The Effect of Rhizophagus irregularis, Bacillus subtilis and Water Regime on the Plant–Microbial Soil System: The Case of Lactuca sativa

Inoculation with beneficial microbes represents a promising solution for sustainable agricultural production; however, knowledge on the effects of inoculants on the indigenous microbial communities remains limited. Here, we evaluated the impact of the arbuscular mycorrhizal fungus Rhizophagus irregularis and the promoting rhizobacterium Bacillus subtilis on the growth of Lactuca sativa. The biomass, the composition, and the enzyme activity (urease, acid phosphatase, and β-glycosidase) of the rhizosphere microbial community at two soil moisture levels (5 and 10% soil water content) were evaluated. Fungal colonization was lower in co-inoculated plants than those only inoculated with R. irregularis. Plant growth was enhanced in co-inoculated and B. subtilis inoculated soils. Bacterial biomass and the composition of the microbial communities responded to the joint effect of inoculant type × water regime while the biomass of the other microbial groups (fungi, actinomycetes, microeukaryotes) was only affected by inoculant type. Co-inoculation enhanced the activity of acid phosphatase, indicating a synergistic effect of the two inoculants. Co-inoculation positively impacted the index reflecting plant–microbial soil functions under both water regimes. We concluded that the interactions between the two inocula as well as between them and the resident rhizosphere microbial community were mainly negative. However, the negative interactions between R. irregularis and B. subtilis were not reflected in plant biomass. The knowledge of the plant and rhizosphere microbial responses to single and co-inoculation and their dependency on abiotic conditions is valuable for the construction of synthetic microbial communities that could be used as efficient inocula.

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Achieving similar root microbiota composition in neighbouring plants through airborne signalling

The ISME Journal ◽

10.1038/s41396-020-00759-z ◽

2020 ◽

Author(s):

Hyun Gi Kong ◽

Geun Cheol Song ◽

Hee-Jung Sim ◽

Choong-Min Ryu

Keyword(s):

Microbial Community ◽

Environmental Changes ◽

Tomato Seedling ◽

Environmental Signals ◽

Plant Volatile ◽

The Status ◽

Plant Growth Promoting ◽

The Impact ◽

First Time ◽

Rhizosphere Microbial Community

Abstract The ability to recognize and respond to environmental signals is essential for plants. In response to environmental changes, the status of a plant is transmitted to other plants in the form of signals such as volatiles. Root-associated bacteria trigger the release of plant volatile organic compounds (VOCs). However, the impact of VOCs on the rhizosphere microbial community of neighbouring plants is not well understood. Here, we investigated the effect of VOCs on the rhizosphere microbial community of tomato plants inoculated with a plant growth-promoting rhizobacterium Bacillus amyloliquefaciens strain GB03 and that of their neighbouring plants. Interestingly, high similarity (up to 69%) was detected in the rhizosphere microbial communities of the inoculated and neighbouring plants. Leaves of the tomato plant treated with strain GB03-released β-caryophyllene as a signature VOC, which elicited the release of a large amount of salicylic acid (SA) in the root exudates of a neighbouring tomato seedling. The exposure of tomato leaves to β-caryophyllene resulted in the secretion of SA from the root. Our results demonstrate for the first time that the composition of the rhizosphere microbiota in surrounding plants is synchronized through aerial signals from plants.

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Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil

Scientific Reports ◽

10.1038/s41598-019-52148-y ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 11

Author(s):

Vanessa L. Brisson ◽

Jennifer E. Schmidt ◽

Trent R. Northen ◽

John P. Vogel ◽

Amélie C. M. Gaudin

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Microbial Community Composition ◽

Microbial Community Analysis ◽

Agricultural System ◽

Community Members ◽

Genetic Groups ◽

Maize Domestication ◽

Rhizosphere Microbial Community

Abstract Maize domestication and breeding have resulted in drastic and well documented changes in aboveground traits, but belowground effects on root system functioning and rhizosphere microbial communities remain poorly understood, despite their critical importance for nutrient and water acquisition. We investigated the rhizosphere microbial community composition and structure of ten Zea mays accessions along an evolutionary transect (two teosinte, three inbred maize lines, and five modern maize hybrids) grown in nutrient depleted soil from a low input agricultural system. Microbial community analysis revealed significant differences in community composition between soil compartments (proximal vs. distal rhizosphere) and between plant genetic groups (teosinte, inbred, and modern hybrid). Only a small portion of the microbial community was differentially selected across plant genetic groups: 3.7% of prokaryotic community members and 4.9% of fungal community members were significantly associated with a specific plant genetic group. Indicator species analysis showed the greatest differentiation between modern hybrids and the other two plant genetic groups. Co-occurrence network analysis revealed that microbial co-occurrence patterns of the inbred maize lines’ rhizosphere were significantly more similar to those of the teosintes than to the modern hybrids. Our results suggest that advances in hybrid development significantly impacted rhizosphere microbial communities and network assembly.

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Cucumber Rhizosphere Microbial Community Response to Biocontrol Agent Bacillus subtilis B068150

Agriculture ◽

10.3390/agriculture6010002 ◽

2015 ◽

Vol 6 (1) ◽

pp. 2 ◽

Cited By ~ 5

Author(s):

Lihua Li ◽

Jincai Ma ◽

A. Ibekwe ◽

Qi Wang ◽

Ching-Hong Yang

Keyword(s):

Bacillus Subtilis ◽

Microbial Community ◽

Biocontrol Agent ◽

Community Response ◽

Rhizosphere Microbial Community

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Hill-based Dissimilarity Indices and Null Models for Analysis of Microbial Community Assembly

10.21203/rs.3.rs-33130/v1 ◽

2020 ◽

Author(s):

Oskar Modin ◽

Raquel Liebana ◽

Soroush Saheb-Alam ◽

Britt-Marie Wilén ◽

Carolina Suarez ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Assembly ◽

Null Model ◽

Amplicon Sequencing ◽

Null Models ◽

Marker Genes ◽

Experimental Systems ◽

Microbial Community Assembly ◽

The Impact

Abstract Background: High-throughput amplicon sequencing of marker genes, such as the 16S rRNA gene in Bacteria and Archaea, provides a wealth of information about the composition of microbial communities. To quantify differences between samples and draw conclusions about factors affecting community assembly, dissimilarity indices are typically used. However, results are subject to several biases and data interpretation can be challenging. The Jaccard and Bray-Curtis indices, which are often used to quantify taxonomic dissimilarity, are not necessarily the most logical choices. Instead, we argue that Hill-based indices, which make it possible to systematically investigate the impact of relative abundance on dissimilarity, should be used for robust analysis of data. In combination with a null model, mechanisms of microbial community assembly can be analyzed. Here, we also introduce a new software, qdiv, which enables rapid calculations of Hill-based dissimilarity indices in combination with null models.Results: Using amplicon sequencing data from two experimental systems, aerobic granular sludge (AGS) reactors and microbial fuel cells (MFC), we show that the choice of dissimilarity index can have considerable impact on results and conclusions. High dissimilarity between replicates because of random sampling effects make incidence-based indices less suited for identifying differences between groups of samples. Determining a consensus table based on count tables generated with different bioinformatic pipelines reduced the number of low-abundant, potentially spurious amplicon sequence variants (ASVs) in the data sets, which led to lower dissimilarity between replicates. Analysis with a combination of Hill-based indices and a null model allowed us to show that different ecological mechanisms acted on different fractions of the microbial communities in the experimental systems.Conclusions: Hill-based indices provide a rational framework for analysis of dissimilarity between microbial community samples. In combination with a null model, the effects of deterministic and stochastic community assembly factors on taxa of different relative abundances can be systematically investigated. Calculations of Hill-based dissimilarity indices in combination with a null model can be done in qdiv, which is freely available as a Python package (https://github.com/omvatten/qdiv). In qdiv, a consensus table can also be determined from several count tables generated with different bioinformatic pipelines.

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A Meta-Omics Analysis Unveils the Shift in Microbial Community Structures and Metabolomics Profiles in Mangrove Sediments Treated with a Selective Actinobacterial Isolation Procedure

Molecules ◽

10.3390/molecules26237332 ◽

2021 ◽

Vol 26 (23) ◽

pp. 7332

Author(s):

Miguel David Marfil-Santana ◽

Anahí Martínez-Cárdenas ◽

Analuisa Ruíz-Hernández ◽

Mario Vidal-Torres ◽

Norma Angélica Márquez-Velázquez ◽

...

Keyword(s):

Microbial Community ◽

Secondary Metabolites ◽

Microbial Communities ◽

Secondary Metabolite ◽

Resistant Bacteria ◽

Mangrove Sediments ◽

Molecular Networking ◽

Mangrove Tree ◽

Enhanced Production ◽

The Impact

Mangrove sediment ecosystems in the coastal areas of the Yucatan peninsula are unique environments, influenced by their karstic origin and connection with the world’s largest underground river. The microbial communities residing in these sediments are influenced by the presence of mangrove roots and the trading chemistry for communication between sediment bacteria and plant roots can be targeted for secondary metabolite research. To explore the secondary metabolite production potential of microbial community members in mangrove sediments at the “El Palmar” natural reserve in Sisal, Yucatan, a combined meta-omics approach was applied. The effects of a cultivation medium reported to select for actinomycetes within mangrove sediments’ microbial communities was also analyzed. The metabolome of the microbial communities was analyzed by high-resolution liquid chromatography-tandem mass spectrometry, and molecular networking analysis was used to investigate if known natural products and their variants were present. Metagenomic results suggest that the sediments from “El Palmar” harbor a stable bacterial community independently of their distance from mangrove tree roots. An unexpected decrease in the observed abundance of actinomycetes present in the communities occurred when an antibiotic-amended medium considered to be actinomycete-selective was applied for a 30-day period. However, the use of this antibiotic-amended medium also enhanced production of secondary metabolites within the microbial community present relative to the water control, suggesting the treatment selected for antibiotic-resistant bacteria capable of producing a higher number of secondary metabolites. Secondary metabolite mining of “El Palmar” microbial community metagenomes identified polyketide synthase and non-ribosomal peptide synthetases’ biosynthetic genes in all analyzed metagenomes. The presence of these genes correlated with the annotation of several secondary metabolites from the Global Natural Product Social Molecular Networking database. These results highlight the biotechnological potential of the microbial communities from “El Palmar”, and show the impact selective media had on the composition of communities of actinobacteria.

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Spatiotemporal Correlations Between Water Quality And Microbial Community of Typical Inflow River Into Taihu Lake, China

10.21203/rs.3.rs-1000115/v1 ◽

2021 ◽

Author(s):

Yajie Zhang ◽

Ye Zhang ◽

Lecheng Wei ◽

Mengyan Li ◽

Weitang Zhu ◽

...

Keyword(s):

Water Quality ◽

Microbial Community ◽

Microbial Communities ◽

Taihu Lake ◽

Wastewater Treatment Plants ◽

Ammonia Nitrogen ◽

Pollution Sources ◽

Storm Water ◽

Urban Wastewater Treatment ◽

The Impact

Abstract Changxing River, which is a typical inflow river into the Taihu Lake and occurs severe algae invasion, is selected to study the effect of different pollution sources on the water quality and ecological system. Four types of pollution sources, including the estuary of Taihu Lake, discharge outlets of urban wastewater treatment plants, storm water outlets, and non-point source agricultural drainage areas are chosen, and next-generation sequencing and multi-variate statistical analyses are used to characterize the microbial communities and reveal their relationship with water physicochemical properties. Results showed that ammonia nitrogen (NH4+-N), total nitrogen (TN), and total phosphorus (TP) are the main pollutant in Changxing River, especially at storm water outlets. At the same time, the diversity of microbial communities was the highest in the summer, and dominant phyla included Proteobacteria (40.9%), Bacteroidetes (21.0%) and Euryarchaeota (6.1%) under the condition of algal bloom. Water temperature (T), air pressure (P), concentrations of TP and CODMn were the important variables for the succession of microbial community. From the perspective of different pollution types, relative abundances of Microcystis and Nostocaceae at the estuary of Taihu Lake were correlated positively with dissolved oxygen (DO) and pH, and Pseudomonas and Arcobacter were correlated positively with concentrations of TN and nitrate nitrogen (NO3--N) at storm water outlets. The results provide a reference for the impact of pollution types on river microbial ecosystem under complex hydrological condition and a guidance for the selection of restoration techniques for polluted rivers entering an important lake.

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Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling

Microbiome ◽

10.1186/s40168-019-0756-9 ◽

2019 ◽

Vol 7 (1) ◽

Cited By ~ 24

Author(s):

Jennifer E. Schmidt ◽

Angela D. Kent ◽

Vanessa L. Brisson ◽

Amélie C. M. Gaudin

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Nitrogen Cycling ◽

Community Composition ◽

Network Structure ◽

Host Selection ◽

Agricultural Management ◽

Plant Selection ◽

Selection Processes ◽

Rhizosphere Microbial Community

Abstract Background Rhizosphere microbial communities are key regulators of plant performance, yet few studies have assessed the impact of different management approaches on the rhizosphere microbiomes of major crops. Rhizosphere microbial communities are shaped by interactions between agricultural management and host selection processes, but studies often consider these factors individually rather than in combination. We tested the impacts of management (M) and rhizosphere effects (R) on microbial community structure and co-occurrence networks of maize roots collected from long-term conventionally and organically managed maize-tomato agroecosystems. We also explored the interaction between these factors (M × R) and how it impacts rhizosphere microbial diversity and composition, differential abundance, indicator taxa, co-occurrence network structure, and microbial nitrogen-cycling processes. Results Host selection processes moderate the influence of agricultural management on rhizosphere microbial communities, although bacteria and fungi respond differently to plant selection and agricultural management. We found that plants recruit management-system-specific taxa and shift N-cycling pathways in the rhizosphere, distinguishing this soil compartment from bulk soil. Rhizosphere microbiomes from conventional and organic systems were more similar in diversity and network structure than communities from their respective bulk soils, and community composition was affected by both M and R effects. In contrast, fungal community composition was affected only by management, and network structure only by plant selection. Quantification of six nitrogen-cycling genes (nifH, amoA [bacterial and archaeal], nirK, nrfA, and nosZ) revealed that only nosZ abundance was affected by management and was higher in the organic system. Conclusions Plant selection interacts with conventional and organic management practices to shape rhizosphere microbial community composition, co-occurrence patterns, and at least one nitrogen-cycling process. Reframing research priorities to better understand adaptive plant-microbe feedbacks and include roots as a significant moderating influence of management outcomes could help guide plant-oriented strategies to improve productivity and agroecosystem sustainability.

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Seasonal Changes in the Rhizosphere Microbial Communities Associated with Field-Grown Genetically Modified Canola (Brassica napus)

Applied and Environmental Microbiology ◽

10.1128/aem.69.12.7310-7318.2003 ◽

2003 ◽

Vol 69 (12) ◽

pp. 7310-7318 ◽

Cited By ~ 132

Author(s):

Kari E. Dunfield ◽

James J. Germida

Keyword(s):

Microbial Community ◽

Transgenic Plants ◽

Transgenic Plant ◽

Microbial Communities ◽

Genetically Modified ◽

Ecological Impact ◽

Growing Season ◽

Field Season ◽

Field Plots ◽

Rhizosphere Microbial Community

ABSTRACT The introduction of transgenic plants into agricultural ecosystems has raised the question of the ecological impact of these plants on nontarget organisms, such as soil bacteria. Although differences in both the genetic structure and the metabolic function of the microbial communities associated with some transgenic plant lines have been established, it remains to be seen whether these differences have an ecological impact on the soil microbial communities. We conducted a 2-year, multiple-site field study in which rhizosphere samples associated with a transgenic canola variety and a conventional canola variety were sampled at six times throughout the growing season. The objectives of this study were to identify differences between the rhizosphere microbial community associated with the transgenic plants and the rhizosphere microbial community associated with the conventional canola plants and to determine whether the differences were permanent or depended on the presence of the plant. Community-level physiological profiles, fatty acid methyl ester profiles, and terminal amplified ribosomal DNA restriction analysis profiles of rhizosphere microbial communities were compared to the profiles of the microbial community associated with an unplanted, fallow field plot. Principal-component analysis showed that there was variation in the microbial community associated with both canola variety and growth season. Importantly, while differences between the microbial communities associated with the transgenic plant variety were observed at several times throughout the growing season, all analyses indicated that when the microbial communities were assessed after winter, there were no differences between microbial communities from field plots that contained harvested transgenic canola plants and microbial communities from field plots that did not contain plants during the field season. Hence, the changes in the microbial community structure associated with genetically modified plants were temporary and did not persist into the next field season.

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Heavy Metal Tolerance Genes Associated With Contaminated Sediments From an E-Waste Recycling River in Southern China

Frontiers in Microbiology ◽

10.3389/fmicb.2021.665090 ◽

2021 ◽

Vol 12 ◽

Author(s):

Shengqiao Long ◽

Hui Tong ◽

Xuxiang Zhang ◽

Shuyu Jia ◽

Manjia Chen ◽

...

Keyword(s):

Heavy Metal ◽

Microbial Community ◽

Microbial Communities ◽

Southern China ◽

Risk Index ◽

River Sediments ◽

Microbial Community Composition ◽

Heavy Metal Tolerance ◽

Waste Recycling ◽

The Impact

Heavy metal pollution that results from electronic waste (e-waste) recycling activities has severe ecological environmental toxicity impacts on recycling areas. The distribution of heavy metals and the impact on the bacteria in these areas have received much attention. However, the diversity and composition of the microbial communities and the characteristics of heavy metal resistance genes (HMRGs) in the river sediments after long-term e-waste contamination still remain unclear. In this study, eight river sediment samples along a river in a recycling area were studied for the heavy metal concentration and the microbial community composition. The microbial community consisted of 13 phyla including Firmicutes (ranging from 10.45 to 36.63%), Proteobacteria (11.76 to 32.59%), Actinobacteria (14.81 to 27.45%), and unclassified bacteria. The abundance of Firmicutes increased along with the level of contaminants, while Actinobacteria decreased. A canonical correspondence analysis (CCA) showed that the concentration of mercury was significantly correlated with the microbial community and species distribution, which agreed with an analysis of the potential ecological risk index. Moreover, manually curated HMRGs were established, and the HMRG analysis results according to Illumina high-throughput sequencing showed that the abundance of HMRGs was positively related to the level of contamination, demonstrating a variety of resistance mechanisms to adapt, accommodate, and live under heavy metal-contaminated conditions. These findings increase the understanding of the changes in microbial communities in e-waste recycling areas and extend our knowledge of the HMRGs involved in the recovery of the ecological environment.

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Phytoremediation of landfill leachate in constructed wetland

Linnaeus Eco-Tech ◽

10.15626/eco-tech.2005.046 ◽

2019 ◽

pp. 441-446

Author(s):

Jaak Truu ◽

Jaanis Juhanson ◽

Mait Kriipsalu ◽

Marit Seene

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Plant Species ◽

Landfill Leachate ◽

Water Samples ◽

Free Water ◽

Vegetation Period ◽

Quality Of Water ◽

Remediation Plan ◽

The Impact

The integrated remediation plan of the Laguja landfill, Estonia, includes creation of aconstructed wetland for treatment of landfill leachate. A mesocosm experiment wasconducted in order to estimate the impact of different plant species on purification efficiencyof wetland. The quality of water in mesocosms was monitored during vegetation period. Allplant treatments enhanced reduction of organic matter (BOD: 87-96%, COD: ca 30%, TOC:ca 50%) as well as ammonia and total nitrogen in water compared to unplanted control.Presence of plants enhanced biodegradative bacterial abundance and activity as well asmetabolic diversity of microbial community in water. Water samples from all plant treatmentswere characterized by distinct microbial communities as revealed by molecular fingerprintingtechniques. Most different from the rest of microbial communities were water samples frommesocosm with plants on floating mats. Our results show that in free-water constructedwetlands with vegetation the purification efficiency is not dependent on plant species, whilestructure of water microbial community differs due to plant species.

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