scholarly journals Dynamics ofPanax ginsengRhizospheric Soil Microbial Community and Their Metabolic Function

2014 ◽  
Vol 2014 ◽  
pp. 1-6 ◽  
Author(s):  
Yong Li ◽  
YiXin Ying ◽  
WanLong Ding
Keyword(s):  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Restriction Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Plant Growth Promoting Bacteria ◽  
Metabolic Function ◽  
Rhizosphere Soils ◽  
Soil Microbial ◽  
Culture Independent ◽  
Plant Growth Promoting

The bacterial communities of 1- to 6-year ginseng rhizosphere soils were characterized by culture-independent approaches, random amplified polymorphic DNA (RAPD), and amplified ribosomal DNA restriction analysis (ARDRA). Culture-dependent method (Biolog) was used to investigate the metabolic function variance of microbe living in rhizosphere soil. Results showed that significant genetic and metabolic function variance were detected among soils, and, with the increasing of cultivating years, genetic diversity of bacterial communities in ginseng rhizosphere soil tended to be decreased. Also we found thatVerrucomicrobia,Acidobacteria, andProteobacteriawere the dominants in rhizosphere soils, but, with the increasing of cultivating years, plant disease prevention or plant growth promoting bacteria, such asPseudomonas,Burkholderia, andBacillus, tended to be rare.

scholarly journals A Degeneration Gradient of Poplar Trees Contributes to the Taxonomic, Functional, and Resistome Diversity of Bacterial Communities in Rhizosphere Soils

2021 ◽  
Vol 22 (7) ◽  
pp. 3438
Author(s):  
Juan Liu ◽  
Xiangwei He ◽  
Jingya Sun ◽  
Yuchao Ma
Keyword(s):  
Soil Fertility ◽  
Microbial Diversity ◽  
Resistance Genes ◽  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Antibiotics Resistance ◽  
Plant Growth Promoting Bacteria ◽  
Soil Microbial Diversity ◽  
Antibiotic Target ◽  
And Function

Bacterial communities associated with roots influence the health and nutrition of the host plant. However, the microbiome discrepancy are not well understood under different healthy conditions. Here, we tested the hypothesis that rhizosphere soil microbial diversity and function varies along a degeneration gradient of poplar, with a focus on plant growth promoting bacteria (PGPB) and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG (antibiotics resistance genes) annotation revealed that available potassium (AK) was correlated with microbial diversity and function. We proposed several microbes, Bradyrhizobium, Sphingomonas, Mesorhizobium, Nocardioides, Variovorax, Gemmatimonadetes, Rhizobacter, Pedosphaera, Candidatus Solibacter, Acidobacterium, and Phenylobacterium, as candidates to reflect the soil fertility and the plant health. The highest abundance of multidrug resistance genes and the four mainly microbial resistance mechanisms (antibiotic efflux, antibiotic target protection, antibiotic target alteration, and antibiotic target replacement) in healthy poplar rhizosphere, corroborated the relationship between soil fertility and microbial activity. This result suggested that healthy rhizosphere soil harbored microbes with a higher capacity and had more complex microbial interaction network to promote plant growing and reduce intracellular levels of antibiotics. Our findings suggested a correlation between the plant degeneration gradient and bacterial communities, and provided insight into the role of high-turnover microbial communities as well as potential PGPB as real-time indicators of forestry soil quality, and demonstrated the inner interaction contributed by the bacterial communities.

Community dynamics of duckweed-associated bacteria upon inoculation of plant growth-promoting bacteria

2020 ◽  
Vol 96 (7) ◽  
Author(s):  
Hidehiro Ishizawa ◽  
Masashi Kuroda ◽  
Daisuke Inoue ◽  
Masaaki Morikawa ◽  
Michihiko Ike
Keyword(s):  
Plant Growth ◽  
Bacterial Communities ◽  
Production Efficiency ◽  
Community Dynamics ◽  
Amplicon Sequencing ◽  
Plant Colonization ◽  
Plant Growth Promoting Bacteria ◽  
Short Period ◽  
Plant Growth Promoting ◽  
Growth Promoting

ABSTRACT Plant growth-promoting bacteria (PGPB) have recently been demonstrated as a promising agent to improve wastewater treatment and biomass production efficiency of duckweed hydrocultures. With a view to their reliable use in aqueous environments, this study analysed the plant colonization dynamics of PGPB and the ecological consequences for the entire duckweed-associated bacterial community. A PGPB strain, Aquitalea magnusonii H3, was inoculated to duckweed at different cell densities or timings in the presence of three environmental bacterial communities. The results showed that strain H3 improved duckweed growth by 11.7–32.1% in five out of nine experiments. Quantitative-PCR and amplicon sequencing analyses showed that strain H3 successfully colonized duckweed after 1 and 3 d of inoculation in all cultivation tests. However, it significantly decreased in number after 7 d, and similar bacterial communities were observed on duckweed regardless of H3 inoculation. Predicted metagenome analysis suggested that genes related to bacterial chemotactic motility and surface attachment systems are consistently enriched through community assembly on duckweed. Taken together, strain H3 dominantly colonized duckweed for a short period and improved duckweed growth. However, the inoculation of the PGPB did not have a lasting impact due to the strong resilience of the natural duckweed microbiome.

scholarly journals Effects of the Biofertilizer OYK (Bacillus sp.) Inoculation on Endophytic Microbial Community in Sweet Potato

Horticulturae ◽  
2020 ◽  
Vol 6 (4) ◽  
pp. 81
Author(s):  
Ahsanul Salehin ◽  
Md Hafizur Rahman Hafiz ◽  
Shohei Hayashi ◽  
Fumihiko Adachi ◽  
Kazuhito Itoh
Keyword(s):  
Plant Growth ◽  
Sweet Potato ◽  
Bacterial Communities ◽  
Ipomoea Batatas ◽  
Diversity Index ◽  
Plant Growth Promoting Bacteria ◽  
Bacillus Sp ◽  
Bacterial Composition ◽  
Plant Growth Promoting ◽  
Growth Promoting

Sweet potato (Ipomoea batatas L.) grows well even in infertile and nitrogen-limited fields, and endophytic bacterial communities have been proposed to be responsible for this ability. Plant-growth-promoting bacteria are considered eco-friendly and are used in agriculture, but their application can interact with endophytic communities in many ways. In this study, a commercial biofertilizer, OYK, consisting of a Bacillus sp., was applied to two cultivars of sweet potato, and the effects on indigenous endophytic bacterial communities in field conditions were examined. A total of 101 bacteria belonging to 25 genera in 9 classes were isolated. Although the inoculated OYK was not detected and significant plant-growth-promoting effects were not observed, the inoculation changed the endophytic bacterial composition, and the changes differed between the cultivars, as follows: Novosphingobium in α-Proteobacteria was dominant; it remained dominant in Beniharuka after the inoculation of OYK, while it disappeared in Beniazuma, with an increase in Sphingomonas and Sphingobium in α-Proteobacteria as well as Chryseobacterium and Acinetobacter in Flavobacteria. The behavior of Bacilli and Actinobacteria also differed between the cultivars. The Shannon diversity index (H) increased after inoculation in all conditions, and the values were similar between the cultivars. Competition of the inoculant with indigenous rhizobacteria and endophytes may determine the fates of the inoculant and the endophytic community.

scholarly journals Effect of Bacillus mesonae H20-5 Treatment on Rhizospheric Bacterial Community of Tomato Plants under Salinity Stress

2021 ◽  
Vol 37 (6) ◽  
pp. 662-672
Author(s):  
Shin Ae Lee ◽  
Hyeon Su Kim ◽  
Mee Kyung Sang ◽  
Jaekyeong Song ◽  
Hang-Yeon Weon
Keyword(s):  
Bacterial Community ◽  
Plant Growth ◽  
Soil Salinity ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Plant Growth Promoting Bacteria ◽  
Tomato Plants ◽  
Rhizosphere Soils ◽  
Salinity Levels

Plant growth-promoting bacteria improve plant growth under abiotic stress conditions. However, their effects on microbial succession in the rhizosphere are poorly understood. In this study, the inoculants of Bacillus mesonae strain H20-5 were administered to tomato plants grown in soils with different salinity levels (EC of 2, 4, and 6 dS/m). The bacterial communities in the bulk and rhizosphere soils were examined 14 days after H20-5 treatment using Illumina MiSeq sequencing of the bacterial 16S rRNA gene. Although the abundance of H20-5 rapidly decreased in the bulk and rhizosphere soils, a shift in the bacterial community was observed following H20-5 treatment. The variation in bacterial communities due to H20-5 treatment was higher in the rhizosphere than in the bulk soils. Additionally, the bacterial species richness and diversity were greater in the H20-5 treated rhizosphere than in the control. The composition and structure of the bacterial communities varied with soil salinity levels, and those in the H20-5 treated rhizosphere soil were clustered. The members of Actinobacteria genera, including Kineosporia, Virgisporangium, Actinoplanes, Gaiella, Blastococcus, and Solirubrobacter, were enriched in the H20-5 treated rhizosphere soils. The microbial co-occurrence network of the bacterial community in the H20-5 treated rhizosphere soils had more modules and keystone taxa compared to the control. These findings revealed that the strain H20-5 induced systemic tolerance in tomato plants and influenced the diversity, composition, structure, and network of bacterial communities. The bacterial community in the H20-5 treated rhizosphere soils also appeared to be relatively stable to soil salinity changes.

scholarly journals Activation of the SA-Associated Plant Defense Pathway Alters the Composition of Soil Bacterial Communities

2021 ◽  
Author(s):  
Jing Zhang ◽  
Peter G.L. Klinkhamer ◽  
Klaas Vrieling ◽  
T. Martijn Bezemer
Keyword(s):  
Plant Growth ◽  
Microbial Communities ◽  
Signaling Pathway ◽  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Soil Microbial Communities ◽  
Core Microbiome ◽  
Soil Microbial ◽  
Soil Bacterial ◽  
Sa Signaling

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.

scholarly journals The Soil Microbiome Influences Grapevine-Associated Microbiota

mBio ◽  
2015 ◽  
Vol 6 (2) ◽  
Author(s):  
Iratxe Zarraonaindia ◽  
Sarah M. Owens ◽  
Pamela Weisenhorn ◽  
Kristin West ◽  
Jarrad Hampton-Marcell ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Management Practices ◽  
Temporal Dynamics ◽  
Spatial Scales ◽  
C:N Ratio ◽  
Soil Microbiome ◽  
Plant Growth Promoting Bacteria ◽  
Organoleptic Properties ◽  
Associated Bacteria ◽  
Plant Growth Promoting

ABSTRACTGrapevine is a well-studied, economically relevant crop, whose associated bacteria could influence its organoleptic properties. In this study, the spatial and temporal dynamics of the bacterial communities associated with grapevine organs (leaves, flowers, grapes, and roots) and soils were characterized over two growing seasons to determine the influence of vine cultivar, edaphic parameters, vine developmental stage (dormancy, flowering, preharvest), and vineyard. Belowground bacterial communities differed significantly from those aboveground, and yet the communities associated with leaves, flowers, and grapes shared a greater proportion of taxa with soil communities than with each other, suggesting that soil may serve as a bacterial reservoir. A subset of soil microorganisms, including root colonizers significantly enriched in plant growth-promoting bacteria and related functional genes, were selected by the grapevine. In addition to plant selective pressure, the structure of soil and root microbiota was significantly influenced by soil pH and C:N ratio, and changes in leaf- and grape-associated microbiota were correlated with soil carbon and showed interannual variation even at small spatial scales. Diazotrophic bacteria, e.g.,Rhizobiaceaeand Bradyrhizobium spp., were significantly more abundant in soil samples and root samples of specific vineyards. Vine-associated microbial assemblages were influenced by myriad factors that shape their composition and structure, but the majority of organ-associated taxa originated in the soil, and their distribution reflected the influence of highly localized biogeographic factors and vineyard management.IMPORTANCEVine-associated bacterial communities may play specific roles in the productivity and disease resistance of their host plant. Also, the bacterial communities on grapes have the potential to influence the organoleptic properties of the wine, contributing to a regional terroir. Understanding that factors that influence these bacteria may provide insights into management practices to shape and craft individual wine properties. We show that soil serves as a key source of vine-associated bacteria and that edaphic factors and vineyard-specific properties can influence the native grapevine microbiome preharvest.

scholarly journals POLYPHASIC CHARACTERIZATION OF Bacillus STRAINS ISOLATED FROM MAIZE

2020 ◽  
Vol 19 ◽  
pp. 18
Author(s):  
ELIANE APARECIDA GOMES ◽  
UBIRACI GOMES DE PAULA LANA ◽  
MARINA ELEUTÉRIO GÓI DE MORAES RODRIGUES ◽  
SYLVIA MORAIS DE SOUSA ◽  
CHRISTIANE ABREU DE OLIVEIRA ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Restriction Analysis ◽  
16S Rrna Gene Sequencing ◽  
Production Quality ◽  
Rrna Gene ◽  
Plant Growth Promoting Bacteria ◽  
Agricultural Practice ◽  
Production Quality Control ◽  
Plant Growth Promoting ◽  
Bacillus Strains

The use of bioinoculants with plant growth-promoting bacteria (PGPB) is a sustainable agricultural practice that has been expanding worldwide. Thus, it is fundamental to characterize these bacteria molecularly to provide better security and traceability for bioinoculants production. This work aimed to identify, characterize and develop specific molecular markers for Bacillus strains related to plant-growing promotion. Five strains were identified as B. pumillus (B32), B. thuringiensis (B116), B. megaterium (B119) and B. subitilis (B2082 and B2084) using 16S rRNA gene sequencing and MALDI-TOF mass spectrometry. Repetitive element palindromic (Rep-PCR) and amplified ribosomal DNA restriction analysis (ARDRA) techniques allowed the discrimination of the strains, except B2082 and B2084 that presented identical genetic profiles, indicating that they are same or genetically close isolates. Moreover, specific molecular markers were developed for B116 and B119 strains and may be used for microbial inoculants production quality control, strains traceability and to detail PGPB colonization.

scholarly journals Biological function of Klebsiella variicola and its effect on the rhizosphere soil of maize seedlings

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9894
Author(s):  
Lijuan Yang ◽  
Kejun Yang
Keyword(s):  
Biological Function ◽  
Rhizosphere Soil ◽  
Potassium Dichromate ◽  
Colorimetric Method ◽  
Soil Salinization ◽  
Available Phosphorus ◽  
Plant Growth Promoting Bacteria ◽  
Alkali Stress ◽  
Maize Seedlings ◽  
Plant Growth Promoting

Background Deterioration of the ecological environment in recent years has led to increasing soil salinization, which severely affects the cultivation of agricultural crops. While research has focused on improving soil environment through the application of pollution-free microbial fertilizers, there are relatively few plant growth-promoting bacteria suitable for saline-alkali environments. Although Klebsiella variicola can adapt to saline-alkali environments to successfully colonize rhizosphere microenvironments, only a few studies have investigated its role in promoting crop growth. Its effect on the crop rhizosphere soil microenvironment is especially unclear. Methods In this study, the biological function of K. variicola and its colonization in maize seedling rhizosphere soil were studied in detail through selective media and ultraviolet spectrophotometry. The effects of K. variicola on the rhizosphere soil microenvironment and the growth of maize seedlings in saline-alkali and neutral soils were systematically analysed using the colorimetric method, the potassium dichromate volumetric method, and the diffusion absorption method. Results Our results showed that K. variicola played a role in indole acetic acid, acetoin, ammonia, phosphorus, and potassium production, as well as in nitrogen fixation. A high level of colonization was observed in the rhizosphere soil of maize seedlings. Following the application of K. variicola in neutral and saline-alkali soils, the nutrient composition of rhizosphere soil of maize seedlings increased in varying degrees, more notably in saline-alkali soil. The content of organic matter, alkali-hydrolysable nitrogen, available phosphorus, available potassium, alkaline phosphatase, sucrase, urease, and catalase increased by 64.22%, 117.39%, 175.64%, 28.63%, 146.08%, 76.77%, 86.60%, and 45.29%, respectively, insaline-alkalisoil. Conclusion K.variicola, therefore, performed a variety of biological functions to promote the growth of maize seedlings and effectively improve the level of soil nutrients and enzymes in the rhizosphere of maize seedlings, undersaline-alkali stress conditions. It played an important role in enhancing the rhizosphere microenvironment of maize seedlings under saline-alkali stress.

scholarly journals The Nexus between Fire and Soil Bacterial Diversity in the African Miombo Woodlands of Niassa Special Reserve, Mozambique

2021 ◽  
Vol 9 (8) ◽  
pp. 1562
Author(s):  
Ivete Sandra Alberto Maquia ◽  
Paula Fareleira ◽  
Isabel Videira e. Castro ◽  
Ricardo Soares ◽  
Denise R. A. Brito ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Fire Regime ◽  
Molecular Taxonomy ◽  
Illumina Miseq ◽  
Plant Growth Promoting Bacteria ◽  
Miombo Woodlands ◽  
Soil Bacterial Diversity ◽  
Pgp Traits ◽  
Plant Growth Promoting ◽  
Ensifer Adhaerens

(1) Background: the Miombo woodlands comprise the most important vegetation from southern Africa and are dominated by tree legumes with an ecology highly driven by fires. Here, we report on the characterization of bacterial communities from the rhizosphere of Brachystegia boehmii in different soil types from areas subjected to different regimes. (2) Methods: bacterial communities were identified through Illumina MiSeq sequencing (16S rRNA). Vigna unguiculata was used as a trap to capture nitrogen-fixing bacteria and culture-dependent methods in selective media were used to isolate plant growth promoting bacteria (PGPB). PGP traits were analysed and molecular taxonomy of the purified isolates was performed. (3) Results: Bacterial communities in the Miombo rhizosphere are highly diverse and driven by soil type and fire regime. Independent of the soil or fire regime, the functional diversity was high, and the different consortia maintained the general functions. A diverse pool of diazotrophs was isolated, and included symbiotic (e.g., Mesorhizobium sp., Neorhizobium galegae, Rhizobium sp., and Ensifer adhaerens), and non-symbiotic (e.g., Agrobacterium sp., Burkholderia sp., Cohnella sp., Microvirga sp., Pseudomonas sp., and Stenotrophomonas sp.) bacteria. Several isolates presented cumulative PGP traits. (4) Conclusions: Although the dynamics of bacterial communities from the Miombo rhizosphere is driven by fire, the maintenance of high levels of diversity and functions remain unchanged, constituting a source of promising bacteria in terms of plant-beneficial activities such as mobilization and acquisition of nutrients, mitigation of abiotic stress, and modulation of plant hormone levels.

scholarly journals Effect of Native American Bean-corn Biculture Planting on Free-living Bacterial Abundance and Plant Growth

2015 ◽  
Vol 12 (4) ◽  
Author(s):  
Heather Miller ◽  
Justin Fiene ◽  
Tamara Marsh
Keyword(s):  
Native American ◽  
Plant Growth ◽  
Plant Biomass ◽  
Plant Growth Promoting Bacteria ◽  
Nitrogen Fixing ◽  
Nitrogen Fixing Bacteria ◽  
Free Living ◽  
Soil Microbial ◽  
Plant Growth Promoting ◽  
Native American Tribes

Native American tribes with bountiful harvests. Today it is widely recognized that this associated intercropping system derives much of its success from symbiotic bacteria (e.g. Rhizobium). These bacteria colonize the roots of leguminous plants, allowing them to fix atmospheric nitrogen into ammonia. However, the effect of this intercropping practice on the microbial community, independent of the effect of the symbiotic nitrogen-fixing bacteria, is not well understood. Therefore, a study was designed to model the effects of simultaneously intercropping bean and corn on the abundance of aerobic heterotrophic, free-living nitrogen-fixing, and symbiotic nitrogen-fixing bacteria, as well as plant growth and fecundity markers. In parallel, the benefits mediated by rhizobia were evaluated by inoculating a duplicate set of treatments with N-Dure, a rhizobia-containing inoculum. Native American varieties of pole-bean (Phaseolus vulgaris L.) and corn (Zea mays mays L.) were planted in monoculture and biculture treatments. All cultivations were maintained under greenhouse conditions for 52 days with daily watering and no additional fertilizer or microbial amendments. Although a significant increase in weight per plant was noted for the inoculated biculture when compared to either the inoculated bean or corn monocultures (p ≤ 0.05), the abundance of heterotrophic and free-living nitrogen-fixing bacteria did not show a significant change from the related controls, with or without inoculation. However, symbiotic nitrogen-fixing bacteria, as measured by root nodulation, increased significantly (p ≤ 0.05) for the inoculated biculture and single planting. Thus, these data confirm that corn benefited from this associated intercropping system as shown by an increase in plant biomass that can be attributed to Rhizobium. However, neither the legume-bacteria symbiotic relationship nor the increase in plant biodiversity resulting from this intercropping practice appears to have had significant effects on the abundance of the two common soil-associated bacterial groups evaluated, though further research would be necessary to fully assess the changes to heterotrophic bacterial diversity at the species level. KEYWORDS: Three Sisters; Nitrogen-fixing Bacteria; Inoculation with Rhizobia; Plant Growth Promoting Bacteria; Soil Microbial Biota; Corn and Bean Simultaneous Planting.

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