scholarly journals Predominance of soil vs root effect in rhizosphere microbiota reassembly

2019 ◽  
Vol 95 (10) ◽  
Author(s):  
Mengli Zhao ◽  
Jun Yuan ◽  
Zongzhuan Shen ◽  
Menghui Dong ◽  
Hongjun Liu ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Disease Incidence ◽  
Bulk Soil ◽  
Pathogen Population ◽  
Root Effect ◽  
Rhizosphere Microbiome ◽  
Distinct Disease ◽  
Pathogenic Microbes ◽  
Disease Suppressive Soil ◽  
Rhizosphere Community

ABSTRACT Rhizosphere community assembly is simultaneously affected by both plants and bulk soils and is vital for plant health. However, it is still unclear how and to what extent disease-suppressive rhizosphere microbiota can be constructed from bulk soil, and the underlying agents involved in the process that render the rhizosphere suppressive against pathogenic microbes remain elusive. In this study, the evolutionary processes of the rhizosphere microbiome were explored based on transplanting plants previously growing in distinct disease-incidence soils to one disease-suppressive soil. Our results showed that distinct rhizoplane bacterial communities were assembled on account of the original bulk soil communities with different disease incidences. Furthermore, the bacterial communities in the transplanted rhizosphere were noticeably influenced by the second disease-suppressive microbial pool, rather than that of original formed rhizoplane microbiota and homogenous nontransplanted rhizosphere microbiome, contributing to a significant decrease in the pathogen population. In addition, Spearman's correlations between relative abundances of bacterial taxa and the abundance of Ralstonia solanacearum indicated Anoxybacillus, Flavobacterium, Permianibacter and Pseudomonas were predicted to be associated with disease-suppressive function formation. Altogether, our results showed that bulk soil played an important role in the process of assembling and reassembling the rhizosphere microbiome of plants.

scholarly journals Rhizosphere Bacteria Exhibit Narrower Environmental Adaptation in Proso Millet Than in Foxtail Millet and Sorghum in Agricultural Fields

2021 ◽  
Author(s):  
Lixin Tian ◽  
Feifei Zhang ◽  
Pengliang Chen ◽  
Panpan Zhang ◽  
Zhijun Gao ◽  
...  
Keyword(s):  
Community Assembly ◽  
Bacterial Communities ◽  
Large Scale ◽  
Foxtail Millet ◽  
Environmental Adaptation ◽  
Rhizosphere Bacteria ◽  
Agricultural Fields ◽  
Proso Millet ◽  
Rhizosphere Community ◽  
Rhizosphere Bacterial Communities

Abstract It is of great ecological significance to understand how the assembly processes of soil microbe communities respond to environmental change. However, the assembly processes of the rhizosphere bacterial communities in three minor grain crops (i.e., foxtail millet, proso millet, and sorghum) across agro-ecosystems are rarely investigated. Here, we investigated the environmental thresholds and phylogenetic signals for ecological preferences of rhizosphere bacterial communities of three minor grain crop taxa across complex environmental gradients to reflect their environmental adaptation. Additionally, we reported environmental factors affecting their community assembly processes based on a large-scale soil survey in agricultural fields across northern China using high-throughput sequencing.. The results demonstrated a narrower range of environmental thresholds and weaker phylogenetic signals for the ecological traits of rhizosphere bacteria in proso millet than in foxtail millet and sorghum fields, while proso millet rhizosphere community was the most phylogenetically clustered. The null model analysis indicated that homogeneous selection belonging to deterministic processes governed the sorghum rhizosphere community, whereas dispersal limitation belonging to stochastic processes was the critical assembly process in the foxtail and proso millet. Mean annual temperature was the decisive factor for adjusting the balance between stochasticity and determinism of the foxtail millet, proso millet, and sorghum rhizosphere communities. A higher temperature resulted in stochasticity in the proso millet and sorghum communities. For the foxtail millet community, the deterministic assembly increased with an increase in temperature. These results contribute to the understanding of root-associated bacterial community assembly processes in agro-ecosystems on a large scale.

scholarly journals Hyperlocal Variation in Soil Iron and Rhizosphere Microbiome Determines Disease Development in Amenity Turfgrass

2020 ◽  
Author(s):  
Ming-Yi Chou ◽  
Smita Shrestha ◽  
Renee Rioux ◽  
Paul Koch
Keyword(s):  
Soil Properties ◽  
Bulk Soil ◽  
Controlled Environment ◽  
Rrna Gene ◽  
Disease Development ◽  
Dollar Spot ◽  
Rhizosphere Microbiome ◽  
Environment Chamber ◽  
Plant Pathosystems ◽  
Important Disease

ABSTRACTDollar spot, caused by the fungal pathogen Clarireedia spp., is an economically important disease of amenity turfgrass in temperate climates worldwide. This disease often occurs in a highly variable manner, even on a local scale with relatively uniform environmental conditions. The objective of this study was to investigate mechanisms behind this local variation, focusing on contributions of the soil and rhizosphere microbiome. Turfgrass, rhizosphere, and bulk soil samples were taken from within a 256 m2 area of healthy turfgrass, transported to a controlled environment chamber, and inoculated with C. jacksonii. Bacterial communities were profiled targeting the 16s rRNA gene, and 16 different soil chemical properties were assessed. Despite their initial uniform appearance, the samples differentiated into highly susceptible and moderately susceptible groups following inoculation in the controlled environment chamber. The highly susceptible samples harbored a unique rhizosphere microbiome with lower relative abundance of antibiotic-producing bacterial taxa and higher predicted abundance of genes associated with xenobiotic biodegradation pathways. In addition, stepwise regression revealed that bulk soil iron content was the only significant soil characteristic that positively regressed with decreased dollar spot susceptibility during the peak disease development stage. These findings suggest that localized variation in soil iron induces the plant to select for a particular rhizosphere microbiome that alters the disease outcome. More broadly, further research in this area may indicate how plot-scale variability in soil properties can drive variable plant disease development through alterations in the rhizosphere microbiome.IMPORTANCEDollar spot is the most economically important disease of amenity turfgrass, and more fungicides are applied targeting dollar spot than any other turfgrass disease. Dollar spot symptoms are small (3-5 cm), circular patches that develop in a highly variable manner within plot-scale even under seemingly uniform conditions. The mechanism behind this variable development is unknown. This study observed that differences in dollar spot development over a 256 m2 area were associated with differences in bulk soil iron concentration and correlated with a particular rhizosphere microbiome. These findings provide important clues for understanding the mechanisms behind the highly variable development of dollar spot, which may offer important clues for innovative control strategies. Additionally, these results also suggest that small changes in soil properties can alter plant activity and hence the plant-associated microbial community which has important implications for a broad array of important agricultural and horticultural plant pathosystems.

scholarly journals Homogenization of Rhizosphere Bacterial Communities by Pea (Pisum sativum L.) Cultivated under Different Conservation Agricultural Practices in the Eastern Himalayas

2019 ◽  
Author(s):  
Diptaraj Chaudhari ◽  
Krishnappa Rangappa ◽  
Anup Das ◽  
Jayanta Layek ◽  
Savita Basavaraju ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Management Practices ◽  
Soil Health ◽  
Agricultural Practices ◽  
Amplicon Sequencing ◽  
Soil Samples ◽  
Residue Management ◽  
Bulk Soil ◽  
Rrna Gene ◽  
North East

AbstractConservation agriculture offers a suitable system to harmonize agriculture with the environment, especially in fragile ecosystems of North-East India. Soil microbes play pivotal roles in ecosystem functioning and act as indispensable indicators of overall fitness of crop plant and soil health. Here we demonstrated that altercations in residue management and tillage practices lead to the development of differential bacterial communities forcing the pea plants to recruit special groups of bacteria leading to highly homogenous rhizosphere communities. Pea rhizosphere and bulk soil samples were collected, and bacterial community structure was estimated by 16S rRNA gene amplicon sequencing and predictive functional analysis was performed using Tax4Fun. The effect on pea plants was evident in the bacterial communities as the overall diversity of rhizosphere samples was significantly higher to that of bulk soil samples. Bacillus, Staphylococcus, Planomicrobium, Enterobacter, Arthrobacter, Nitrobacter, Geobacter, and Sphingomonas were noticed as the most abundant genera in the rhizosphere and bulk soil samples. The abundance of Firmicutes and Proteobacteria altered significantly in the rhizosphere and bulk samples, which was further validated by qPCR. Selection of specific taxa by pea plant was indicated by the higher values of mean proportion of Rhizobium, Pseudomonas, Pantoea, Nitrobacter, Enterobacter and Sphingomonas in rhizosphere samples, and Massilia, Paenibacillus and Planomicrobium in bulk soil samples. Tillage and residue management treatments did not significantly alter the bacterial diversity, while their influence was observed on the abundance of few genera. Recorded results revealed that pea plant selects specific taxa into its rhizosphere plausibly to meet its requirements for nutrient uptake and stress amelioration under the different tillage and residue management practices.

scholarly journals Changes in bulk soil affect the disease-suppressive rhizosphere microbiome against Fusarium wilt disease

2020 ◽  
Vol 7 (3) ◽  
pp. 307
Author(s):  
Lin FU ◽  
Wu XIONG ◽  
Francisco DINI-ANDREOTE ◽  
Beibei WANG ◽  
Chengyuan TAO ◽  
...  
Keyword(s):  
Fusarium Wilt ◽  
Wilt Disease ◽  
Bulk Soil ◽  
Rhizosphere Microbiome ◽  
Fusarium Wilt Disease

Bacterial communities on food court tables and cleaning equipment in a shopping mall

2012 ◽  
Vol 141 (8) ◽  
pp. 1647-1651 ◽  
Author(s):  
S. DINGSDAG ◽  
N. V. COLEMAN
Keyword(s):  
Bacterial Communities ◽  
Shopping Mall ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Cross Contamination ◽  
Cleaning Equipment ◽  
Public Health Threat ◽  
Culture Independent ◽  
The Subject ◽  
Pathogenic Microbes

SUMMARYThe food court at a shopping mall is a potential transfer point for pathogenic microbes, but to date, this environment has not been the subject of detailed molecular microbiological study. We used a combination of culture-based and culture-independent approaches to investigate the types and numbers of bacteria present on food court tables, and on a food court cleaning cloth. Bacteria were found at 102–105 c.f.u./m2on food court tables and 1010 c.f.u./m2on the cleaning cloth. Tag-pyrosequencing of amplified 16S rRNA genes revealed that the dominant bacterial types on the cleaning cloth were genera known to include pathogenic species (Stenotrophomonas,Aeromonas), and that these genera were also evident at lower levels on table surfaces, suggesting possible cross-contamination. The evidence suggests a public health threat is posed by bacteria in the food court, and that this may be due to cross-contamination between cleaning equipment and table surfaces.

scholarly journals Comparison and interpretation of characteristics of Rhizosphere microbiomes of three blueberry varieties

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yan Zhang ◽  
Wei Wang ◽  
Zhangjun Shen ◽  
Jingjing Wang ◽  
Yajun Chen ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Rhizosphere Soil ◽  
Alpha Diversity ◽  
Distribution Patterns ◽  
Soil Samples ◽  
Bulk Soil ◽  
Core Microbiome ◽  
Rhizosphere Microbiome ◽  
Vital Functions

Abstract Background Studies on the rhizosphere microbiome of various plants proved that rhizosphere microbiota carries out various vital functions and can regulate the growth and improve the yield of plants. However, the rhizosphere microbiome of commercial blueberry was only reported by a few studies and remains elusive. Comparison and interpretation of the characteristics of the rhizosphere microbiome of blueberry are critical important to maintain its health. Results In this study, a total of 20 rhizosphere soil samples, including 15 rhizosphere soil samples from three different blueberry varieties and five bulk soil samples, were sequenced with a high-throughput sequencing strategy. Based on these sequencing datasets, we profiled the taxonomical, functional, and phenotypic compositions of rhizosphere microbial communities for three different blueberry varieties and compared our results with a previous study focused on the rhizosphere microbiome of blueberry varieties. Our results demonstrated significant differences in alpha diversity and beta diversity of rhizosphere microbial communities of different blueberry varieties and bulk soil. The distribution patterns of taxonomical, functional, and phenotypic compositions of rhizosphere microbiome differ across the blueberry varieties. The rhizosphere microbial communities of three different blueberry varieties could be distinctly separated, and 28 discriminative biomarkers were selected to distinguish these three blueberry varieties. Core rhizosphere microbiota for blueberry was identified, and it contained 201 OTUs, which were mainly affiliated with Proteobacteria, Actinobacteria, and Acidobacteria. Moreover, the interactions between OTUs of blueberry rhizosphere microbial communities were explored by a co-occurrence network of OTUs from an ecological perspective. Conclusions This pilot study explored the characteristics of blueberry’s rhizosphere microbial community, such as the beneficial microorganisms and core microbiome, and provided an integrative perspective on blueberry’s rhizosphere microbiome, which beneficial to blueberry health and production.

scholarly journals Colonization of Naive Roots from Populus tremula × alba Involves Successive Waves of Fungi and Bacteria with Different Trophic Abilities

2021 ◽  
Vol 87 (6) ◽  
Author(s):  
F. Fracchia ◽  
L. Mangeot-Peter ◽  
L. Jacquot ◽  
F. Martin ◽  
C. Veneault-Fourrey ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Laser Scanning Microscopy ◽  
Fungal Communities ◽  
Bulk Soil ◽  
Confocal Laser ◽  
Community Members ◽  
Root Microbiome ◽  
Over Time

ABSTRACT Through their roots, trees interact with a highly complex community of microorganisms belonging to various trophic guilds and contributing to tree nutrition, development, and protection against stresses. Tree roots select for specific microbial species from the bulk soil communities. The root microbiome formation is a dynamic process, but little is known on how the different microorganisms colonize the roots and how the selection occurs. To decipher whether the final composition of the root microbiome is the product of several waves of colonization by different guilds of microorganisms, we planted sterile rooted cuttings of gray poplar obtained from plantlets propagated in axenic conditions in natural poplar stand soil. We analyzed the root microbiome at different time points between 2 and 50 days of culture by combining high-throughput Illumina MiSeq sequencing of the fungal ribosomal DNA internal transcribed spacer and bacterial 16S rRNA amplicons with confocal laser scanning microscopy observations. The microbial colonization of poplar roots took place in three stages, but bacteria and fungi had different dynamics. Root bacterial communities were clearly different from those in the soil after 2 days of culture. In contrast, if fungi were also already colonizing roots after 2 days, the initial communities were very close to that in the soil and were dominated by saprotrophs. They were slowly replaced by endophytes and ectomycorhizal fungi. The replacement of the most abundant fungal and bacterial community members observed in poplar roots over time suggest potential competition effect between microorganisms and/or a selection by the host. IMPORTANCE The tree root microbiome is composed of a very diverse set of bacterial and fungal communities. These microorganisms have a profound impact on tree growth, development, and protection against different types of stress. They mainly originate from the bulk soil and colonize the root system, which provides a unique nutrient-rich environment for a diverse assemblage of microbial communities. In order to better understand how the tree root microbiome is shaped over time, we observed the composition of root-associated microbial communities of naive plantlets of poplar transferred in natural soil. The composition of the final root microbiome relies on a series of colonization stages characterized by the dominance of different fungal guilds and bacterial community members over time. Our observations suggest an early stabilization of bacterial communities, whereas fungal communities are established following a more gradual pattern.

scholarly journals Response of Root-Associated Bacterial Communities to Different Degrees of Soft Rot Damage in Amorphophallus konjac Under a Robinia pseudoacacia Plantation

2021 ◽  
Vol 12 ◽  
Author(s):  
Fei He
Keyword(s):  
Community Composition ◽  
Bacterial Communities ◽  
Disease Incidence ◽  
Robinia Pseudoacacia ◽  
Alpha Diversity ◽  
Soft Rot ◽  
Rrna Gene ◽  
Illumina Hiseq ◽  
Amorphophallus Konjac ◽  
Damage Degree

Bacterial soft rot is a destructive disease that restricts the development of the konjac (Amorphophallus konjac K. Koch ex N.E.Br) industry. The objective of this study was to investigate how soft rot disease affects bacterial communities associated with the roots of konjac plants growing under a pure Robinia pseudoacacia plantation. Three sampling sites affected by different degrees of soft rot damage were selected based on the disease incidence [0%, non-diseased (ND); 4.2%, moderately diseased (MD); and 18.6%, highly diseased (HD)]. The variation in soil and root bacterial diversity and community composition among the sampling sites was determined by Illumina HiSeq sequencing of the V3–V4 hypervariable regions of the bacterial 16S rRNA gene. The results showed that the contents of soil organic matter and available nutrients (N, P, and K) increased with increasing damage degree, whereas higher damage degree resulted in lower soil pH and enzymatic activity (sucrase, urease, catalase, and polyphenol oxidase). The composition of root-associated bacterial communities differed among the three sampling sites. Proteobacteria was the most dominant bacterial phylum in all soil and root samples. Pseudomonas, Bacillus, Rhizobium, and Streptomyces were the most abundant in all samples from the ND sites, whereas Pectobacterium carotovorum and Serratia were predominant in the samples from the MD and HD sites. The abundance and alpha diversity of root-associated bacteria were significantly higher (p < 0.05) in the ND sites than in the diseased sites. The results suggested pronounced differences in the abundance, alpha diversity, and community composition of bacteria associated with the roots of konjac plants affected by different degrees of soft rot damage. Such differences in bacterial community structure were related to dynamic changes in soil variables, especially soil available potassium content, sucrase activity, and urease activity. Analysis of the dominant root-associated bacterial taxa offers an approach to predict the damage degree due to soft rot in konjac and provides evidence for the prevention of this soil-borne disease via microecological regulation.

scholarly journals Deep-rooted plant species recruit distinct bacterial communities in 3 m deep subsoil

2021 ◽  
Author(s):  
Frederik Bak ◽  
Annemette Lyhne-Kjaerbye ◽  
Stacie Tardif ◽  
Dorte Bodin Dresboell ◽  
Mette Haubjerg Nicolaisen
Keyword(s):  
Plant Species ◽  
Bacterial Communities ◽  
Soil Bacteria ◽  
Climatic Changes ◽  
N Cycling ◽  
Bulk Soil ◽  
Rrna Gene ◽  
Carbon Supply ◽  
Gene Copies ◽  
Beneficial Traits

Deep-rooted plants can obtain water and nutrients from the subsurface, making them more resilient to climatic changes such as drought. In addition, the deeper root network also allow the plants to recruit bacteria from a larger reservoir in the soil. These bacteria might contribute to nutrient acquisition and provide other plant beneficial traits to the plant. However, the deep rhizosphere communities' compositions and their assembly dynamics are unknown. Here, we show, using three perennial crops, Kernza, lucerne and rosinweed, grown in 4 m RootTowers, that deep rhizosphere bacterial communities are plant specific, but clearly distinct from the shallow communities. We found that the diversity decreased with depth in the rhizosphere, whereas abundance of 16S rRNA gene copies did not change with depth in lucerne and rosinweed. Furthermore, we identified a subgroup (4-8%) of ASVs in the rhizosphere communities that could not be retrieved in the corresponding bulk soil communities. The abundances of genes determined by qPCR involved in N-cycling: amoA, nifH, nirK, nirS and nosZ differed significantly between plant species, suggesting differences in N content in the root exudates of the plant species. Our results suggest that colonization of the rhizosphere by bulk soil bacteria is not limited by carbon supply, but rather by dispersal. Furthermore, the abundance of N cycling genes indicate that deep rhizosphere bacteria have the potential to provide N through nitrogen fixation.

scholarly journals Maize residues changes soil fungal composition and decrease soil microbial co-ocurrence networks complexity

2019 ◽  
Author(s):  
José F. Cobo-Díaz ◽  
Fabienne Legrand ◽  
Gaétan Le Floch ◽  
Adeline Picot
Keyword(s):  
Bacterial Communities ◽  
Environmental Samples ◽  
Crop Residues ◽  
Disease Incidence ◽  
Soil Microbial ◽  
Rotation System ◽  
Previous Crop ◽  
Maize Residues ◽  
Mesocosm Experiments ◽  
Lower Complexity

ABSTRACTFusarium graminearum (Fg) can cause different diseases in cereals and maize crops worldwide, and a correct management of previous crop residues could decrease disease incidence and/or severity. Bacterial, fungal and Fusarium communities were studied by metabarcoding approach in 8 agricultural fields with wheat-maize rotation system in Brittany, France, during three years. Additionally, shift in microbial communities were evaluated under mesocosm experiments in soils amended or not with maize residues and/or Fg isolate. Bacterial communities composition were highly influenced by crop soil origin in both environmental and mesocosm soils, while bacteria co-occurrence network complexity was decreased by maize residues in environmental samples and Fg treatment in mesocosm samples. Maize residues altered slightly bacteria-fungi co-occurrence networks, while all treatments on mesoscosm experiments showed lower complexity in bacteria-fungi networks than Control Soil treatment. A clear input of fungal genera Epicoccum, Fusarium, Vishniacozyma, Articulospora, Papiliotrema, Sarocladium, Xenobotryosphaeria, Ramularia, Cladosporium, Cryptococcus and Bullera from maize residues to soil were observed for both environmental and mesocosm samples. Moreover, an increase of F. graminearum and F. avenaceum was observed in soils whe maize residues were presented. Finally, microbial co-occurrence networks reported some OTUs significant correlated to Fusarium spp. OTUs, such as those assigned to Epicoccum, Vishniacozyma and Sarocladium fungal genera, previously reported as efficient biocontrol agents versus Fusarium spp. Moreover, a decrease of complexity was observed for soil bacterial and bacterial-fungal networks due to maize addition in both environmental and mesocoms communities.

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