The soil pH and heavy metals revealed their impact on soil microbial community

Journal of Environmental Management, Journal Year: 2022, Volume and Issue: 321, P. 115770 - 115770

Published: Aug. 30, 2022

Language: Английский

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Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples

Environmental Science & Technology, Journal Year: 2023, Volume and Issue: 57(26), P. 9713 - 9721

Published: June 13, 2023

Surveillance of antibiotic resistance genes (ARGs) has been increasingly conducted in environmental sectors to complement the surveys human and animal under "One-Health" framework. However, there are substantial challenges comparing synthesizing results multiple studies that employ different test methods approaches bioinformatic analysis. In this article, we consider commonly used quantification units (ARG copy per cell, ARG genome, density, 16S rRNA gene, RPKM, coverage, PPM, etc.) for profiling ARGs suggest a universal unit cell) reporting such biological measurements samples improving comparability surveillance efforts.

Language: Английский

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Ecological insights into soil health according to the genomic traits and environment-wide associations of bacteria in agricultural soils

ISME Communications, Journal Year: 2023, Volume and Issue: 3(1)

Published: Jan. 9, 2023

Soil microbiomes are sensitive to current and previous soil conditions, bacterial 'bioindicators' of biological, physical, chemical properties have considerable potential for health assessment. However, the lack ecological or physiological information most microorganisms limits our ability interpret associations bioindicators and, thus, their utility guiding management. We identified tillage intensity twelve used rate using a 16S rRNA gene-based survey farmland across North America. then inferred genomic traits evaluated environment-wide (EWAS) with respect agricultural management practice, disturbance, plant 89 studies from agroecosystems. Most were either positively correlated biological (e.g., organic matter) negatively physical properties. Higher ratings corresponded smaller genome size higher coding density, while lower larger genomes rrn copy number. Community-weighted explained variation in ratings. EWAS linked prominent impacts environmental disturbances. Our findings provide insights into relevant management, illustrating tight coupling microbiome function.

Language: Английский

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Flexible and cost-effective genomic surveillance of P. falciparum malaria with targeted nanopore sequencing

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Feb. 15, 2024

Abstract Genomic surveillance of Plasmodium falciparum malaria can provide policy-relevant information about antimalarial drug resistance, diagnostic test failure, and the evolution vaccine targets. Yet large low complexity genome P. complicates development genomic methods, while resource constraints in endemic regions limit their deployment. Here, we demonstrate an approach for targeted nanopore sequencing from dried blood spots (DBS) that enables cost-effective low-resource settings. We release software facilitates flexible design amplicon panels use this to two target . The generate 3–4 kbp reads eight sixteen targets respectively, covering key drug-resistance associated genes, antigens, polymorphic markers csp validate our on mock field samples, demonstrating robust coverage, accurate variant calls within coding sequences, ability explore within-sample diversity detect deletions underlying rapid failure.

Language: Английский

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Megasphaera elsdenii: Its Role in Ruminant Nutrition and Its Potential Industrial Application for Organic Acid Biosynthesis

Microorganisms, Journal Year: 2024, Volume and Issue: 12(1), P. 219 - 219

Published: Jan. 21, 2024

The Gram-negative, strictly anaerobic bacterium Megasphaera elsdenii was first isolated from the rumen in 1953 and is common mammalian gastrointestinal tract. Its ability to use either lactate or glucose as its major energy sources for growth has been well documented, although it can also ferment amino acids into ammonia branched-chain fatty acids, which are factors other bacteria. ruminal abundance of M. usually increases animals fed grain-based diets due (the product rapid sugar fermentation), especially at a low pH (<5.5). proposed potential dietary probiotic prevent acidosis feedlot cattle high-producing dairy cows. However, this associated with milk fat depression (MFD) cows, proving causative role remained elusive. This review summarizes unique physiology intriguing functional community health productivity host animal. In addition effects rumen, produce C2–C7 carboxylic acids—potential precursors industrial fuel chemical production—is examined.

Language: Английский

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Unveiling novel features and phylogenomic assessment of indigenous Priestia megaterium AB-S79 using comparative genomics

Microbiology Spectrum, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 19, 2025

ABSTRACT Priestia megaterium strain AB-S79 isolated from active gold mine soil previously expressed in vitro heavy metal resistance and has a 5.7 Mb genome useful for biotechnological exploitation. This study used web-based bioinformatic resources to analyze P. genomic relatedness, decipher its secondary metabolite biosynthetic gene clusters (BGCs), better comprehend taxa. Genes were highly conserved across the 14 P . genomes examined here. The pangenome reflected total of 61,397 protein-coding genes, 59,745 homolog protein family hits, 1,652 singleton hits. There also 7,735 families, including 1,653 families 6,082 families. OrthoVenn3 comparison sequences with 13 other strains, 7 spp., 6 Bacillus spp. highlighted AB-S79’s unique evolutionary trait. antiSMASH identified two key transcription factor binding site regulators genome: zinc-responsive repressor (Zur) antibiotic production activator (AbrC3), plus putative enzymes biosynthesis terpenes ranthipeptides. harbors BGCs siderophores (synechobactins schizokinens), phosphonate, dienelactone hydrolase protein, phenazine (phzF), which is significant this study. Phosphonate particularly showed specificity sp. validating effect expansion contraction. looks be viable source value-added compounds. Thus, contributes theoretical framework systematic metabolic genetic exploitation sp., value-yielding strains. IMPORTANCE explores microbial natural product discovery using mining, focusing on Key findings highlight potential , AB-S79, applications. research shows limited output Africa, emphasizing importance native AB-S79. Additionally, underlines strain’s diverse capabilities, reinforcing suitability as model cell factories foundational role future

Language: Английский

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Taxonomic and environmental distribution of bacterial amino acid auxotrophies

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Nov. 22, 2023

Many microorganisms are auxotrophic-unable to synthesize the compounds they require for growth. With this work, we quantify prevalence of amino acid auxotrophies across a broad diversity bacteria and habitats. We predicted biosynthetic capabilities 26,277 unique bacterial genomes spanning 12 phyla using metabolic pathway model validated with empirical data. Amino auxotrophy is widespread phyla, but conservatively estimate that majority taxa (78.4%) able all acids. Our estimates indicate more prevalent among obligate intracellular parasites in free-living genomic attributes characteristic 'streamlined' life history strategies. communities found habitats investigate environmental associations auxotrophy, data compiled from 3813 samples major aquatic, terrestrial, engineered environments. Auxotrophic were abundant host-associated environments (including human oral cavity gut) fermented food products, auxotrophic being relatively rare soil aquatic systems. Overall, work contributes complete understanding tree ecological contexts which can be successful strategy.

Language: Английский

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Genomic Legacies of Ancient Adaptation Illuminate GC-Content Evolution in Bacteria

Microbiology Spectrum, Journal Year: 2022, Volume and Issue: 11(1)

Published: Dec. 13, 2022

GC content has been shown to be an important factor in microbial ecology and evolution, the genomic of bacteria can characterized by great intergenomic heterogeneity, high intragenomic homogeneity, strong phylogenetic inertia, as well being associated with environment. Current hypotheses concerning direct selection or mutational biases cannot explain these features simultaneously.

Language: Английский

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Edaphic controls on genome size and GC content of bacteria in soil microbial communities

Soil Biology and Biochemistry, Journal Year: 2022, Volume and Issue: 178, P. 108935 - 108935

Published: Dec. 26, 2022

Language: Английский

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Warmer and drier ecosystems select for smaller bacterial genomes in global soils

iMeta, Journal Year: 2023, Volume and Issue: 2(1)

Published: Jan. 3, 2023

Abstract Bacterial genome size reflects bacterial evolutionary processes and metabolic lifestyles, with implications for microbial community assembly ecosystem functions. However, to understand the extent of genome‐mediated responses environmental selections, we require studies that observe distributions along gradients representing different conditions soil bacteria normally encounter. In this study, used surface soils collected from 237 sites across globe analyzed how (e.g., carbon nutrients, aridity, pH, temperature) affect occurrences at level using profiling. We a joint species distribution model quantify effects environments on found aridity was major regulator warmer drier selecting smaller genomes. Drought‐induced physiological constraints growth water scarcity cell metabolisms) may have led these correlations. This finding suggests increasing cover by ecosystems result in simplifications reduction size.

Language: Английский

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