The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms

FEMS Microbiology Reviews, Год журнала: 2013, Номер 37(5), С. 634 - 663

Опубликована: Июнь 24, 2013

Microbial communities play a pivotal role in the functioning of plants by influencing their physiology and development. While many members rhizosphere microbiome are beneficial to plant growth, also pathogenic microorganisms colonize striving break through protective microbial shield overcome innate defense mechanisms order cause disease. A third group that can be found true opportunistic human bacteria, which carried on or tissue may disease when introduced into debilitated humans. Although importance for growth has been widely recognized, vast majority no knowledge exists. To enhance health, it is essential know microorganism present what they doing. Here, we review main functions how impact health We discuss involved multitrophic interactions chemical dialogues occur rhizosphere. Finally, highlight several strategies redirect reshape favor health.

Язык: Английский

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Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe

Proceedings of the National Academy of Sciences, Год журнала: 2015, Номер 112(35), С. 10967 - 10972

Опубликована: Авг. 17, 2015

Significance Human activities have resulted in large increases the availability of nutrients terrestrial ecosystems worldwide. Although plant community responses to elevated been well studied, soil microbial remain poorly understood, despite their critical importance ecosystem functioning. Using DNA-sequencing approaches, we assessed response communities experimentally added nitrogen and phosphorus at 25 grassland sites across globe. Our results demonstrate that composition these shifts consistent ways with nutrient inputs there are corresponding ecological attributes members. This study represents an important step forward for understanding connection between inputs, communities, altered

Язык: Английский

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Archaeal and bacterial ammonia-oxidisers in soil: the quest for niche specialisation and differentiation

Trends in Microbiology, Год журнала: 2012, Номер 20(11), С. 523 - 531

Опубликована: Сен. 7, 2012

Язык: Английский

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Microbiomes in light of traits: A phylogenetic perspective

Science, Год журнала: 2015, Номер 350(6261)

Опубликована: Ноя. 5, 2015

A focus on the phenotypic characteristics of microorganisms-their traits-offers a path for interpreting growing amount microbiome data. We review key aspects microbial traits, as well approaches used to assay their phylogenetic distribution. Recent studies reveal that traits are differentially conserved across tree life and appear be in hierarchical fashion, possibly linked biochemical complexity. These results suggest predictive framework whereby genetic (or taxonomic) resolution variation among samples provides information about under selection. The organizational parallels seen human free-living microbiomes seem support this idea. Developments may offer predictions not only how composition responds changing environmental conditions, but also these changes alter health or functioning human, engineered, systems.

Язык: Английский

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Microbial functional genes involved in nitrogen fixation, nitrification and denitrification in forest ecosystems

Soil Biology and Biochemistry, Год журнала: 2014, Номер 75, С. 11 - 25

Опубликована: Апрель 13, 2014

Язык: Английский

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Diversity, Physiology, and Niche Differentiation of Ammonia-Oxidizing Archaea

Applied and Environmental Microbiology, Год журнала: 2012, Номер 78(21), С. 7501 - 7510

Опубликована: Авг. 25, 2012

Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, has been suggested have a central part global biogeochemical nitrogen cycle since oxygenation Earth. The cultivation several ammonia-oxidizing archaea (AOA) as well discovery that archaeal monooxygenase (amo)-like gene sequences are nearly ubiquitously distributed in environment and outnumber their bacterial counterparts many habitats fundamentally revised our understanding nitrification. Surprising insights into physiological distinctiveness AOA mirrored by recognition phylogenetic uniqueness these microbes, which fall within novel phylum now known Thaumarchaeota. relative importance nitrification, compared bacteria (AOB), is still under debate. This minireview provides synopsis current knowledge diversity physiology AOA, factors controlling ecology, role carbon cycling potential involvement production greenhouse gas nitrous oxide. It emphasizes activity-based analyses studies formulates priorities for future research.

Язык: Английский

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Global biogeography of microbial nitrogen-cycling traits in soil

Proceedings of the National Academy of Sciences, Год журнала: 2016, Номер 113(29), С. 8033 - 8040

Опубликована: Июль 18, 2016

Microorganisms drive much of the Earth’s nitrogen (N) cycle, but we still lack a global overview abundance and composition microorganisms carrying out soil N processes. To address this gap, characterized biogeography microbial traits, defined as eight N-cycling pathways, using publically available metagenomes. The relative frequency pathways varied consistently across soils, such that frequencies individual were positively correlated samples. Habitat type, carbon, largely explained total pathway in sample. In contrast, could not identify major drivers taxonomic functional groups. Further, dominant genera encoding generally similar among habitat types. samples also revealed an unexpectedly high bacteria required for dissimilatory nitrate reduction to ammonium, little-studied process soil. Finally, phylogenetic analysis showed some groups seem be specialists or generalists. For instance, taxa within Deltaproteobacteria encoded all whereas those Cyanobacteria primarily three pathways. Overall, trait-based approach provides baseline investigating relationship between diversity cycling soils.

Язык: Английский

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Nitrification and nitrifiers in acidic soils

Soil Biology and Biochemistry, Год журнала: 2017, Номер 116, С. 290 - 301

Опубликована: Ноя. 5, 2017

Язык: Английский

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High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats

mBio, Год журнала: 2015, Номер 6(1)

Опубликована: Янв. 27, 2015

Understanding the structure, functions, activities and dynamics of microbial communities in natural environments is one grand challenges 21st century science. To address this challenge, over past decade, numerous technologies have been developed for interrogating communities, which some are amenable to exploratory work (e.g., high-throughput sequencing phenotypic screening) others depend on reference genes or genomes phylogenetic functional gene arrays). Here, we provide a critical review synthesis most commonly applied "open-format" "closed-format" detection technologies. We discuss their characteristics, advantages, disadvantages within context environmental applications focus analysis complex systems, such as those soils, diversity high few. In addition, crucial issues considerations associated with applying complementary molecular important ecological questions.

Язык: Английский

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The global-scale distributions of soil protists and their contributions to belowground systems

Science Advances, Год журнала: 2020, Номер 6(4)

Опубликована: Янв. 24, 2020

Protists are ubiquitous in soil, where they key contributors to nutrient cycling and energy transfer. However, protists have received far less attention than other components of the soil microbiome. We used amplicon sequencing soils from 180 locations across six continents investigate ecological preferences their functional contributions belowground systems. complemented these analyses with shotgun metagenomic 46 validate identities more abundant protist lineages. found that most dominated by consumers, although parasites phototrophs particularly tropical arid ecosystems, respectively. The best predictors composition (primarily annual precipitation) fundamentally distinct those shaping bacterial archaeal communities (namely, pH). Some bacteria co-occur globally, highlighting potential importance largely undescribed interactions. Together, this study allowed us identify living our work providing a cross-ecosystem perspective on factors structuring likely functioning.

Язык: Английский

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