scholarly journals Microbial Diversity Associated with Odor Modification for Production of Fertilizers from Chicken Litter

2006 ◽  
Vol 72 (6) ◽  
pp. 4105-4114 ◽  
Author(s):  
Julie J. Enticknap ◽  
Hirofumi Nonogaki ◽  
Allen R. Place ◽  
Russell T. Hill
Keyword(s):  
Microbial Diversity ◽  
Agricultural Soil ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Viable Solution ◽  
Soil Actinomycetes ◽  
Chicken Litter ◽  
Gradient Gel Electrophoresis ◽  
Total Community ◽  
Processing Steps ◽  
Selection Of

ABSTRACT Litter from the chicken industry can present several environmental challenges, including offensive odors and runoff into waterways leading to eutrophication. An economically viable solution to the disposal of waste from chicken houses is treatment to produce a natural, granulated fertilizer that can be commercially marketed for garden and commercial use. Odor of the final product is important in consumer acceptance, and an earthy odor is desirable. By understanding and manipulating the microbial processes occurring during this process, it may be possible to modify the odors produced. Geosmin and related volatiles produced by soil actinomycetes are responsible for earthy odors, and actinomycetes are likely to be present in the composting manure. Bacterial communities at each stage of the process were analyzed by culturing studies and denaturing gradient gel electrophoresis (DGGE). The processing steps changed the culturable bacterial community, but the total community was shown by DGGE to be stable throughout the process. A local agricultural soil was analyzed in parallel as a potential source of geosmin-producing actinomycetes. This agricultural soil had higher microbial diversity than the compost at both the culturable and the molecular levels. Actinomycete bacteria were isolated and analyzed by AromaTrax, a gas chromatography-olfactometry system. This system enables the odor production of individual isolates to be monitored, allowing for rational selection of strains for augmentation experiments to improve the odor of the final fertilizer product.

scholarly journals Selection of Sphingomonadaceae at the Base of Laccaria proxima and Russula exalbicans Fruiting Bodies

2009 ◽  
Vol 75 (7) ◽  
pp. 1979-1989 ◽  
Author(s):  
F. G. Hidde Boersma ◽  
Jan A. Warmink ◽  
Fernando A. Andreote ◽  
Jan Dirk van Elsas
Keyword(s):  
Ectomycorrhizal Fungi ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bulk Soil ◽  
Fruiting Bodies ◽  
Community Structures ◽  
Specific Pcr ◽  
Laccaria Proxima ◽  
The Family ◽  
Gradient Gel Electrophoresis ◽  
Selection Of

ABSTRACT The dense hyphal network directly underneath the fruiting bodies of ectomycorrhizal fungi might exert strong influences on the bacterial community of soil. Such fruiting bodies might serve as hot spots for bacterial activity, for instance by providing nutrients and colonization sites in soil. Here, we assessed the putative selection of specific members of the Sphingomonadaceae family at the bases of the fruiting bodies of the ectomycorrhizal fungi Laccaria proxima and Russula exalbicans in comparison to the adjacent bulk soil. To do so, we used a previously designed Sphingomonadaceae-specific PCR-denaturing gradient gel electrophoresis (DGGE) system and complemented this with analyses of sequences from a Sphingomonadaceae-specific clone library. The analyses showed clear selective effects of the fruiting bodies of both fungi on the Sphingomonadaceae community structures. The effect was especially prevalent with R. exalbicans. Strikingly, similar fungi sampled approximately 100 m apart showed similar DGGE patterns, while corresponding bulk soil-derived patterns differed from each other. However, the mycospheres of L. proxima and R. exalbicans still revealed divergent community structures, indicating that different fungi select for different members of the Sphingomonadaceae family. Excision of specific bands from the DGGE patterns, as well as analyses of the clone libraries generated from both habitats, revealed fruiting body-specific Sphingomonadaceae types. It further showed that major groups from the mycospheres of R. exalbicans and L. proxima did not cluster with known bacteria from the database, indicating new groups within the family of Sphingomonadaceae present in these environments.

scholarly journals Evaluation of quantitative polymerase chain reaction to assessnosZgene prevalence in mixed microbial communities

2007 ◽  
Vol 53 (5) ◽  
pp. 636-642 ◽  
Author(s):  
Steven D. Siciliano ◽  
Wai Ma ◽  
Shane Powell
Keyword(s):  
Polymerase Chain Reaction ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Ralstonia Eutropha ◽  
Quantitative Polymerase Chain Reaction ◽  
Chain Reaction ◽  
Pcr Products ◽  
Gradient Gel Electrophoresis ◽  
Total Community ◽  
Polymerase Chain ◽  
Template Dna

The usefulness of quantitative polymerase chain reaction (QPCR) to measure nosZ gene prevalence in a multi-template reaction was assessed by comparing 19 nosZ template DNA samples and 91 model communities. Efficiencies of the QPCR varied but were not significantly different among nosZ genotypes and were not linked to genetic distance from Ralstonia eutropha . nosZ genotype QPCR efficiencies obtained from isolated denitrifiers were higher (84.8%) than those obtained from excised denaturing gradient gel electrophoresis bands or clones of PCR products from total community DNA (ca. 60%). Analysis of the model communities indicated that QPCR accurately predicts gene prevalence in communities composed of up to six templates.

The Influence of Applying Microbial Amendments to Soil and Plants on the Microbial Diversity in the Rhizosphere Soil of Garlic

2021 ◽  
Vol 15 (4) ◽  
pp. 528-535
Author(s):  
Yang Li ◽  
Sushuang Liu ◽  
Xiangui Yang ◽  
Choufei Wu ◽  
Quanxin Gao ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Rhizosphere Soil ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Soil Treatment ◽  
Bacillus Sp ◽  
Bacterial Strains ◽  
Water Control ◽  
Depth Analysis ◽  
Gradient Gel Electrophoresis ◽  
Plant Treatment

With the environmental problems brought about by the excessive use of fertilizers and pesticides, numerous biological amendments have been developed and used in recent years. This study, through in-depth analysis of the effects of two different microbial amendments on the microbial diversity in the garlic rhizosphere, provides a theoretical basis and data support for farmers to select microbial amendments. In the experiment, two different microbial amendments were applied to garlic, and its rhizosphere soil was collected after 10, 20, 30, and 40 days. The polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) was used to analyze bacterial diversity in the garlic rhizosphere soil. The total abundance and diversity of microbial flora in the rhizosphere soil of garlic increased after application of microbial amendments to soil or plants. Plant growth was significantly better in the soil treatment than the plant treatment and the water control. The two dominant bacteria of uncultured gamma proteobacterium and Uncultured Gemmatimonadete existed only in the soil treatment. After 40 day of treatment, the abundance in the rhizosphere soil of these four bacterial strains (Uncultured Bacillus sp. clone D.an-22, Mesorhizobium sp., uncultured gamma proteobacterium, and Pseudomonas boreopolis) was greater in the soil than the plant treatment and the control. The irrigation of microbial amendments not only influenced the structure and abundance of rhizosphere microorganisms, and also promoted the colonization by microorganisms. The five bacterial strains of uncultured gamma proteobacterium, Uncultured Gemmatimonadetes, Uncultured Bacillus sp. clone D.an-22, Mesorhizobium sp., Pseudomonas boreopolis could facilitate the growth and enhance resistance of garlic, establishing a foundation for the use of microbial amendments and providing new ideas and methods for environmental management and protection.

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