scholarly journals Interactions between plants and soil shaping the root microbiome under abiotic stress

2019 ◽  
Vol 476 (19) ◽  
pp. 2705-2724 ◽  
Author(s):  
Kyle Hartman ◽  
Susannah G. Tringe
Keyword(s):  
Abiotic Stress ◽  
Microbial Communities ◽  
Abiotic Stress Tolerance ◽  
Soil Microbial Communities ◽  
Terrestrial Ecosystems ◽  
Stress Conditions ◽  
Bulk Soil ◽  
Future Research ◽  
Soil Microbial ◽  
Root Microbiome

Abstract Plants growing in soil develop close associations with soil microorganisms, which inhabit the areas around, on, and inside their roots. These microbial communities and their associated genes — collectively termed the root microbiome — are diverse and have been shown to play an important role in conferring abiotic stress tolerance to their plant hosts. In light of growing concerns over the threat of water and nutrient stress facing terrestrial ecosystems, especially those used for agricultural production, increased emphasis has been placed on understanding how abiotic stress conditions influence the composition and functioning of the root microbiome and the ultimate consequences for plant health. However, the composition of the root microbiome under abiotic stress conditions will not only reflect shifts in the greater bulk soil microbial community from which plants recruit their root microbiome but also plant responses to abiotic stress, which include changes in root exudate profiles and morphology. Exploring the relative contributions of these direct and plant-mediated effects on the root microbiome has been the focus of many studies in recent years. Here, we review the impacts of abiotic stress affecting terrestrial ecosystems, specifically flooding, drought, and changes in nitrogen and phosphorus availability, on bulk soil microbial communities and plants that interact to ultimately shape the root microbiome. We conclude with a perspective outlining possible directions for future research needed to advance our understanding of the complex molecular and biochemical interactions between soil, plants, and microbes that ultimately determine the composition of the root microbiome under abiotic stress.

Alkaline soil pH affects bulk soil, rhizosphere and root endosphere microbiomes of plants growing in a Sandhills ecosystem

2021 ◽  
Vol 97 (4) ◽  
Author(s):  
Lucas Dantas Lopes ◽  
Jingjie Hao ◽  
Daniel P Schachtman
Keyword(s):  
Microbial Communities ◽  
Plant Species ◽  
Soil Ph ◽  
Soil Microbial Communities ◽  
Bulk Soil ◽  
Strong Impact ◽  
Alkaline Soil ◽  
Alkaline Soils ◽  
Soil Microbial ◽  
Soil Rhizosphere

ABSTRACT Soil pH is a major factor shaping bulk soil microbial communities. However, it is unclear whether the belowground microbial habitats shaped by plants (e.g. rhizosphere and root endosphere) are also affected by soil pH. We investigated this question by comparing the microbial communities associated with plants growing in neutral and strongly alkaline soils in the Sandhills, which is the largest sand dune complex in the northern hemisphere. Bulk soil, rhizosphere and root endosphere DNA were extracted from multiple plant species and analyzed using 16S rRNA amplicon sequencing. Results showed that rhizosphere, root endosphere and bulk soil microbiomes were different in the contrasting soil pH ranges. The strongest impact of plant species on the belowground microbiomes was in alkaline soils, suggesting a greater selective effect under alkali stress. Evaluation of soil chemical components showed that in addition to soil pH, cation exchange capacity also had a strong impact on shaping bulk soil microbial communities. This study extends our knowledge regarding the importance of pH to microbial ecology showing that root endosphere and rhizosphere microbial communities were also influenced by this soil component, and highlights the important role that plants play particularly in shaping the belowground microbiomes in alkaline soils.

scholarly journals On Maintenance and Metabolisms in Soil Microbial Communities

2022 ◽  
Author(s):  
Paul Dijkstra ◽  
Weichao Wu ◽  
Michaela Dippold ◽  
Egbert Schwartz ◽  
Bruce Hungate ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Metabolic Flux ◽  
Soil Microbial Communities ◽  
Soil Ecology ◽  
Future Research ◽  
Flux Analysis ◽  
Maintenance Energy ◽  
Substrate Use ◽  
Soil Microbial ◽  
Use Efficiency

Abstract Biochemistry is an essential yet often undervalued aspect of soil ecology, especially in soil C cycling. We assume based on tradition, intuition or hope that the complexity of biochemistry is confined to the microscopic world, and can be ignored when dealing with whole soil systems. This opinion paper draws attention to patterns caused by basic biochemical processes that permeate the world of ecosystem processes. From these patterns, we can estimate activities of the biochemical reactions of the central C metabolic network and gain insights into the ecophysiology of microbial biosynthesis and growth and maintenance energy requirements; important components of Carbon Use Efficiency (CUE).The biochemical pathways used to metabolize glucose vary from soil to soil, with mostly glycolysis in some soils, and pentose phosphate or Entner-Doudoroff pathways in others. However, notwithstanding this metabolic diversity, glucose use efficiency is high and thus substrate use for maintenance energy and overflow respiration is low in these three soils. These results contradict current dogma based on four decades of research in soil ecology. We identify three main shortcomings in our current understanding of substrate use efficiency: 1) in numeric and conceptual models, we lack appreciation of the strategies that microbes employ to quickly reduce energy needs in response to starvation; 2) production of exudates and microbial turnover affect whole-soil CUE more than variation in maintenance energy demand; and 3) whether tracer experiments can be used to measure the long-term substrate use efficiency of soil microbial communities depends critically on the ability of non-growing cells to take up tracer substrates, how biosynthesis responds to these substrates, as well as on how cellular activities scale to the community level.To move the field of soil ecology forward, future research must consider the details of microbial ecophysiology and develop new tools that enable direct measurement of microbial functioning in intact soils. We submit that 13C metabolic flux analysis is one of those new tools.

scholarly journals Microbial Inoculants and Their Impact on Soil Microbial Communities: A Review

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Darine Trabelsi ◽  
Ridha Mhamdi
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Future Research ◽  
Bacterial Strains ◽  
Microbial Inoculants ◽  
Soil Microbial ◽  
Functional Capabilities ◽  
Plant Soil ◽  
Taxonomic Groups ◽  
The Impact

The knowledge of the survival of inoculated fungal and bacterial strains in field and the effects of their release on the indigenous microbial communities has been of great interest since the practical use of selected natural or genetically modified microorganisms has been developed. Soil inoculation or seed bacterization may lead to changes in the structure of the indigenous microbial communities, which is important with regard to the safety of introduction of microbes into the environment. Many reports indicate that application of microbial inoculants can influence, at least temporarily, the resident microbial communities. However, the major concern remains regarding how the impact on taxonomic groups can be related to effects on functional capabilities of the soil microbial communities. These changes could be the result of direct effects resulting from trophic competitions and antagonistic/synergic interactions with the resident microbial populations, or indirect effects mediated by enhanced root growth and exudation. Combination of inoculants will not necessarily produce an additive or synergic effect, but rather a competitive process. The extent of the inoculation impact on the subsequent crops in relation to the buffering capacity of the plant-soil-biota is still not well documented and should be the focus of future research.

Patterns and drivers of soil microbial communities in Tibetan alpine and global terrestrial ecosystems

2016 ◽  
Vol 43 (10) ◽  
pp. 2027-2039 ◽  
Author(s):  
Yong-Liang Chen ◽  
Jin-Zhi Ding ◽  
Yun-Feng Peng ◽  
Fei Li ◽  
Gui-Biao Yang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Terrestrial Ecosystems ◽  
Soil Microbial

scholarly journals Impact of Water Stress on Microbial Community and Activity in Sandy and Loamy Soils

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1429 ◽  
Author(s):  
Sylwia Siebielec ◽  
Grzegorz Siebielec ◽  
Agnieszka Klimkowicz-Pawlas ◽  
Anna Gałązka ◽  
Jarosław Grządziel ◽  
...  
Keyword(s):  
Water Stress ◽  
Microbial Communities ◽  
Bacterial Diversity ◽  
Water Deficit ◽  
Enzyme Activities ◽  
Soil Microbial Communities ◽  
Stress Conditions ◽  
Drought Period ◽  
Soil Microbial ◽  
Level 2

Prolonged drought and extreme precipitation can have a significant impact on the activity and structure of soil microbial communities. The aim of the study was to assess the impact of drought length on the dynamics of mineral nitrogen, enzyme activities and bacterial diversity in two soils of different texture (sand and silt loam, according to USDA classification). An additional objective was to evaluate the effect of compost on the alleviation of soil microbial responses to stress conditions, i.e. alternating periods of drought and excessive soil moisture. The pot study was carried out in a greenhouse under controlled conditions. Compost was added at an amount equal to 3% of soil to the sandy soil, which was characterised by a significantly lower water retention capacity. Specific levels of water stress conditions were created through application of drought and soil watering periods. For each soil, four levels of moisture regimes were set-up, including optimal conditions kept at 60% of field water holding capacity, and three levels of water stress: The low level—2 week period without watering; the medium level—1 month drought period followed by watering to full but short-term soil saturation with water; and the high level—2 month drought period followed by full and long-term saturation with the same total amount of water, as in other variants. The soil water regime strongly modified the activities of dehydrogenases and acid and alkaline phosphatase, as well as the bacterial diversity. Loamy soil exhibited greater resistance to the inhibition of soil enzymatic activity. After irrigation, following both a 1 month and 2 month drought, the enzyme activities and nitrification largely recovered in soil with a loamy texture. Drought induced substantial shifts in the functional diversity of bacterial communities. The use of such C substrates, as carboxylic and acetic acids, was strongly inhibited by water deficit. Water deficit induced changes in the relative abundances of particular phyla, for example, an increase in Acidobacteria or a decrease in Verrucomicrobia. The study clearly proves the greater susceptibility of microbial communities to drought in sandy soils and the important role of exogenous organic matter in protecting microbial activity in drought periods.

Terrestrial ecosystems

2018 ◽  
Author(s):  
Pierre Taberlet ◽  
Aurélie Bonin ◽  
Lucie Zinger ◽  
Eric Coissac
Keyword(s):  
Microbial Communities ◽  
Functional Diversity ◽  
Soil Microbial Communities ◽  
Terrestrial Ecosystems ◽  
Single Species ◽  
Freshwater Ecology ◽  
Species Detection ◽  
Soil Microbial

Chapter 14 “Terrestrial ecosystems” focuses on the use of eDNA analysis for the study of terrestrial organisms, especially those found in or associated with soil. While eDNA-based analyses have rapidly gained momentum in the freshwater ecology community, first for single-species detection and more recently for diversity surveys, their success has been less immediate among terrestrial ecologists. Soil microbiologists are a notable exception, as they quickly realized that targeting DNA directly in the environment could free them from cultivating microorganisms prior to any community census. This chapter first addresses the particularities of detectability, persistence, and mobility of eDNA in soil. Then, it revisits several remarkable studies dealing with the characterization of plant, earthworm, or soil microbial communities, as well as soil functional diversity. Finally, Chapter 14 reviews one of the most fascinating opportunities offered by eDNA metabarcoding (i.e., the possibility to carry out multitaxa diversity surveys).

scholarly journals Organic Amendments to Avocado Crops Induce Suppressiveness and Influence the Composition and Activity of Soil Microbial Communities

2015 ◽  
Vol 81 (10) ◽  
pp. 3405-3418 ◽  
Author(s):  
Nuria Bonilla ◽  
Carmen Vida ◽  
Maira Martínez-Alonso ◽  
Blanca B. Landa ◽  
Nuria Gaju ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Root Rot ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Organic Amendments ◽  
Bulk Soil ◽  
White Root Rot ◽  
Content Type ◽  
Soil Microbial

ABSTRACTOne of the main avocado diseases in southern Spain is white root rot caused by the fungusRosellinia necatrixPrill. The use of organic soil amendments to enhance the suppressiveness of natural soil is an inviting approach that has successfully controlled other soilborne pathogens. This study tested the suppressive capacity of different organic amendments againstR. necatrixand analyzed their effects on soil microbial communities and enzymatic activities. Two-year-old avocado trees were grown in soil treated with composted organic amendments and then used for inoculation assays. All of the organic treatments reduced disease development in comparison to unamended control soil, especially yard waste (YW) and almond shells (AS). The YW had a strong effect on microbial communities in bulk soil and produced larger population levels and diversity, higher hydrolytic activity and strong changes in the bacterial community composition of bulk soil, suggesting a mechanism of general suppression. Amendment with AS induced more subtle changes in bacterial community composition and specific enzymatic activities, with the strongest effects observed in the rhizosphere. Even if the effect was not strong, the changes caused by AS in bulk soil microbiota were related to the direct inhibition ofR. necatrixby this amendment, most likely being connected to specific populations able to recolonize conducive soil after pasteurization. All of the organic amendments assayed in this study were able to suppress white root rot, although their suppressiveness appears to be mediated differentially.

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