Soil feedbacks of plant diversity on soil microbial communities and subsequent plant growth

Abstract Background and aimsMany plant species grow better in sterilized than in live soil. Foliar application of SA mitigates this negative effect of live soil on the growth of the plant Jacobaea vulgaris. To examine what causes the positive effect of SA application on plant growth in live soils, we analyzed the effects of SA application on the composition of active rhizosphere bacteria in the live soil. Methods We studied this over four consecutive plant cycles (generations), using mRNA sequencing of the microbial communities in the rhizosphere of J. vulgaris. ResultsOur study shows that the composition of the rhizosphere bacterial communities of J. vulgaris greatly differed among generations. Application of SA resulted in both increases and decreases in a number of active bacterial genera in the rhizosphere soil, but the genera that were affected by the treatment differed among generations. In the first generation, there were no genera that were significantly affected by the SA treatment, indicating that induction of the SA defense pathway in plants does not lead to immediate changes in the soil microbial community. 89 species out of the total 270 (32.4%) were present in all generations in all soils of SA-treated and control plants suggesting that these make up the “core” microbiome. On average in each generation, 72.9% of all genera were present in both soils. Application of SA to plants significantly up-regulated genera of Caballeronia, unclassified Cytophagaceae, Crinalium and Candidatus Thermofonsia Clade 2, and down-regulated genera of Thermomicrobiales, unclassified Rhodobacterales, Paracoccus and Flavihumibacter. While the functions of many of these bacteria are poorly understood, bacteria of the genus Caballeronia play an important role in fixing nitrogen and promoting plant growth, and hence this suggests that activation of the SA signaling pathway in J. vulgaris plants may select for bacterial genera that are beneficial to the plant. ConclusionsOverall, our study shows that aboveground activation of defenses in the plant affects soil microbial communities and, as soil microbes can greatly influence plant performance, this implies that induction of plant defenses can lead to complex above-belowground feedbacks. Further studies should examine how activation of the SA signaling pathway in the plant changes the functional genes of the rhizosphere soil bacterial community.

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Development of soil microbial communities for promoting sustainability in agriculture and a global carbon fix

10.7287/peerj.preprints.789 ◽

2015 ◽

Author(s):

David Johnson ◽

Joe Ellington ◽

Wesley Eaton

Keyword(s):

Plant Growth ◽

Microbial Communities ◽

Soil Microbial Communities ◽

Soil Conditions ◽

Management Approach ◽

Total System ◽

Soil C ◽

Soil Microbial ◽

Respiration Rates ◽

Agriculture Management

The goals of this research were to explore alternative agriculture management practices in both greenhouse and field trials that do not require the use of synthetic and/or inorganic nutrient amendments but instead would emulate mechanisms operating in natural ecosystems, between plant and Soil Microbial Communities (SMC), for plant nutrient acquisition and growth. Greenhouse plant-growth trials, implementing a progression of soil conditions with increasing soil carbon (C) (C= 0.14% to 5.3%) and associated SMC population with increasing Fungal to Bacterial ratios (F:B) ( from 0.04 to 3.68), promoted a) increased C partitioning into plant shoot and plant fruit partitions (m=4.41, r2=0.99), b) significant quantities of plant photosynthate, 49%-97% of Total System New C (CTSN), partitioned towards increasing soil C c) four times reduction in soil C respiration (CR) as F:B ratios increased, starting with 44% of initial treatment soil C content respired in bacterial-dominant soils (low F:B), to 11% of soil C content respired in higher fertility fungal-dominant soils (Power Regression, r2=0.90; p=0.003). Plant growth trials in fields managed for increased soil C content and enhanced SMC population and structure (increased F:B) demonstrated: a) dry aboveground biomass production rates (g m-2) of ~1,980 g in soils initiating SMC enhancement (soil C=0.87, F:B= 0.80) with observed potentials of 8,450 g in advanced soils (soil C=7.6%, F:B=4.3) b) a 25-times increase in active soil fungal biomass and a ~7.5 times increase in F:B over a 19 month application period to enhance SMC and c) reduced soil C respiration rates, from 1.25 g C m-2 day-1 in low fertility soils (soil C= 0.6%, F:B= 0.25) with only a doubling of respiration rates to 2.5 g C m-2 day-1 in a high-fertility soil with an enhanced SMC (F:B= 4.3) and >7 times more soil C content (soil C= 7.6%). Enhancing SMC population and F:B structure in a 4.5 year agricultural field study promoted annual average capture and storage of 10.27 metric tons soil C ha-1 year -1 while increasing soil macro-, meso- and micro-nutrient availability offering a robust, cost-effective carbon sequestration mechanism within a more productive and long-term sustainable agriculture management approach.

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Soil inoculation with the biocontrol agent Clonostachys rosea and the mycorrhizal fungus Glomus intraradices results in mutual inhibition, plant growth promotion and alteration of soil microbial communities

Soil Biology and Biochemistry ◽

10.1016/j.soilbio.2006.06.003 ◽

2006 ◽

Vol 38 (12) ◽

pp. 3453-3462 ◽

Cited By ~ 41

Author(s):

Sabine Ravnskov ◽

Birgit Jensen ◽

Inge M.B. Knudsen ◽

Lars Bødker ◽

Dan Funck Jensen ◽

...

Keyword(s):

Plant Growth ◽

Microbial Communities ◽

Glomus Intraradices ◽

Biocontrol Agent ◽

Growth Promotion ◽

Mycorrhizal Fungus ◽

Soil Microbial Communities ◽

Mutual Inhibition ◽

Clonostachys Rosea ◽

Soil Microbial

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Decoupling plant-growth from land-use legacies in soil microbial communities

Soil Biology and Biochemistry ◽

10.1016/j.soilbio.2007.11.020 ◽

2008 ◽

Vol 40 (5) ◽

pp. 1059-1068 ◽

Cited By ~ 30

Author(s):

Andrew Kulmatiski ◽

Karen H. Beard

Keyword(s):

Land Use ◽

Plant Growth ◽

Microbial Communities ◽

Soil Microbial Communities ◽

Soil Microbial ◽

Land Use Legacies

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Relationships between Arabidopsis genotype-specific biomass accumulation and associated soil microbial communities

Botany ◽

10.1139/cjb-2012-0217 ◽

2013 ◽

Vol 91 (2) ◽

pp. 123-126 ◽

Cited By ~ 34

Author(s):

Akifumi Sugiyama ◽

Matthew G. Bakker ◽

Dayakar V. Badri ◽

Daniel K. Manter ◽

Jorge M. Vivanco

Keyword(s):

Microbial Community ◽

Plant Growth ◽

Growth Performance ◽

Microbial Communities ◽

Soil Microbial Communities ◽

454 Sequencing ◽

Biomass Accumulation ◽

The United States ◽

Natural Soil ◽

Soil Microbial

Rhizosphere microbial communities are impacted by resident plant species and have reciprocal effects on their host plants. We collected resident soil from five wild populations of Arabidopsis in the United States and Europe in an effort to characterize the impacts of natural soil microbiomes on Arabidopsis growth performance. The microbial communities present in these soils showed differences in community structure as assessed by 454 sequencing and in metabolic activity. While pathogens associated with the Brassica family were rare, diverse genera of potential plant growth promoting rhizobacteria were detected. Seed corresponding to the five Arabidopsis genotypes was grown in resident and nonresident soils to determine relationships among plant growth performance and soil microbial community and edaphic characteristics. Arabidopsis genotypes demonstrated different patterns of relationship between biomass accumulation and microbial community characteristics. This work sheds light on the bacterial populations naturally associated with Arabidopsis and suggests implications of the rhizosphere microbiome for plant growth performance.

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