scholarly journals Influence of Forest Trees on the Distribution of Mineral Weathering-Associated Bacterial Communities of the Scleroderma citrinum Mycorrhizosphere

2010 ◽  
Vol 76 (14) ◽  
pp. 4780-4787 ◽  
Author(s):  
Christophe Calvaruso ◽  
Marie-Pierre Turpault ◽  
Elisabeth Leclerc ◽  
Jacques Ranger ◽  
Jean Garbaye ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Mycorrhizal Fungus ◽  
Mineral Weathering ◽  
Bulk Soil ◽  
Limiting Factor ◽  
Bacterial Isolates ◽  
Tree Roots ◽  
Nutrient Mobilization ◽  
Scleroderma Citrinum ◽  
Significant Enrichment

ABSTRACT In acidic forest soils, availability of inorganic nutrients is a tree-growth-limiting factor. A hypothesis to explain sustainable forest development proposes that tree roots select soil microbes involved in central biogeochemical processes, such as mineral weathering, that may contribute to nutrient mobilization and tree nutrition. Here we showed, by combining soil analyses with cultivation-dependent analyses of the culturable bacterial communities associated with the widespread mycorrhizal fungus Scleroderma citrinum, a significant enrichment of bacterial isolates with efficient mineral weathering potentials around the oak and beech mycorrhizal roots compared to bulk soil. Such a difference did not exist in the rhizosphere of Norway spruce. The mineral weathering ability of the bacterial isolates was assessed using a microplaque assay that measures the pH and the amount of iron released from biotite. Using this microplate assay, we demonstrated that the bacterial isolates harboring the most efficient mineral weathering potential belonged to the Burkholderia genus. Notably, previous work revealed that oak and beech harbored very similar pHs in the 5- to 10-cm horizon in both rhizosphere and bulk soil environments. In the spruce rhizosphere, in contrast, the pH was significantly lower than that in bulk soil. Because the production of protons is one of the main mechanisms responsible for mineral weathering, our results suggest that certain tree species have developed indirect strategies for mineral weathering in nutrient-poor soils, which lie in the selection of bacterial communities with efficient mineral weathering potentials.

scholarly journals Effect of the Mycorrhizosphere on the Genotypic and Metabolic Diversity of the Bacterial Communities Involved in Mineral Weathering in a Forest Soil

2007 ◽  
Vol 73 (9) ◽  
pp. 3019-3027 ◽  
Author(s):  
S. Uroz ◽  
C. Calvaruso ◽  
M. P. Turpault ◽  
J. C. Pierrat ◽  
C. Mustin ◽  
...  
Keyword(s):  
Carbon Metabolism ◽  
Mycorrhizal Fungi ◽  
Bacterial Species ◽  
Mineral Weathering ◽  
Bulk Soil ◽  
Rrna Gene ◽  
Bacterial Isolates ◽  
Bacterial Strains ◽  
Gene Sequence Analysis ◽  
Scleroderma Citrinum

ABSTRACT To date, several bacterial species have been described as mineral-weathering agents which improve plant nutrition and growth. However, the possible relationships between mineral-weathering potential, taxonomic identity, and metabolic ability have not been investigated thus far. In this study, we characterized a collection of 61 bacterial strains isolated from Scleroderma citrinum mycorrhizae, the mycorrhizosphere, and the adjacent bulk soil in an oak forest. The ability of bacteria to weather biotite was assessed with a new microplate bioassay that measures the pH and the quantity of iron released from this mineral. We showed that weathering bacteria occurred more frequently in the vicinity of S. citrinum than in the bulk soil. Moreover, the weathering efficacy of the mycorrhizosphere bacterial isolates was significantly greater than that of the bulk soil isolates. All the bacterial isolates were identified by partial 16S rRNA gene sequence analysis as members of the genera Burkholderia, Collimonas, Pseudomonas, and Sphingomonas, and their carbon metabolism was characterized by the BIOLOG method. The most efficient isolates belonged to the genera Burkholderia and Collimonas. Multivariate analysis resulted in identification of three metabolic groups, one of which contained mainly bacterial isolates associated with S. citrinum and exhibiting high mineral-weathering potential. Therefore, our results support the hypothesis that by its carbon metabolism this fungus selects in the bulk soil reservoir a bacterial community with high weathering potential, and they also address the question of functional complementation between mycorrhizal fungi and bacteria in the ectomycorrhizal complex for the promotion of tree nutrition.

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.

Isolation and characterization of bacteria from the rhizosphere and bulk soil of Stellera chamaejasme L.

2015 ◽  
Vol 61 (3) ◽  
pp. 171-181 ◽  
Author(s):  
Haiyan Cui ◽  
Xiaoyan Yang ◽  
Dengxue Lu ◽  
Hui Jin ◽  
Zhiqiang Yan ◽  
...  
Keyword(s):  
Bulk Soil ◽  
Growth Stages ◽  
Bacterial Isolates ◽  
Phenotypic Properties ◽  
Isolation And Characterization ◽  
Fruiting Stage ◽  
Major Shift ◽  
Stellera Chamaejasme ◽  
Bacterial Groups

This study is the first to describe the composition and characteristics of culturable bacterial isolates from the rhizosphere and bulk soil of the medicinal plant Stellera chamaejasme L. at different growth stages. Using a cultivation-dependent approach, a total of 148 isolates showing different phenotypic properties were obtained from the rhizosphere and bulk soil. Firmicutes and Actinobacteria were the major bacterial groups in both the rhizosphere and bulk soil at all 4 growth stages of S. chamaejasme. The diversity of the bacterial community in the rhizosphere was higher than that in bulk soil in flowering and fruiting stages. The abundance of bacterial communities in the rhizosphere changed with the growth stages and had a major shift at the fruiting stage. Dynamic changes of bacterial abundance and many bacterial groups in the rhizosphere were similar to those in bulk soil. Furthermore, most bacterial isolates exhibited single or multiple biochemical activities associated with S. chamaejasme growth, which revealed that bacteria with multiple physiological functions were abundant and widespread in the rhizosphere and bulk soil. These results are essential (i) for understanding the ecological roles of bacteria in the rhizosphere and bulk soil and (ii) as a foundation for further evaluating their efficacy as effective S. chamaejasme growth-promoting rhizobacteria.

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 Cultivable Bacterial Communities in Brines from Perennially Ice-Covered and Pristine Antarctic Lakes: Ecological and Biotechnological Implications

2020 ◽  
Vol 8 (6) ◽  
pp. 819 ◽  
Author(s):  
Carmen Rizzo ◽  
Antonella Conte ◽  
Maurizio Azzaro ◽  
Maria Papale ◽  
Alessandro C. Rappazzo ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Extracellular Polymeric Substances ◽  
Rrna Gene ◽  
Bacterial Isolates ◽  
Antarctic Lakes ◽  
Bacterial Response ◽  
Victoria Land ◽  
Boulder Clay ◽  
Aliphatic And Aromatic Hydrocarbons ◽  
Sequence Similarities

The diversity and biotechnological potentialities of bacterial isolates from brines of three Antarctic lakes of the Northern Victoria Land (namely Boulder Clay and Tarn Flat areas) were first explored. Cultivable bacterial communities were analysed mainly in terms of bacterial response to contaminants (i.e., antibiotics and heavy metals) and oxidation of contaminants (i.e., aliphatic and aromatic hydrocarbons and polychlorobiphenyls). Moreover, the biosynthesis of biomolecules (antibiotics, extracellular polymeric substances and enzymes) with applications for human health and environmental protection was assayed. A total of 74 and 141 isolates were retrieved from Boulder Clay and Tarn Flat brines, respectively. Based on 16S rRNA gene sequence similarities, bacterial isolates represented three phyla, namely Proteobacteria (i.e., Gamma- and Alphaproteobacteria), Bacteroidetes and Actinobacteria, with differences encountered among brines. At genus level, Rhodobacter, Pseudomonas, Psychrobacter and Leifsonia members were dominant. Results obtained from this study on the physiological and enzymatic features of cold-adapted isolates from Antarctic lake brines provide interesting prospects for possible applications in the biotechnological field through future targeted surveys. Finally, findings on contaminant occurrence and bacterial response suggest that bacteria might be used as bioindicators for tracking human footprints in these remote polar areas.

scholarly journals Mineral Types and Tree Species Determine the Functional and Taxonomic Structures of Forest Soil Bacterial Communities

2016 ◽  
Vol 83 (5) ◽  
Author(s):  
Y. Colin ◽  
O. Nicolitch ◽  
M.-P. Turpault ◽  
S. Uroz
Keyword(s):  
Nutrient Cycling ◽  
Incubation Period ◽  
Tree Species ◽  
Bacterial Communities ◽  
Forest Ecosystems ◽  
Mineral Weathering ◽  
Content Type ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
Mineral Type

ABSTRACT Although minerals represent important soil constituents, their impact on the diversity and structure of soil microbial communities remains poorly documented. In this study, pure mineral particles with various chemistries (i.e., obsidian, apatite, and calcite) were considered. Each mineral type was conditioned in mesh bags and incubated in soil below different tree stands (beech, coppice with standards, and Corsican pine) for 2.5 years to determine the relative impacts of mineralogy and mineral weatherability on the taxonomic and functional diversities of mineral-associated bacterial communities. After this incubation period, the minerals and the surrounding bulk soil were collected to determine mass loss and to perform soil analyses, enzymatic assays, and cultivation-dependent and -independent analyses. Notably, our 16S rRNA gene pyrosequencing analyses revealed that after the 2.5-year incubation period, the mineral-associated bacterial communities strongly differed from those of the surrounding bulk soil for all tree stands considered. When focusing only on minerals, our analyses showed that the bacterial communities associated with calcite, the less recalcitrant mineral type, significantly differed from those that colonized obsidian and apatite minerals. The cultivation-dependent analysis revealed significantly higher abundances of effective mineral-weathering bacteria on the most recalcitrant minerals (i.e., apatite and obsidian). Together, our data showed an enrichment of Betaproteobacteria and effective mineral-weathering bacteria related to the Burkholderia and Collimonas genera on the minerals, suggesting a key role for these taxa in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems. IMPORTANCE Forests are usually developed on nutrient-poor and rocky soils, while nutrient-rich soils have been dedicated to agriculture. In this context, nutrient recycling and nutrient access are key processes in such environments. Deciphering how soil mineralogy influences the diversity, structure, and function of soil bacterial communities in relation to the soil conditions is crucial to better understanding the relative role of the soil bacterial communities in nutrient cycling and plant nutrition in nutrient-poor environments. The present study determined in detail the diversity and structure of bacterial communities associated with different mineral types incubated for 2.5 years in the soil under different tree species using cultivation-dependent and -independent analyses. Our data showed an enrichment of specific bacterial taxa on the minerals, specifically on the most weathered minerals, suggesting that they play key roles in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems.

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 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 Bacterial biofilm production and water stress resistance by rhizobacteria associated to sugarcane (Saccharum officinarum) Linnaeus (POACEAE)

2021 ◽  
Vol 6 (2) ◽  
pp. 1899-1909
Author(s):  
Yamina Montaldo ◽  
Tania Marta Carvalho dos Santos ◽  
João Manoel da Silva ◽  
Crísea Cristina Nascimento de Cristo ◽  
Cícero Eduardo Ramalho Neto
Keyword(s):  
Water Stress ◽  
Water Activity ◽  
Culture Medium ◽  
Plant Protection ◽  
Bacterial Biofilm ◽  
Limiting Factor ◽  
Bacterial Isolates ◽  
Water Restriction ◽  
Production Ratio ◽  
Biofilm Production

ABSTRACT: The water restriction is a limiting factor in agricultural production. Some rhizobacteria, to live in symbiosis with the plant, can benefit plant growth. Among the skills of micro-organisms is the ability to survive in extreme environments, such as water stress, as well as having the biofilm production ability. The objective of this study was to evaluate the potential of four bacterial isolates from sugarcane rhizosphere as resistance to water restriction and biofilm production. A qualitative and other quantitative assay to produce biofilm was conducted. The qualitative assay was based on colorimetry with crystal violet. The qualitative test was developed by the violet colorimetric ratio of technical and optical density at 540 nm. Bacterial growth testing in low water activity was developed by inoculating the bacterial isolates in the TSA culture medium (10%) supplemented with sorbitol (405 gL-1) at 28 °C, yielding the corresponding Aw value 0.919. All strains were able to produce biofilms in both tests however isolated Bacillus subtilis was most effective, with the greatest biofilm production ratio. All isolates were also skilled in the growing culture medium with low water activity. KEYWORDS: plant protection, rhizobacteria, plant gowth promotion, symbiosis.

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