Embracing the unknown: disentangling the complexities of the soil microbiome

Nature Reviews Microbiology, Год журнала: 2017, Номер 15(10), С. 579 - 590

Опубликована: Авг. 21, 2017

Язык: Английский

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Development of a Prokaryotic Universal Primer for Simultaneous Analysis of Bacteria and Archaea Using Next-Generation Sequencing

PLoS ONE, Год журнала: 2014, Номер 9(8), С. e105592 - e105592

Опубликована: Авг. 21, 2014

For the analysis of microbial community structure based on 16S rDNA sequence diversity, sensitive and robust PCR amplification is a critical step. To obtain accurate composition data, must be free bias; however, amplifying all species with equal efficiency from sample containing large variety microorganisms remains challenging. Here, we designed universal primer V3-V4 hypervariable region prokaryotic for simultaneous detection Bacteria Archaea in fecal samples crossbred pigs (Landrace × Large white Duroc) using an Illumina MiSeq next-generation sequencer. In-silico showed that newly primers matched approximately 98.0% 94.6% rRNA gene sequences Ribosomal Database Project database. each sequencing reaction performed primer, average 69,330 (± 20,482) reads were obtained, which archaeal genes comprised 1.2% to 3.2% reads. In addition, frequency belonging phylum Verrucomicrobia, including members classes Verrucomicrobiae Opitutae, was higher NGS than bacterial primer. Importantly, this new set had markedly lower bias most previously primers. Our findings demonstrate present study will permit Archaea, therefore allow more comprehensive understanding structures environmental samples.

Язык: Английский

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Mineral protection of soil carbon counteracted by root exudates

Nature Climate Change, Год журнала: 2015, Номер 5(6), С. 588 - 595

Опубликована: Март 27, 2015

Язык: Английский

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Nitrogen fertilization directly affects soil bacterial diversity and indirectly affects bacterial community composition

Soil Biology and Biochemistry, Год журнала: 2015, Номер 92, С. 41 - 49

Опубликована: Окт. 22, 2015

Язык: Английский

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Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change

Microbiology and Molecular Biology Reviews, Год журнала: 2017, Номер 81(2)

Опубликована: Апрель 12, 2017

The ecology of forest soils is an important field research due to the role forests as carbon sinks. Consequently, a significant amount information has been accumulated concerning their ecology, especially for temperate and boreal forests. Although most studies have focused on fungi, soil bacteria also play roles in this environment. In soils, inhabit multiple habitats with specific properties, including bulk soil, rhizosphere, litter, deadwood habitats, where communities are shaped by nutrient availability biotic interactions. Bacteria contribute range essential processes involved cycling carbon, nitrogen, phosphorus. They take part decomposition dead plant biomass highly fungal mycelia. rhizospheres trees, interact roots mycorrhizal fungi commensalists or mycorrhiza helpers. mediate critical steps nitrogen cycle, N fixation. Bacterial respond effects global change, such climate warming, increased levels dioxide, anthropogenic deposition. This response, however, often reflects specificities each studied ecosystem, it still impossible fully incorporate into predictive models. understanding bacterial advanced dramatically recent years, but incomplete. exact extent contribution ecosystem will be recognized only future, when activities all community members simultaneously.

Язык: Английский

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Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems

Microbiome, Год журнала: 2018, Номер 6(1)

Опубликована: Авг. 21, 2018

Soil microbiomes play an important role in the services and functioning of terrestrial ecosystems. However, little is known their vertical responses to restoration process contributions soil nutrient cycling subsurface profiles. Here, we investigated community assembly bacteria, archaea, fungi along (i.e., depths 0–300 cm) horizontal distance from trees 30–90 profiles a chronosequence reforestation sites that represent over 30 years restoration. In superficial layers (0–80 cm), bacterial fungal diversity decreased, whereas archaeal increased with increasing depth. As proceeded time, spatial variation communities while increased. Vertical distributions were more related properties, may be driven by gradient effect roots extending tree. Bacterial beta-diversity strongly multi-nutrient soil, respectively, playing major roles deep layers. Taken together, these results reveal new perspective on at fine scale single trees. Distinct response patterns underpinned as function during ex-arable land.

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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Changes in extracellular enzyme activity and microbial community structure with soil depth at the Luquillo Critical Zone Observatory

Soil Biology and Biochemistry, Год журнала: 2014, Номер 75, С. 237 - 247

Опубликована: Май 5, 2014

Язык: Английский

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How to study deep roots—and why it matters

Frontiers in Plant Science, Год журнала: 2013, Номер 4

Опубликована: Янв. 1, 2013

The drivers underlying the development of deep root systems, whether genetic or environmental, are poorly understood but evidence has accumulated that rooting could be a more widespread and important trait among plants than commonly anticipated from their share biomass. Even though distinct classification "deep roots" is missing to date, roots provide functions for individual such as nutrient water uptake can also shape plant communities by hydraulic lift. Subterranean fauna microbial highly influenced resources provided in rhizosphere influence soil paedogenesis carbon storage. Despite recent technological advances, study remains inherently time-consuming, technically demanding costly, which explains why yet given attention they deserve. While state-of-the-art technologies promising laboratory studies involving relatively small volumes, remain limited use situ observation roots. Thus, basic techniques destructive sampling observations at transparent interfaces with (e.g., windows) have been known used decades observe near surface, must adapted specific requirements observation. In this review, we successively address major physical, biogeochemical ecological emphasise significance illustrate knowledge. second part describe main methodological options measure roots, providing researchers interested field root/rhizosphere comprehensive overview. Addressed methodologies excavations, trenches coring approaches, minirhizotrons, access shafts, caves mines, indirect approaches tracer-based techniques.

Язык: Английский

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Convergence of gut microbiomes in myrmecophagous mammals

Molecular Ecology, Год журнала: 2013, Номер 23(6), С. 1301 - 1317

Опубликована: Авг. 29, 2013

Mammals have diversified into many dietary niches. Specialized myrmecophagous (ant- and termite-eating) placental mammals represent a textbook example of evolutionary convergence driven by extreme diet specialization. Armadillos, anteaters, aardvarks, pangolins aardwolves thus provide model system for understanding the potential role gut microbiota in convergent adaptation to myrmecophagy. Here, we expand upon previous mammalian microbiome studies using high-throughput barcoded Illumina sequencing 16S rRNA gene characterize composition 15 species representing all lineages their close relatives from zoo- field-collected samples. We confirm that both phylogeny drive evolution microbiota, with cases global composition, but also examples phylogenetic inertia. Our results reveal specialized myrmecophages as spectacular case large-scale composition. Indeed, neighbour-net networks beta-diversity plots based on UniFrac distances show significant clustering (anteaters, aardvarks aardwolves), even though they belong phylogenetically distant different orders. The aardwolf, which diverged carnivorous hyenas only last 10 million years, experienced shift its become more similar other myrmecophages. These be major driving factor over timescales. This study sets scene future metagenomic aiming at evaluating functional content microbiomes

Язык: Английский

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