scholarly journals A dynamic rhizosphere interplay between tree roots and soil bacteria under drought

2021 ◽  
Author(s):  
Yaara Oppenheimer-Shaanan ◽  
Gilad Jakoby ◽  
Maya Starr ◽  
Romiel Karliner ◽  
Gal Eilon ◽  
...  
Keyword(s):  
Forest Soil ◽  
Root Exudates ◽  
Soil Bacteria ◽  
Bacterial Species ◽  
Root Exudation ◽  
Pseudomonas Stutzeri ◽  
Nitrogen Sources ◽  
Microbial Interactions ◽  
Tree Roots ◽  
Custom Made

Root exudates are thought to play an important role in plant-microbial interactions. In return for nutrition, soil bacteria can increase the bioavailability of soil minerals. However, root exudates typically decrease in situations such as drought, calling into question the efficacy of bacteria-dependent mineral uptake in such stress. Here we tested the hypothesis of exudate-driven microbial priming on Cupressus saplings grown in forest soil in custom-made rhizotron boxes. A 1-month imposed drought and concomitant inoculations with Bacillus subtilis and Pseudomonas stutzeri, bacteria species isolated from the forest soil, were applied using factorial design. Direct bacteria counts and visualization by confocal microscopy showed that both bacteria associated with Cupressus roots. Interestingly, root exudation rates increased with bacteria under drought. Forty four metabolites in exudates were significantly different in concentration between irrigated and drought trees, including phenolic acid compounds and quinate, that were shown to be used as carbon and nitrogen sources by both bacterial species. Importantly, soil phosphorous bioavailability was maintained only in inoculated trees, mitigating drought-induced decrease in leaf phosphorus and iron. Our observations of increased root exudation rate when drought and inoculation regimes were combined, support the idea of root recruitment of beneficial bacteria.

scholarly journals A dynamic rhizosphere interplay between tree roots and soil bacteria under drought stress

2021 ◽  
Author(s):  
Yaarao Oppenheimer-Shaanan ◽  
Gilad Jakoby ◽  
Maya Laurenci Starr ◽  
Romiel Karliner ◽  
Gal Eilon ◽  
...  
Keyword(s):  
Forest Soil ◽  
Soil Bacteria ◽  
Bacterial Species ◽  
Root Exudation ◽  
Nitrogen Sources ◽  
Microbial Interactions ◽  
Tree Roots ◽  
Carbon And Nitrogen ◽  
Custom Made ◽  
Exudation Rate

<p>Root exudates are thought to play an important role in plant-microbial interactions. In return, soil bacteria can increase the bioavailability of soil minerals, which is typically decreasing in situations such as drought. Here we describe an exudate-driven microbial priming on <em>Cupressus</em> saplings grown outside in forest soil in custom-made rhizotron boxes. A 1-month imposed drought and inoculations with <em>Bacillus subtilis </em>and <em>Pseudomonas</em> <em>stutzeri</em>, bacteria species forest soil isolation, were applied in a factorial design. We revealed that both bacteria associated with <em>Cupressus</em> roots and were more abundant in rhizosphere than in bulk soil. Moreover, root exudation rate increased in inoculated trees under drought with >100 first identified metabolites from <em>Cupressus</em> roots. Among these metabolites, phenolic acid compounds, quinate, and others, were used as carbon and nitrogen sources by both bacterial species. Furthermore, soil phosphorous bioavailability was maintained only in inoculated trees, where a drought-induced decrease in leaf phosphorus and iron was prevented. We provide evidence that changes in exudation rate and composition under drought and bacteria inoculation, support the idea of root recruitment of beneficial bacteria. In turn, trees secreted further carbon source to the rhizosphere and hosted more bacteria, benefited from improved nutrition.</p>

DNA Isolation from Recalcitrant Materials Such as Tree Roots, Bark, and Forest Soil for the Detection of Fungal Pathogens by Polymerase Chain Reaction

1998 ◽  
Vol 262 (1) ◽  
pp. 79-82 ◽  
Author(s):  
Günther Bahnweg ◽  
Steffen Schulze ◽  
Evelyn M. Möller ◽  
Hilkea Rosenbrock ◽  
Christian Langebartels ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Forest Soil ◽  
Fungal Pathogens ◽  
Dna Isolation ◽  
Chain Reaction ◽  
Tree Roots ◽  
Polymerase Chain

scholarly journals Microcolony Cultivation on a Soil Substrate Membrane System Selects for Previously Uncultured Soil Bacteria

2005 ◽  
Vol 71 (12) ◽  
pp. 8714-8720 ◽  
Author(s):  
Belinda C. Ferrari ◽  
Svend J. Binnerup ◽  
Michael Gillings
Keyword(s):  
Soil Bacteria ◽  
Bacterial Species ◽  
Membrane System ◽  
Soil Extract ◽  
Growth Strategy ◽  
Soil Slurry ◽  
Polycarbonate Membrane ◽  
Microbiological Methods ◽  
Candidate Division ◽  
Excessive Nutrients

ABSTRACT Traditional microbiological methods of cultivation recover less than 1% of the total bacterial species, and the culturable portion of bacteria is not representative of the total phylogenetic diversity. Classical cultivation strategies are now known to supply excessive nutrients to a system and therefore select for fast-growing bacteria that are capable of colony or biofilm formation. New approaches to the cultivation of bacteria which rely on growth in dilute nutrient media or simulated environments are beginning to address this problem of selection. Here we describe a novel microcultivation method for soil bacteria that mimics natural conditions. Our soil slurry membrane system combines a polycarbonate membrane as a growth support and soil extract as the substrate. The result is abundant growth of uncharacterized bacteria as microcolonies. By combining microcultivation with fluorescent in situ hybridization, previously “unculturable” organisms belonging to cultivated and noncultivated divisions, including candidate division TM7, can be identified by fluorescence microscopy. Successful growth of soil bacteria as microcolonies confirmed that the missing culturable majority may have a growth strategy that is not observed when traditional cultivation indicators are used.

Localizing metabolic synthesis in microbial cultures with kinetic mass spectrometry imaging (kMSI)

2016 ◽  
Author(s):  
Katherine B. Louie ◽  
Benjamin P. Bowen ◽  
Rebecca Lau ◽  
Trent R. Northen
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectrometry Imaging ◽  
Shewanella Oneidensis ◽  
Pseudomonas Stutzeri ◽  
Isotopic Analysis ◽  
Microbial Interactions ◽  
Microbial Biofilms ◽  
High Lipid ◽  
New Synthesis ◽  
Species Specific

Mass spectrometry imaging (MSI) has emerged as a powerful technique enabling spatially defined imaging of metabolites within microbial biofilms. Here, we extend this approach to enable differentiation of newly synthesized versus pre-existing metabolites across a co-culture. This is accomplished by MS imaging two soil microbes, Shewanella oneidensis MR1 and Pseudomonas stutzeri RCH2, that were administered heavy water (D2O) during growth on agar plates. For two species-specific diglyceride (DG) lipids, isotopic analysis was performed on each spectra collected across the co-culture to determine the relative amount of newly synthesized versus pre-existing lipid. Here, highest levels of new synthesis of RCH2 lipid was localized to border regions adjacent to S. oneidensis MR1, while the MR1 lipid showed highest levels in regions further from RCH2. Interestingly, regions of high lipid abundance did not correspond to the regions with highest new lipid biosynthesis. Given the simplicity and generality of using D2O as a stable isotopic probe combined with the accessibility of kMSI to a range of MSI instrumentation, this approach has broad application for improving our understanding of how microbial interactions influence metabolite biosynthesis.

scholarly journals Effects of tobacco–peanut relay intercropping on soil bacteria community structure

2019 ◽  
Vol 69 (13) ◽  
pp. 1531-1536 ◽  
Author(s):  
Lin Gao ◽  
Xin-min Liu ◽  
Yong-mei Du ◽  
Hao Zong ◽  
Guo-ming Shen
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Soil Bacteria ◽  
Pathogenic Bacteria ◽  
Bacterial Species ◽  
Continuous Cropping ◽  
Soil Microbial ◽  
Relay Intercropping ◽  
Bacteria Community Structure

Abstract Purpose A reasonable cultivation pattern is beneficial to maintain soil microbial activity and optimize the structure of the soil microbial community. To determine the effect of tobacco−peanut (Nicotiana tabacum−Arachis hypogaea) relay intercropping on the microbial community structure in soil, we compared the effects of relay intercropping and continuous cropping on the soil bacteria community structure. Methods We collected soil samples from three different cropping patterns and analyzed microbial community structure and diversity using high-throughput sequencing technology. Result The number of operational taxonomic units (OTU) for bacterial species in the soil was maximal under continuous peanut cropping. At the phylum level, the main bacteria identified in soil were Proteobacteria, Actinobacteria, and Acidobacteria, which accounted for approximately 70% of the total. The proportions of Actinobacteria and Firmicutes increased, whereas the proportion of Proteobacteria decreased in soil with tobacco–peanut relay intercropping. Moreover, the proportions of Firmicutes and Proteobacteria among the soil bacteria further shifted over time with tobacco–peanut relay intercropping. At the genus level, the proportions of Bacillus and Lactococcus increased in soil with tobacco–peanut relay intercropping. Conclusion The community structure of soil bacteria differed considerably with tobacco–peanut relay intercropping from that detected under peanut continuous cropping, and the proportions of beneficial bacteria (the phyla Actinobacteria and Firmicutes, and the genera Bacillus and Lactococcus) increased while the proportion of potentially pathogenic bacteria (the genera Variibacter and Burkholderia) decreased. These results provide a basis for adopting tobacco–peanut relay intercropping to improve soil ecology and microorganisms, while making better use of limited cultivable land.

scholarly journals Stoichiometry constrains microbial response to root exudation- insights from a model and a field experiment in a temperate forest

2013 ◽  
Vol 10 (2) ◽  
pp. 821-838 ◽  
Author(s):  
J. E. Drake ◽  
B. A. Darby ◽  
M.-A. Giasson ◽  
M. A. Kramer ◽  
R. P. Phillips ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Microbial Biomass ◽  
Field Experiment ◽  
Microbial Activity ◽  
Root Exudates ◽  
Microbial Respiration ◽  
Root Exudation ◽  
N Availability ◽  
Rhizosphere Soils ◽  
Wide Range

Abstract. Plant roots release a wide range of chemicals into soils. This process, termed root exudation, is thought to increase the activity of microbes and the exoenzymes they synthesize, leading to accelerated rates of carbon (C) mineralization and nutrient cycling in rhizosphere soils relative to bulk soils. The nitrogen (N) content of microbial biomass and exoenzymes may introduce a stoichiometric constraint on the ability of microbes to effectively utilize the root exudates, particularly if the exudates are rich in C but low in N. We combined a theoretical model of microbial activity with an exudation experiment to test the hypothesis that the ability of soil microbes to utilize root exudates for the synthesis of additional biomass and exoenzymes is constrained by N availability. The field experiment simulated exudation by automatically pumping solutions of chemicals often found in root exudates ("exudate mimics") containing C alone or C in combination with N (C : N ratio of 10) through microlysimeter "root simulators" into intact forest soils in two 50-day experiments. The delivery of C-only exudate mimics increased microbial respiration but had no effect on microbial biomass or exoenzyme activities. By contrast, experimental delivery of exudate mimics containing both C and N significantly increased microbial respiration, microbial biomass, and the activity of exoenzymes that decompose low molecular weight components of soil organic matter (SOM, e.g., cellulose, amino sugars), while decreasing the activity of exoenzymes that degrade high molecular weight SOM (e.g., polyphenols, lignin). The modeling results were consistent with the experiments; simulated delivery of C-only exudates induced microbial N-limitation, which constrained the synthesis of microbial biomass and exoenzymes. Exuding N as well as C alleviated this stoichiometric constraint in the model, allowing for increased exoenzyme production, the priming of decomposition, and a net release of N from SOM (i.e., mineralization). The quantity of N released from SOM in the model simulations was, under most circumstances, in excess of the N in the exudate pulse, suggesting that the exudation of N-containing compounds can be a viable strategy for plant-N acquisition via a priming effect. The experimental and modeling results were consistent with our hypothesis that N-containing compounds in root exudates affect rhizosphere processes by providing substrates for the synthesis of N-rich microbial biomass and exoenzymes. This study suggests that exudate stoichiometry is an important and underappreciated driver of microbial activity in rhizosphere soils.

Plants colonized by AM fungi regulate further root colonization by AM fungi through altered root exudation

1999 ◽  
Vol 77 (6) ◽  
pp. 891-897 ◽  
Author(s):  
Alexandra Pinior ◽  
Urs Wyss ◽  
Yves Piché ◽  
Horst Vierheilig
Keyword(s):  
Root Exudates ◽  
Glomus Mosseae ◽  
Glomus Intraradices ◽  
Root Colonization ◽  
Root Exudation ◽  
Axenic Culture ◽  
Am Fungi ◽  
Hyphal Growth ◽  
Gigaspora Rosea ◽  
Stimulation Of

The effect of root exudates from non-mycorrhizal and mycorrhizal cucumber (Cucumis sativus L.) plants colonized by one of three arbuscular mycorrhizal fungi (Gigaspora rosea Nicolson & Schenck, Glomus intraradices Smith & Schenck, or Glomus mosseae (Nicolson & Gerdemann) Gerd. & Trappe) on hyphal growth of Gi. rosea and G. intraradices in axenic culture and on root colonization by G. mosseae in soil was investigated. Root exudates from non-mycorrhizal cucumber plants clearly stimulated hyphal growth, whereas root exudates from all mycorrhizal cucumber plants tested showed no stimulation of the hyphal growth of Gi. rosea and only a slight stimulation of the hyphal growth of G. intraradices. Moreover, root exudates from all mycorrhizal cucumber plants inhibited root colonization by G. mosseae compared with the water-treated controls. These results suggest that plants colonized by AM fungi regulate further mycorrhization via their root exudates.Key words: Glomales, Gigaspora rosea, Glomus intraradices, Glomus mosseae, root exudates, regulation.

scholarly journals Impact of Logging and Forest Conversion to Oil Palm Plantations on Soil Bacterial Communities in Borneo

2013 ◽  
Vol 79 (23) ◽  
pp. 7290-7297 ◽  
Author(s):  
Larisa Lee-Cruz ◽  
David P. Edwards ◽  
Binu M. Tripathi ◽  
Jonathan M. Adams
Keyword(s):  
Forest Soil ◽  
Oil Palm ◽  
Bacterial Communities ◽  
Soil Bacteria ◽  
Forest Conversion ◽  
Soil Bacterial Communities ◽  
Oil Palm Plantation ◽  
Β Diversity ◽  
Logged Forest ◽  
Soil Bacterial

ABSTRACTTropical forests are being rapidly altered by logging and cleared for agriculture. Understanding the effects of these land use changes on soil bacteria, which constitute a large proportion of total biodiversity and perform important ecosystem functions, is a major conservation frontier. Here we studied the effects of logging history and forest conversion to oil palm plantations in Sabah, Borneo, on the soil bacterial community. We used paired-end Illumina sequencing of the 16S rRNA gene, V3 region, to compare the bacterial communities in primary, once-logged, and twice-logged forest and land converted to oil palm plantations. Bacteria were grouped into operational taxonomic units (OTUs) at the 97% similarity level, and OTU richness and local-scale α-diversity showed no difference between the various forest types and oil palm plantations. Focusing on the turnover of bacteria across space, true β-diversity was higher in oil palm plantation soil than in forest soil, whereas community dissimilarity-based metrics of β-diversity were only marginally different between habitats, suggesting that at large scales, oil palm plantation soil could have higher overall γ-diversity than forest soil, driven by a slightly more heterogeneous community across space. Clearance of primary and logged forest for oil palm plantations did, however, significantly impact the composition of soil bacterial communities, reflecting in part the loss of some forest bacteria, whereas primary and logged forests did not differ in composition. Overall, our results suggest that the soil bacteria of tropical forest are to some extent resilient or resistant to logging but that the impacts of forest conversion to oil palm plantations are more severe.

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