scholarly journals Inter-Kingdom Networks of Canola Microbiome Reveal Bradyrhizobium as Keystone Species and Underline the Importance of Bulk Soil in Microbial Studies to Enhance Canola Production.

2021 ◽  
Author(s):  
Jean-Baptiste Floc'h ◽  
Chantal Hamel ◽  
Mario Laterriere ◽  
Breanne Tidemann ◽  
Marc St-Arnaud ◽  
...  
Keyword(s):  
Microbial Community ◽  
Network Analysis ◽  
Hot Spots ◽  
Keystone Species ◽  
Cropping System ◽  
Bulk Soil ◽  
Canadian Prairies ◽  
Rotation System ◽  
Bradyrhizobium Sp ◽  
Microbial Environment

Abstract The subterranean microbiota of plants are of great importance for plant growth and health, as root-associated microbes can perform crucial ecological functions. As the microbial environment of roots is extremely diverse, identifying keystone microorganisms in plant roots, rhizosphere and bulk soil is a necessary step towards understanding the network of influence within the microbial community associated with roots and enhancing its beneficial elements. To target these hot spots of microbial interaction, we used inter-kingdom network analysis on the canola growth phase of a long-term cropping system diversification experiment conducted at four locations in the Canadian prairies. Our aims were: to verify whether bacterial and fungal communities of canola roots, rhizosphere and bulk soil are related and influenced by diversification of the crop rotation system; to determine whether there are common or specific core fungi and bacteria in the roots, rhizosphere, and bulk soil under canola grown in different environments and with different levels of cropping system diversification; and to identify hub taxa at the inter-kingdom level that could play an important ecological role in the microbiota of canola. Our results showed that fungi were influenced by crop diversification but not by bacteria. We found no core microbiota in canola roots but identified three core fungi in the rhizosphere, one core mycobiota in the bulk soil and one core bacteria shared by the rhizosphere and bulk soil. We identified two bacterial and one fungal hub taxa in the inter-kingdom networks of the canola rhizosphere, and one bacterial and two fungal hub taxa in the bulk soil. Among these inter-kingdom hub taxa, Bradyrhizobium sp. and Mortierella sp. are particularly influential on the microbial community and the plant. To our knowledge, this is the first inter-kingdom network analysis utilized to identify hot spots of interaction in canola microbial communities.

Microbial community structure and abundance in the rhizosphere and bulk soil of a tomato cropping system that includes cover crops

2014 ◽  
Vol 77 ◽  
pp. 42-50 ◽  
Author(s):  
Jude E. Maul ◽  
Jeffrey S. Buyer ◽  
R. Michael Lehman ◽  
Steve Culman ◽  
Christopher B. Blackwood ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Cover Crops ◽  
Cropping System ◽  
Bulk Soil

Diversity of Root Bacteria from Peanut Cropping Systems

2004 ◽  
Vol 31 (2) ◽  
pp. 86-91 ◽  
Author(s):  
D. T. Gooden ◽  
H. D. Skipper ◽  
J. H. Kim ◽  
K. Xiong
Keyword(s):  
Fatty Acids ◽  
Biological Control ◽  
Gas Chromatography ◽  
Cropping Systems ◽  
Cropping System ◽  
Critical Research ◽  
Chromatography Analysis ◽  
Rotation System ◽  
Gas Chromatography Analysis ◽  
Peanut Production

Abstract Rhizobacteria play an important role in sustainable agriculture via plant growth and biological control of pests in a number of ecosystems. Understanding the interactions of crop rotation and rhizobacteria on peanut production is a critical research need. Development of a database on the rhizobacteria obtained from continuous and rotational fields of peanut was initiated in 1997 and terminated in 2000. Peanut was planted in monoculture for 4 yr. In rotational plots, peanut, cotton, corn, and peanut were planted in sequence. Rhizobacteria were isolated from the roots of crop plants grown in a Norfolk soil near Florence, SC. These isolates were identified by composition of fatty acids from gas chromatography analysis (GC/FAME). Arthrobacter and Bacillus were the major genera from non-rhizosphere soils. At initiation of this study in July 1997, the plots selected for continuous peanut had more diversity in rhizobacteria than those plots selected for rotation. In July 2000, rhizobacteria diversity was greater from peanut roots in the rotation cropping system than continuous peanut. Even though rhizobacteria diversity was greater in the rotation system, higher peanut yields were recorded in the continuous peanut system in 2000. Burkholderia spp. were always isolated from the peanut and other crop rhizospheres at each sampling date.

scholarly journals Changes in Microbial Community Composition and Function during a Polyaromatic Hydrocarbon Phytoremediation Field Trial

2003 ◽  
Vol 69 (1) ◽  
pp. 483-489 ◽  
Author(s):  
Steven D. Siciliano ◽  
James J. Germida ◽  
Kathy Banks ◽  
Charles W. Greer
Keyword(s):  
Microbial Community ◽  
Festuca Arundinacea ◽  
Rhizosphere Soil ◽  
Microbial Community Composition ◽  
Hydrocarbon Degradation ◽  
Bulk Soil ◽  
Catabolic Gene ◽  
Soil Microbial ◽  
Catabolic Genes ◽  
And Function

ABSTRACT The purpose of this study was to investigate the mechanism by which phytoremediation systems promote hydrocarbon degradation in soil. The composition and degradation capacity of the bulk soil microbial community during the phytoremediation of soil contaminated with aged hydrocarbons was assessed. In the bulk soil, the level of catabolic genes involved in hydrocarbon degradation (ndoB, alkB, and xylE) as well as the mineralization of hexadecane and phenanthrene was higher in planted treatment cells than in treatment cells with no plants. There was no detectable shift in the 16S ribosomal DNA (rDNA) composition of the bulk soil community between treatments, but there were plant-specific and -selective effects on specific catabolic gene prevalence. Tall Fescue (Festuca arundinacea) increased the prevalence of ndoB, alkB, and xylE as well as naphthalene mineralization in rhizosphere soil compared to that in bulk soil. In contrast, Rose Clover (Trifolium hirtum) decreased catabolic gene prevalence and naphthalene mineralization in rhizosphere soil. The results demonstrated that phytoremediation systems increase the catabolic potential of rhizosphere soil by altering the functional composition of the microbial community. This change in composition was not detectable by 16S rDNA but was linked to specific functional genotypes with relevance to petroleum hydrocarbon degradation.

scholarly journals Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic Management

2021 ◽  
Vol 12 ◽  
Author(s):  
Ahmad Nuruddin Khoiri ◽  
Supapon Cheevadhanarak ◽  
Jiraporn Jirakkakul ◽  
Sudarat Dulsawat ◽  
Peerada Prommeenate ◽  
...  
Keyword(s):  
Microbial Community ◽  
Organic Farming ◽  
Keystone Species ◽  
Taxonomic Diversity ◽  
Plant Growth Promoting Bacteria ◽  
Shotgun Metagenomics ◽  
Mesorhizobium Loti ◽  
Metagenome Analysis ◽  
Microbial Network ◽  
Plant Growth Promoting

Converting conventional farms to organic systems to improve ecosystem health is an emerging trend in recent decades, yet little is explored to what extent and how this process drives the taxonomic diversity and functional capacity of above-ground microbes. This study was, therefore, conducted to investigate the effects of agricultural management, i.e., organic, transition, and conventional, on the structure and function of sugarcane phyllosphere microbial community using the shotgun metagenomics approach. Comparative metagenome analysis exhibited that farming practices strongly influenced taxonomic and functional diversities, as well as co-occurrence interactions of phyllosphere microbes. A complex microbial network with the highest connectivity was observed in organic farming, indicating strong resilient capabilities of its microbial community to cope with the dynamic environmental stressors. Organic farming also harbored genus Streptomyces as the potential keystone species and plant growth-promoting bacteria as microbial signatures, including Mesorhizobium loti, Bradyrhizobium sp. SG09, Lactobacillus plantarum, and Bacillus cellulosilyticus. Interestingly, numerous toxic compound-degrading species were specifically enriched in transition farming, which might suggest their essential roles in the transformation of conventional to organic farming. Moreover, conventional practice diminished the abundance of genes related to cell motility and energy metabolism of phyllosphere microbes, which could negatively contribute to lower microbial diversity in this habitat. Altogether, our results demonstrated the response of sugarcane-associated phyllosphere microbiota to specific agricultural managements that played vital roles in sustainable sugarcane production.

scholarly journals Chemical composition of soil organic carbon changed by long-term monoculture cropping system in Chinese black soil

2018 ◽  
Vol 64 (No. 11) ◽  
pp. 557-563 ◽  
Author(s):  
Yunfa Qiao ◽  
Shujie Miao ◽  
Yingxue Li ◽  
Xin Zhong
Keyword(s):  
Chemical Composition ◽  
Organic Carbon ◽  
Soil Organic Carbon ◽  
Relative Proportion ◽  
Cropping System ◽  
Black Soil ◽  
Chemical Compositions ◽  
Crop Species ◽  
Rotation System

Monoculture is common to meet commodity grain requirements in Northeast China. The effect of long-term monoculture on chemical composition of soil organic carbon (SOC) remains unclear. This study was done to evaluate how changes in chemical compositions of SOC responded to long-term monoculture. To achieve this objective, the chemical compositions of SOC in maize-soybean rotation, continuous soybean and continuous maize were characterized with the nuclear magnetic resonance technique. Two main components, O-alkyl and aromatic C, showed a wider range of relative proportion in monoculture than rotation system across soil profiles, but no difference was observed between two monoculture systems. Pearson’s analysis showed a significant relationship between plant-C and OCH<sub>3</sub>/NCH, alkyl C or alkyl O-C-O, and the A/O-A was closely related to plant-C. The findings indicated a greater influence of monoculture on the chemical composition of SOC compared to rotation, but lower response to crop species.

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