A communal catalogue reveals Earth’s multiscale microbial diversity

Nature, Journal Year: 2017, Volume and Issue: 551(7681), P. 457 - 463

Published: Oct. 31, 2017

Abstract Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding its fundamental structure. Despite recent advances in DNA sequencing, a lack standardized protocols common analytical frameworks impedes comparisons among studies, hindering development global inferences about life on Earth. Here we present meta-analysis community samples collected by hundreds researchers for Earth Microbiome Project. Coordinated new methods, particularly use exact sequences instead clustered operational taxonomic units, enable bacterial archaeal ribosomal RNA gene to be followed across multiple studies allow us explore patterns at an unprecedented scale. The result is both reference database giving context sequence data framework incorporating from future fostering increasingly complete characterization Earth’s diversity.

Language: Английский

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Understanding the holobiont: the interdependence of plants and their microbiome

Current Opinion in Microbiology, Journal Year: 2017, Volume and Issue: 38, P. 188 - 196

Published: July 19, 2017

Language: Английский

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Fertilization Shapes Bacterial Community Structure by Alteration of Soil pH

Frontiers in Microbiology, Journal Year: 2017, Volume and Issue: 8

Published: July 18, 2017

Application of chemical fertilizer or manure can affect soil microorganisms directly by supplying nutrients and indirectly altering pH. However, it remains uncertain which effect mostly shapes microbial community structure. We determined bacterial diversity structure 454 pyrosequencing the V1-V3 regions 16S rRNA genes after 7-years (2007-2014) applying nitrogen, phosphorus potassium (NPK) fertilizers, composted their combination to acidic (pH 5.8), near-neutral 6.8) alkaline 8.4) Eutric Regosol in a maize-vegetable rotation southwest China. In soil, nutrient sources did not Operational Taxonomic Unit (OTU) richness Shannon index, despite higher available N, P, K, organic carbon fertilized than unfertilized soil. contrast, OTU index were significantly lower soils under NPK combination, corresponded with changes Permutational multivariate analysis variance showed that was affected across these three soils, but PCoA ordination patterns indicated less distinct among near-neural soils. Distance-based redundancy structures altered pH any properties The relative abundance (%) most phyla dominant Proteobacteria (24.6%), Actinobacteria (19.7%), Chloroflexi (15.3%) Acidobacteria (12.6%); medium Bacterioidetes (5.3%), Planctomycetes (4.8%), Gemmatimonadetes (4.5%), Firmicutes (3.4%), Cyanobacteria (2.1%), Nitrospirae (1.8%), candidate division TM7 (1.0%); least abundant Verrucomicrobia (0.7%), Armatimonadetes (0.6%), WS3 (0.4%) Fibrobacteres (0.3%). addition, more whereas Gemmatimonadetes, conclude fertilization, shaped rather direct addition.

Language: Английский

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Ammonium nitrogen content is a dominant predictor of bacterial community composition in an acidic forest soil with exogenous nitrogen enrichment

The Science of The Total Environment, Journal Year: 2017, Volume and Issue: 624, P. 407 - 415

Published: Dec. 17, 2017

Language: Английский

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Responses of the rhizosphere bacterial community in acidic crop soil to pH: Changes in diversity, composition, interaction, and function

The Science of The Total Environment, Journal Year: 2019, Volume and Issue: 700, P. 134418 - 134418

Published: Sept. 12, 2019

Language: Английский

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Altered activities of extracellular soil enzymes by the interacting global environmental changes

Global Change Biology, Journal Year: 2023, Volume and Issue: 29(8), P. 2067 - 2091

Published: Jan. 19, 2023

Abstract Soil enzymes are crucial in mediating ecosystems' responses to environmental drivers, so that the comprehension of their sensitivity drivers global change can help make predictions future scenarios and design tailored interventions biomanipulation. Drivers usually act combination two or more, indirect effects one driver acting through modification another often occur, yet most both manipulative meta‐analysis studies available tend focus on direct effect single activity specific soil enzymes. One biggest challenges is, therefore, represented by difficulty assessing interactions between different due complexity disentangling from combined ones. In this review, after elucidating general mechanisms enzyme production regulation, we display state‐of‐the‐art knowledge direct, main activities, identify gaps research, plus analyse how reverberate biomanipulation techniques for improvement ecosystem services. We conclude qualitative but not quantitative outcomes be predicted some such as warming + drought CO 2 , while other ones, results controversial: basic research will have center holistic approach. A trend toward overall increase activities acceleration biogeochemical cycles persist, until an inflection caused factors shifts microbial communities changes carbon use efficiency. Applied develop refinement “in situ” analytical systems study support bioengineering better tailoring

Language: Английский

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Rhizosphere Microorganisms Supply Availability of Soil Nutrients and Induce Plant Defense

Microorganisms, Journal Year: 2024, Volume and Issue: 12(3), P. 558 - 558

Published: March 11, 2024

Plant health is necessary for food security, which a key determinant of secure and sustainable production systems. Deficiency soil nutrients invasion plant pathogens or insects are the main destroyers world’s production. Synthetic fertilizers chemical-based pesticides frequently employed to combat problems. However, these have negative impacts on microbial ecosystems ecosystem functioning. Rhizosphere microorganisms demonstrated their potency improve manage encourage growth, resulting in increased yield quality by converting organic inorganic substances around rhizosphere zone into available nutrients. Besides regulating nutrient availability growth enhancement, rhizobacteria fungi can restrict that cause disease secreting inhibitory chemicals boosting immunity pests pathogens. Thus, viewed as viable, alluring economic approaches agriculture biofertilizers biopesticides. This review provides an overview role inducing defenses. Moreover, discussion presented surrounding recent consequences employing strategy towards improving fertilization effectiveness, encouraging stronger, more pest-resistant plants.

Language: Английский

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Do Added Microplastics, Native Soil Properties, and Prevailing Climatic Conditions Have Consequences for Carbon and Nitrogen Contents in Soil? A Global Data Synthesis of Pot and Greenhouse Studies

Environmental Science & Technology, Journal Year: 2024, Volume and Issue: 58(19), P. 8464 - 8479

Published: May 3, 2024

Microplastics threaten soil ecosystems, strongly influencing carbon (C) and nitrogen (N) contents. Interactions between microplastic properties climatic edaphic factors are poorly understood. We conducted a meta-analysis to assess the interactive effects of (type, shape, size, content), native (texture, pH, dissolved organic (DOC)) (precipitation temperature) on C N contents in soil. found that low-density polyethylene reduced total (TN) content, whereas biodegradable polylactic acid led decrease (SOC). Microplastic fragments especially depleted TN, reducing aggregate stability, increasing N-mineralization leaching, consequently C/N ratio. size affected outcomes; those <200 μm both TN SOC Mineralization-induced nutrient losses were greatest at 1 2.5% weight. Sandy soils suffered highest contamination-induced depletion. Alkaline showed depletion, suggesting high degradability. In low-DOC soils, contamination caused 2-fold greater depletion than with DOC. Sites precipitation temperature had conclusion, there complex interactions determining impacts health. always risks but severity depends characteristics, properties, conditions, potential exacerbation by greenhouse emission-induced climate change.

Language: Английский

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The pH optimum of soil exoenzymes adapt to long term changes in soil pH

Soil Biology and Biochemistry, Journal Year: 2019, Volume and Issue: 138, P. 107601 - 107601

Published: Sept. 16, 2019

Language: Английский

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Co‐occurrence of antibiotic, biocide, and heavy metal resistance genes in bacteria from metal and radionuclide contaminated soils at the Savannah River Site

Microbial Biotechnology, Journal Year: 2020, Volume and Issue: 13(4), P. 1179 - 1200

Published: May 3, 2020

Summary Contaminants such as heavy metals may contribute to the dissemination of antimicrobial resistance (AMR) by enriching gene determinants via co‐selection mechanisms. In present study, a survey was performed on soils collected from four areas at Savannah River Site (SRS), South Carolina, USA, with varying contaminant profiles: relatively pristine (Upper Three Runs), (Ash Basins), radionuclides (Pond B) and metal (Tim’s Branch). Using 16S rRNA amplicon sequencing, we explored structure diversity soil bacterial communities. Sites legacies and/or radionuclide contamination displayed significantly lower compared reference site. Metagenomic analysis indicated that multidrug vancomycin antibiotic genes (ARGs) (MRGs) including those associated copper, arsenic, iron, nickel zinc were prominent in all However, significant differences found relative abundance certain ARGs MRGs metal/radionuclide contaminated Co‐occurrence patterns revealed ARG/MRG subtypes predominant taxa Acidobacteriaceae , Bradyrhizobium Mycobacterium Streptomyces Verrumicrobium Actinomadura Solirubacterales. Overall, study emphasizes potential risk human activities AMR environment.

Language: Английский

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