Rhizosphere effect alters the soil microbiome composition and C, N transformation in an arid ecosystem

Agricultural over-fertilization may adversely impact plant−microbial interactions affecting crop yield. It is unclear if soil microbiomes respond quickly to changes in fertilizer inputs once conditioned to specific nutrient regimes. We conducted a growth chamber study assessing the compositional and functional resilience of root-associated microbiomes of Medicago sativa to nutrient regime changes, and consequences for plant growth. Plants were grown with a common starting soil microbiome under four nutrient treatments: control (no fertilizer), organic phosphorus (compost added), low inorganic P (low triple superphosphate, TSP) and high inorganic P (high TSP). After several conditioning generations, in which microbiomes from rhizospheres of high biomass plants were transferred forward, microbiome composition was distinct across the four treatments. The resulting microbiomes were then transplanted into each of the nutrient treatments, leading generally to functional changes in hydrolytic enzyme activity and taxonomic convergence with other microbiomes transplanted into the same nutrient regime. However, high inorganic P-conditioned microbiomes were resistant to compositional change. Correspondingly, M. sativa grown with high inorganic P-conditioned microbiomes had lower biomass, fewer nodules, and lower %N than plants grown under the same nutrient regime with other microbiomes. These findings suggest that excessive inorganic P fertilization may change microbiomes such that they negatively affect plant growth.

Download Full-text

Rethinking Invasion Impacts across Multiple Field Sites Using European Swallowwort (Vincetoxicum rossicum) as a Model Invader

Invasive Plant Science and Management ◽

10.1017/inp.2018.22 ◽

2018 ◽

Vol 11 (3) ◽

pp. 109-116 ◽

Cited By ~ 2

Author(s):

Grant L. Thompson ◽

Terrence H. Bell ◽

Jenny Kao-Kniffin

Keyword(s):

Enzyme Activities ◽

New York State ◽

Extracellular Enzyme ◽

Growth Patterns ◽

Soil Microbiome ◽

Microbial Composition ◽

Similar Time ◽

Microbiome Composition ◽

Extracellular Enzyme Activities ◽

Vincetoxicum Rossicum

AbstractEuropean swallowwort [Vincetoxicum rossicum (Kleopow) Barbarich] is found in the northeastern United States and southeastern Canada. It forms dense growth patterns that reduce plant and insect biodiversity, and lab assays show that it produces allelopathic compounds that affect microbial activity. Consequently, we hypothesized that V. rossicum alters soil microbiome composition and activity in invaded habitats, which may impact ecosystem properties and processes. We sampled soil from a similar time point within a growing season at each of five sites in New York State where V. rossicum was both present and absent. We measured bacterial and fungal microbiome composition, available soil nitrogen (N), soil respiration (CO2 flux), and soil extracellular enzyme activities. Microbial composition varied across field sites, but only fungal composition was affected by invasion. No significant differences were found between the invaded and uninvaded plots at any of the sites for available soil ammonium, nitrate, or respiration, though extractable N varied greatly between sites. Microbial hydrolytic extracellular enzyme activities suggest decreased protein degradation and increased oxidative enzyme activity with V. rossicum invasion, which is relevant to soil N and carbon cycling processes. Although V. rossicum impacted rhizosphere microbial composition and activity, it was not associated with large perturbations in ecosystem function when examined across multiple invasion sites during this short-term study.

Download Full-text

Rhizosphere Microbiome Regulates the Growth of Mustard under Organic Greenhouse Cultivation

Agriculture ◽

10.3390/agriculture11100987 ◽

2021 ◽

Vol 11 (10) ◽

pp. 987

Author(s):

Ting-Chung Liu ◽

Hui-Mei Peng ◽

Seth Wollney ◽

Chang-Hui Shen

Keyword(s):

Soil Microbiome ◽

Physiochemical Properties ◽

Tropical Regions ◽

Microbiome Composition ◽

Vegetable Growth ◽

Rhizosphere Microbiome ◽

Organic Cultivation ◽

Greenhouse Cultivation ◽

Next Generation Sequencing Ngs ◽

The Impact

Organic cultivation can improve soil fertility and biodiversity through the preservation of soil organic matter. Meanwhile, greenhouse cultivation can provide a controlled environment and therefore enables the management of every aspect of plant growth. In recent years, the combination of organic and greenhouse cultivation has slowly become a popular option in tropical regions to prevent the unpredictable impact of weather. Although it is known that organic cultivation significantly increases the density and species of microorganisms, the impact of soil microbiome on short-term vegetable growth under organic greenhouse cultivation is still not elucidated. In this study, we examined soil physiochemical properties as well as the rhizosphere microbiome from healthy and diseased mustard plants under organic greenhouse cultivation. Through next generation sequencing (NGS) analysis, our results revealed that the rhizosphere microbiome structure of healthy mustard plants was significantly different from those of the diseased mustard plants under organic greenhouse cultivation. Our findings suggest that soil microbiome composition can influence the growth of the vegetable significantly. As such, we have shown the impact of soil microbiome on vegetable growth under organic greenhouse cultivation and provide a possible strategy for sustainable agriculture.

Download Full-text

Effects of Different Fertilizer Treatments on Rhizosphere Soil Microbiome Composition and Functions

Land ◽

10.3390/land9090329 ◽

2020 ◽

Vol 9 (9) ◽

pp. 329

Author(s):

Yanan Li ◽

Chengyu Wang ◽

Tianye Wang ◽

Yutao Liu ◽

Shuxia Jia ◽

...

Keyword(s):

Nitrate Nitrogen ◽

Organic Fertilizer ◽

Differentially Expressed Gene ◽

Fertilizer Application ◽

Chemical Fertilizer ◽

Soil Microbiome ◽

Fertilizer Treatment ◽

N Fixation ◽

Microbiome Composition

Fertilization influences the soil microbiome. However, little is known about the effects of long-term fertilization on soil microbial metabolic pathways. In this study, we investigated the soil microbiome composition and function and microbial participation in the N cycle according to the Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) functional annotation of different genes in a metagenomic analysis after long-term fertilization. Fertilizer application significantly changed the soil C/N ratio. Chemical fertilizer (NPK) treatment decreased soil pH, and chemical fertilizer combined with straw (NPK+S0.5) treatment increased ammonium nitrogen (NH4+-N) but decreased nitrate nitrogen (NO3−-N). NPK, NPK+S0.5 and S0.5 applications did not change the soil microbiome composition or dominant phylum but changed the relative abundances of microbiome components. Moreover, fertilizer significantly influenced metabolic processes, cellular processes and single-organism processes. Compared with a no-fertilizer treatment (CK), the NPK treatment resulted in more differentially expressed gene (DEG) pathways than the NPK+S0.5 and S0.5 treatments, and these pathways significantly correlated with soil nitrate nitrogen (NO3−-N), available phosphorus (AP) and the moisture content of soil (MC). KEGG analysis found that fertilizer application mainly affected the ribosome, photosynthesis and oxidative phosphorylation pathways. S0.5 and NPK+S0.5 increased microbial nitrogen fixation, and NPK and NPK+S0.5 decreased amoA and amoB and accelerated denitrification. Thus, organic fertilizer increased N fixation and nitrification, and inorganic N fertilizer accelerated denitrification. We found that the function of the soil microbiome under different fertilizer applications could be important for the rational application of fertilizer and for environmental and sustainable development.

Download Full-text

Soil hydrology drives ecological niche differentiation in a native prairie microbiome

FEMS Microbiology Ecology ◽

10.1093/femsec/fiz163 ◽

2019 ◽

Vol 96 (1) ◽

Cited By ~ 2

Author(s):

James S Griffin ◽

Loren A Haug ◽

Vivien A Rivera ◽

Liliana M Hernandez Gonzalez ◽

John J Kelly ◽

...

Keyword(s):

Hydrological Regime ◽

Niche Differentiation ◽

Soil Microbiome ◽

Sand Ridge ◽

Edaphic Factors ◽

Soil Hydrology ◽

Data Set ◽

Microbiome Composition ◽

Terrestrial Environments ◽

The Impact

ABSTRACT While the impacts of soil moisture on soil microbiome diversity and composition are well characterized, the influence of hydrological regime has been overlooked. As precipitation patterns are altered by climate change, understanding the impact of soil hydrology on community structure and function is critical. In this work, water level was continuously monitored for over a year in a Midwestern prairie-wetland at 10 cm depth increments up to a depth of 120 cm in 10 locations. We analyzed microbiome composition and edaphic factors in soil cores collected from this unique spatially distributed, longitudinal data set. We demonstrate that the fraction of time that each sample was inundated explains more variability in diversity and composition across this site than other commonly assessed edaphic factors, such as soil pH or depth. Finally, we show that these compositional changes influence abundance of ammonia oxidizers. The observed patterns in community composition and diversity are fundamentally regulated by the interaction of water with a structured landscape, particularly an elevated sand ridge characterized by drier conditions and a lower-lying wetland with more clayey soils. Similar processes are generally expected to influence the biogeography of many terrestrial environments, as morphology, hydrology and soil properties generally co-vary.

Download Full-text

Temporal turnover of the soil microbiome composition is guild‐specific

Ecology Letters ◽

10.1111/ele.13896 ◽

2021 ◽

Author(s):

Tijana Martinović ◽

Iñaki Odriozola ◽

Tereza Mašínová ◽

Barbara Doreen Bahnmann ◽

Petr Kohout ◽

...

Keyword(s):

Soil Microbiome ◽

Microbiome Composition ◽

Temporal Turnover

Download Full-text

Pasture Management Intensification Shifts the Soil Microbiome Composition and Ecosystem Functions

SSRN Electronic Journal ◽

10.2139/ssrn.3973503 ◽

2021 ◽

Author(s):

Daniela Tomazelli ◽

Osmar Klauberg-Filho ◽

Sandra Denise Camargo Mendes ◽

Tiago Celso Baldissera ◽

Fábio Cervo Garagorry ◽

...

Keyword(s):

Soil Microbiome ◽

Ecosystem Functions ◽

Pasture Management ◽

Microbiome Composition

Download Full-text

Initial soil microbiome composition and functioning predetermine future plant health

Science Advances ◽

10.1126/sciadv.aaw0759 ◽

2019 ◽

Vol 5 (9) ◽

pp. eaaw0759 ◽

Cited By ~ 29

Author(s):

Zhong Wei ◽

Yian Gu ◽

Ville-Petri Friman ◽

George A. Kowalchuk ◽

Yangchun Xu ◽

...

Keyword(s):

Plant Pathogen ◽

Plant Protection ◽

Soil Microbiome ◽

Antimicrobial Compounds ◽

Disease Dynamics ◽

Microbiome Composition ◽

Disease Outcomes ◽

Initial Soil ◽

Genes Encoding ◽

Plant Pathogen Interactions

Plant-pathogen interactions are shaped by multiple environmental factors, making it difficult to predict disease dynamics even in relatively simple agricultural monocultures. Here, we explored how variation in the initial soil microbiome predicts future disease outcomes at the level of individual plants. We found that the composition and functioning of the initial soil microbiome predetermined whether the plants survived or succumbed to disease. Surviving plant microbiomes were associated with specific rare taxa, highly pathogen-suppressing Pseudomonas and Bacillus bacteria, and high abundance of genes encoding antimicrobial compounds. Microbiome-mediated plant protection could subsequently be transferred to the next plant generation via soil transplantation. Together, our results suggest that small initial variation in soil microbiome composition and functioning can determine the outcomes of plant-pathogen interactions under natural field conditions.

Download Full-text

Bacterial compatibility and immobilization with biochar improved tebuconazole degradation, soil microbiome composition and functioning

Journal of Hazardous Materials ◽

10.1016/j.jhazmat.2020.122941 ◽

2020 ◽

Vol 398 ◽

pp. 122941 ◽

Cited By ~ 5

Author(s):

Tong Sun ◽

Jingbo Miao ◽

Muhammad Saleem ◽

Haonan Zhang ◽

Yong Yang ◽

...

Keyword(s):

Soil Microbiome ◽

Microbiome Composition

Download Full-text

Soil microbiome of the postmining areas in polar ecosystems in surroundings of Nadym, Western Siberia, Russia

Open Agriculture ◽

10.1515/opag-2019-0070 ◽

2019 ◽

Vol 4 (1) ◽

pp. 684-696

Author(s):

Grigory Gladkov ◽

Anastasiia Kimeklis ◽

Alexei Zverev ◽

Elizaveta Pershina ◽

Ekaterina Ivanova ◽

...

Keyword(s):

16S Rrna ◽

Driving Force ◽

Western Siberia ◽

Microbial Mats ◽

Plant Cover ◽

Soil Microbiome ◽

Microbiome Composition ◽

Bacterial Phyla ◽

Arctic Soils ◽

Disturbed Soils

AbstractLocalization of agriculture with the aim of local food support has become a very urgent topic for Yamal region. The most fertile soils of this region are sandy textured anthropogenically affected soils. Microbiomes from disturbed soils of the Nadym region were studied using analysis of 16S rRNA metagenomic libraries. It was shown that plant cover is a driving force of microbiome composition. Forest soils covered with aeolian transfers from the quarry retaids a typical forest microbiome with the following dominant bacterial phyla: Proteobateria, Acidobacteria, Verrucomicrobia, Planctomycetes and Bacteroidetes. However, it contains significantly less Planctomycetes, which indicates greater aridity of the soil. The microbiomes of the overgrown quarries were strikingly differ from the soil microbiome and resemble those of arctic soils being dominated by Proteobacteria, Chloroflexi, Acidobacteria and Cyanobacteria. Absence of dense vegetation cover and availability of nutrients facilitated the formation of autotrophic microbial mats. The microbiome of the lower horizons of the quarry is characterised by Proteobacteria, Actinobacteria and Firmicutes. Presumably, most of the time these bacteria reside in a dormant state with short periods of activity due to nutrient uptake from the upper horizons.

Download Full-text