomena at the single-cell level bacteria; however, potential this approach is ultimately limited by availability methods to faithfully segment cells independent their or optical characteristics. Here, we present Omnipose, a deep neural network image-segmentation algorithm. Unique outputs such as gradient distance field allow Omnipose accurately on which current algorithms, including its predecessor, Cellpose, produce errors. We show that achieves unprecedented segmentation performance mixed bacterial cultures, antibiotic-treated elongated branched morphology. Furthermore, benefits extend non-bacterial subjects, varied imaging modalities three-dimensional objects. Finally, demonstrate utility characterization extreme phenotypes arise during interbacterial antagonism. Our results distinguish powerful tool characterizing diverse arbitrarily shaped cell types from data.

Language: Английский

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Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities

Nature Biotechnology, Journal Year: 2022, Volume and Issue: 40(5), P. 711 - 719

Published: Jan. 3, 2022

Language: Английский

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Nitrogen cycling and microbial cooperation in the terrestrial subsurface

The ISME Journal, Journal Year: 2022, Volume and Issue: 16(11), P. 2561 - 2573

Published: Aug. 8, 2022

The nitrogen cycle plays a major role in aquatic transformations, including the terrestrial subsurface. However, variety of transformations remains understudied. To determine how cycling microorganisms respond to different aquifer chemistries, we sampled groundwater with varying nutrient and oxygen contents. Genes transcripts involved nitrogen-cycling pathways were quantified from 55 26 sites, respectively, metagenomes metatranscriptomes analyzed subset oxic dysoxic sites (0.3-1.1 mg/L bulk dissolved oxygen). Nitrogen-cycling mechanisms (e.g. ammonia oxidation, denitrification, dissimilatory nitrate reduction ammonium) prevalent highly redundant, regardless site-specific physicochemistry or availability, present 40% reconstructed genomes, suggesting that is core function communities. Transcriptional activity for nitrification, nitrite-dependent anaerobic methane oxidation (anammox) occurred simultaneously groundwater, indicating availability oxic-anoxic interfaces. Concurrent by these indicates potential synergisms through metabolite exchange across interfaces nitrite Fragmented denitrification pathway encoding transcription was widespread among bacteria, although considerable proportion associated transcriptional driven complete denitrifiers, especially under conditions. Despite large differences transcription, capacity final steps largely invariant conditions, most genes N2O reductases atypical Sec-dependant type, energy-efficiency prioritization. Results provide insights into cooperative relationships communities, richness complexity metabolic leading loss fixed nitrogen.

Language: Английский

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Organic fertilizer compost alters the microbial composition and network structure in strongly acidic soil

Applied Soil Ecology, Journal Year: 2024, Volume and Issue: 195, P. 105263 - 105263

Published: Jan. 5, 2024

Language: Английский

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Cutting edge tools in the field of soil microbiology

Current Research in Microbial Sciences, Journal Year: 2024, Volume and Issue: 6, P. 100226 - 100226

Published: Jan. 1, 2024

The study of the whole genetic material contained within microbial populations found in a certain environment is made possible by metagenomics. This technique enables thorough knowledge variety, function, and interactions communities that are notoriously difficult to research. Due limitations conventional techniques such as culturing PCR-based methodologies, soil microbiology particularly challenging field. Metagenomics has emerged an effective for overcoming these obstacles shedding light on dynamic nature soil. review focuses principle metagenomics techniques, their potential applications diversity analysis. effectiveness target-based determining function individual genes microorganisms ecosystems also highlighted. Targeted metagenomics, including high-throughput sequencing stable-isotope probing, essential studying taxa complex ecosystems. Shotgun may reveal bacteria, composition, impacted land use management. Sanger, Next Generation Sequencing, Illumina, Ion Torrent revolutionise microbiome Oxford Nanopore Technology (ONT) Pacific Biosciences (PacBio)'s third fourth generation systems long-read technology. GeoChip, clone libraries, metabarcoding help comprehend communities. article indicates improve environmental management agriculture despite existing limitations.Metagenomics revolutionised research revealing complete diversity, anticipated continue defining future some limitations, difficulty locating appropriate method specific genes.

Language: Английский

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Lake salinization on the Qinghai–Tibetan Plateau alters viral community composition and lifestyles

Communications Earth & Environment, Journal Year: 2025, Volume and Issue: 6(1)

Published: Jan. 25, 2025

Language: Английский

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Phylogenetic Signal, Congruence, and Uncertainty across Bacteria and Archaea

Molecular Biology and Evolution, Journal Year: 2021, Volume and Issue: 38(12), P. 5514 - 5527

Published: Aug. 26, 2021

Abstract Reconstruction of the Tree Life is a central goal in biology. Although numerous novel phyla bacteria and archaea have recently been discovered, inconsistent phylogenetic relationships are routinely reported, many inter-phylum inter-domain evolutionary remain unclear. Here, we benchmark different marker genes often used constructing multidomain trees present set that perform best for constructed from concatenated alignments. We use recently-developed Certainty metrics to assess confidence our results obviate complications traditional bootstrap-based metrics. Given vastly disparate number genomes available archaea, also assessed impact taxon sampling on tree construction. Our demonstrate biases between representation taxonomic groups can dramatically topology resulting trees. Inspection highest-quality supports division most into Terrabacteria Gracilicutes, with Thermatogota Synergistota branching earlier these superphyla. This inclusion Patescibacteria within as sister group Chloroflexota instead basal-branching lineage. For Archaea, three monophyletic lineages (DPANN, Euryarchaeota, TACK/Asgard), although note basal placement DPANN may still represent an artifact caused by biased sequence composition. findings provide robust standardized framework reconstruction be evaluate uncertainty conflicting topologies Life.

Language: Английский

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Symbiosis between Candidatus Patescibacteria and Archaea Discovered in Wastewater-Treating Bioreactors

mBio, Journal Year: 2022, Volume and Issue: 13(5)

Published: Aug. 31, 2022

One highly diverse phylogenetic group of Bacteria, Ca . Patescibacteria, remains poorly understood, but, from the few cultured representatives and metagenomic investigations, they are thought to live symbiotically or parasitically with other bacteria even eukarya.

Language: Английский

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The economical lifestyle of CPR bacteria in groundwater allows little preference for environmental drivers

Environmental Microbiome, Journal Year: 2021, Volume and Issue: 16(1)

Published: Dec. 1, 2021

The highly diverse Cand. Patescibacteria are predicted to have minimal biosynthetic and metabolic pathways, which hinders understanding of how their populations differentiate in response environmental drivers or host organisms. Their mechanisms employed cope with oxidative stress largely unknown. Here, we utilized genome-resolved metagenomics investigate the adaptive genome repertoire oxic anoxic groundwaters, infer putative ranges.Within six groundwater wells, was most dominant (up 79%) super-phylum across 32 metagenomes sequenced from DNA retained on 0.2 0.1 µm filters after sequential filtration. Of reconstructed 1275 metagenome-assembled genomes (MAGs), 291 high-quality MAGs were classified as Patescibacteria. Paceibacteria Microgenomates enriched exclusively fractions, whereas candidate division ABY1 Gracilibacteria fractions. On average, smaller filter fractions had 22% genomes, 13.4% lower replication measures, higher proportion rod-shape determining proteins, genomic features suggesting type IV pili mediated cell-cell attachments. Near-surface wells harbored rates than downstream characterized by longer water residence time. Except prevalence superoxide dismutase genes groundwaters (83%), no major phylogenetic differences observed. abundant MAG encoded a nitrate transporter, nitrite reductase, F-type ATPase, an alternative energy conservation mechanism. consistently co-occurred one another members phyla Nanoarchaeota, Bacteroidota, Nitrospirota, Omnitrophota. Among fractions,, only 8% showed significant one-to-one correlation, mostly Motility transport related certain similar other (Omnitrophota, Proteobacteria Nanoarchaeota).Other stress, found little evidence for niche adaptation groundwaters. Given that could detect specific preference few MAGs, speculate majority is able attach multiple hosts just long enough loot exchange supplies.

Language: Английский

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