scholarly journals High-methionine soybean has no significant effect on nitrogen-transforming bacteria in rhizosphere soil

2018 ◽  
Vol 64 (No. 3) ◽  
pp. 108-113 ◽  
Author(s):  
Liang Jingang ◽  
Luan Ying ◽  
Jiao Yue ◽  
Sun Shi ◽  
Wu Cunxiang ◽  
...  
Keyword(s):  
Community Composition ◽  
Rhizosphere Soil ◽  
Microbial Community Composition ◽  
Potential Effect ◽  
Ammonia Oxidizing Bacteria ◽  
Nitrogen Fixing ◽  
Transgenic Soybean ◽  
Bacterial Populations ◽  
Microbial Functional Groups ◽  
Microbial Groups

Transgenic plants may induce shifts in the microbial community composition that in turn alter microbially-mediated nutrient cycling in soil. Studies of how specific microbial groups respond to genetically modified (GM) planting help predict potential impacts upon processes performed by these groups. This study investigated the effect of transgenic high-methionine soybean cv. ZD91 on nitrogen-fixing and ammonia-oxidizing bacterial populations. A difference in nitrogen-fixing or ammonia-oxidizing bacteria community composition was not found, suggesting that cv. ZD91 does not alter the bacterial populations in rhizosphere soil. This study increases our understanding of the potential effect of transgenic soybean on microbial functional groups within soil by suggesting that nitrogen-transforming bacteria may be useful for future investigations on the GM crops impact in the soil ecosystem.

scholarly journals First Insights into the Microbiome of a Mangrove Tree Reveal Significant Differences in Taxonomic and Functional Composition among Plant and Soil Compartments

2019 ◽  
Vol 7 (12) ◽  
pp. 585 ◽  
Author(s):  
Witoon Purahong ◽  
Dolaya Sadubsarn ◽  
Benjawan Tanunchai ◽  
Sara Fareed Mohamed Wahdan ◽  
Chakriya Sansupa ◽  
...  
Keyword(s):  
Community Composition ◽  
Rhizosphere Soil ◽  
Plant Root ◽  
Nifh Gene ◽  
Nitrogen Fixing ◽  
Ecological Functions ◽  
Rhizophora Stylosa ◽  
Bacterial Phyla ◽  
Mangrove Tree ◽  
Mangrove Ecosystems

Mangrove forest trees play important ecological functions at the interface between terrestrial and marine ecosystems. However, despite playing crucial roles in plant health and productivity, there is little information on microbiomes of the tree species in mangrove ecosystems. Thus, in this study we aimed to characterize the microbiome in soil (rhizosphere) and plant (root, stem, and leaf endosphere) compartments of the widely distributed mangrove tree Rhizophora stylosa. Surprisingly, bacterial operational taxonomic units (OTUs) were only confidently detected in rhizosphere soil, while fungal OTUs were detected in all soil and plant compartments. The major detected bacterial phyla were affiliated to Proteobacteria, Actinobacteria, Planctomycetes, and Chloroflexi. Several nitrogen-fixing bacterial OTUs were detected, and the presence of nitrogen-fixing bacteria was confirmed by nifH gene based-PCR in all rhizosphere soil samples, indicating their involvement in N acquisition in the focal mangrove ecosystem. We detected taxonomically (54 families, 83 genera) and functionally diverse fungi in the R. stylosa mycobiome. Ascomycota (mainly Dothideomycetes, Eurotiomycetes, Sordariomycetes) were most diverse in the mycobiome, accounting for 86% of total detected fungal OTUs. We found significant differences in fungal taxonomic and functional community composition among the soil and plant compartments. We also detected significant differences in fungal OTU richness (p < 0.002) and community composition (p < 0.001) among plant compartments. The results provide the first information on the microbiome of rhizosphere soil to leaf compartments of mangrove trees and associated indications of ecological functions in mangrove ecosystems.

scholarly journals Density-Based Separation of Microbial Functional Groups in Activated Sludge

2020 ◽  
Vol 17 (1) ◽  
pp. 376
Author(s):  
Lin Li ◽  
Yaqi You ◽  
Krishna Pagilla
Keyword(s):  
Activated Sludge ◽  
Functional Groups ◽  
Ammonia Oxidizing Bacteria ◽  
Biological Phosphorus Removal ◽  
Domestic Water ◽  
Microbial Functional Groups ◽  
Nitrite Oxidizing Bacteria ◽  
And Performance ◽  
Microbial Groups ◽  
Polyphosphate Accumulating Organisms

Mechanistic understanding of how activated sludge (AS) solids density influences wastewater treatment processing is limited. Because microbial groups often generate and store intracellular inclusions during certain metabolic processes, it is hypothesized that some microorganisms, like polyphosphate-accumulating organisms (PAOs), would have higher biomass densities. The present study developed a density-based separation approach and applied it to suspended growth AS in two full-scale domestic water resource recovery facilities (WRRFs). Incorporating quantitative real-time PCR (qPCR) and fluorescence in situ hybridization (FISH) analyses, the research demonstrated the effectiveness of density-based separation in enriching key microbial functional groups, including ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB) and PAOs, by up to 90-fold in target biomass fractions. It was observed that WRRF process functionalities have significant influence on density-based enrichment, such that maximum enrichments were achieved in the sludge fraction denser than 1.036 g/cm3 for the enhanced biological phosphorus removal (EBPR) facility and in the sludge fraction lighter than 1.030 g/cm3 for the non-EBPR facility. Our results provide important information on the relationship between biomass density and enrichment of microbial functional groups in AS, contributing to future designs of enhanced biological treatment processes for improved AS settleability and performance.

scholarly journals Successive DNA extractions improve characterization of soil microbial communities

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2915 ◽  
Author(s):  
Mauricio R. Dimitrov ◽  
Annelies J. Veraart ◽  
Mattias de Hollander ◽  
Hauke Smidt ◽  
Johannes A. van Veen ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Dna Extraction ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Soil Samples ◽  
Soil Microbial ◽  
Dna Yield ◽  
Microbial Groups

Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1–374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition.

Membrane bioreactor versus conventional activated sludge system: population dynamics of nitrifiers

2005 ◽  
Vol 52 (10-11) ◽  
pp. 417-425 ◽  
Author(s):  
R. Manser ◽  
W. Gujer ◽  
H. Siegrist
Keyword(s):  
Activated Sludge ◽  
Community Composition ◽  
Membrane Bioreactor ◽  
Membrane Separation ◽  
Heterotrophic Bacteria ◽  
Microbial Community Composition ◽  
Laser Scanning Microscopy ◽  
Nitrifying Bacteria ◽  
Ammonia Oxidizing Bacteria ◽  
Conventional Activated Sludge

Although membrane bioreactors have attracted increasing attention in recent years, little research has been undertaken on the influence of the membrane separation on the microbial community composition. This paper compares the startup behaviour and the performance of the subsequent eight months of a membrane bioreactor with a conventional activated sludge pilot plant. Both plants were operated in parallel at the same sludge age and treated the same domestic wastewater. The identification of the nitrifying community composition using fluorescent in situ hybridization revealed only minor differences between the two reactors for both ammonia-oxidizing bacteria and nitrite-oxidizing bacteria. Accordingly, both systems exhibited the same maximum nitrification rates. Confocal laser scanning microscopy showed that the aggregates formed by nitrifying bacteria were located mostly in the inner part of the flocs and were overgrown by heterotrophic bacteria. It is concluded that the membrane separation itself does affect neither the nitrifying community composition nor the nitrification performance. However, impacts on kinetic parameters are emphasized.

scholarly journals Mycorrhization of Quercus acutissima with Chinese black truffle significantly altered the host physiology and root-associated microbiomes

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6421 ◽  
Author(s):  
Xiaoping Zhang ◽  
Lei Ye ◽  
Zongjing Kang ◽  
Jie Zou ◽  
Xiaoping Zhang ◽  
...  
Keyword(s):  
Plant Physiology ◽  
Soil Properties ◽  
Host Plant ◽  
Community Composition ◽  
Rhizosphere Soil ◽  
Early Stage ◽  
Microbial Community Composition ◽  
Symbiotic Relationship ◽  
Black Truffle ◽  
Quercus Acutissima

Background Our aim was to explore how the ectomycorrhizae of an indigenous tree,Quercus acutissima, with a commercial truffle, Chinese black truffle (Tuber indicum), affects the host plant physiology and shapes the associated microbial communities in the surrounding environment during the early stage of symbiosis. Methods To achieve this, changes in root morphology and microscopic characteristics, plant physiology indices, and the rhizosphere soil properties were investigated when six-month-old ectomycorrhizae were synthesized. Meanwhile, next-generation sequencing technology was used to analyze the bacterial and fungal communities in the root endosphere and rhizosphere soil inoculated with T. indicum or not. Results The results showed that colonization by T. indicum significantly improved the activity of superoxide dismutase in roots but significantly decreased the root activity. The biomass, leaf chlorophyll content and root peroxidase activity did not obviously differ. Ectomycorrhization of Q. acutissima with T. indicum affected the characteristics of the rhizosphere soil, improving the content of organic matter, total nitrogen, total phosphorus and available nitrogen. The bacterial and fungal community composition in the root endosphere and rhizosphere soil was altered by T. indicum colonization, as was the community richness and diversity. The dominant bacteria in all the samples were Proteobacteria and Actinobacteria, and the dominant fungi were Eukaryota_norank, Ascomycota, and Mucoromycota. Some bacterial communities, such as Streptomyces, SM1A02, and Rhizomicrobium were more abundant in the ectomycorrhizae or ectomycorrhizosphere soil. Tuber was the second-most abundant fungal genus, and Fusarium was present at lower amounts in the inoculated samples. Discussion Overall, the symbiotic relationship between Q. acutissima and T. indicum had an obvious effect on host plant physiology, soil properties, and microbial community composition in the root endosphere and rhizosphere soil, which could improve our understanding of the symbiotic relationship between Q. acutissima and T. indicum, and may contribute to the cultivation of truffle.

scholarly journals Effect of Litter-Derived Dissolved Organic Carbon Addition on Forest Soil Microbial Community Composition

2021 ◽  
Vol 1 ◽  
Author(s):  
Min Wang ◽  
Qiuxiang Tian ◽  
Chang Liao ◽  
Rudong Zhao ◽  
Feng Liu
Keyword(s):  
Microbial Community ◽  
Microbial Biomass ◽  
Organic Carbon ◽  
Dissolved Organic Carbon ◽  
Community Composition ◽  
Soil Microbial Biomass ◽  
Microbial Community Composition ◽  
Soil Microbial ◽  
Significant Difference ◽  
Microbial Groups

The input of dissolved organic carbon (DOC) into soil affects soil organic carbon mineralization and microbial community composition by changing carbon availability. However, up to now, there is little knowledge about the microbial groups that utilize the added DOC and how the incorporation process may vary over time. In this study, we added 13C-labeled litter-derived DOC (treatment) or pure water (control) to a forest soil from different layers to investigate the effects of DOC addition on soil microbial biomass and community composition in a 180-d laboratory incubation experiment. Soil microbial phospholipid fatty acid (PLFA) were measured to assess changes in the microbial community composition. The 13C incorporation into microbial biomass and PLFAs was analyzed to trace the microbial utilization of litter-derived DOC. Our results indicated that DOC addition increased the biomass of gram-negative bacteria, gram-positive bacteria, fungi, and actinomycetes, but the microbial community composition manifested a similar trend for both treatment and control soils at the end of incubation. Proportions of added DOC in different depths of soil microbial PLFAs had no significant difference. Moreover, 17:0 cy and 15:0 PLFAs which are described as the bacterial biomarkers had a greater amount of 13C incorporation than other PLFAs for the topsoil, which indicated that 13C-labeled litter-derived DOC was more easily assimilated by some specific bacterial community. Soil microbial biomass and the incorporation of 13C into PLFA reached its maximum around 30 days after DOC addition and then rapidly reduced to the level comparable to control. Overall, this study demonstrated that the incorporation of 13C-labeled litter-derived DOC into PLFA in different depth soil had no significant difference, and the incorporation of 13C by bacteria was higher than other microbial groups.

scholarly journals The influence of microbial community dynamics on anaerobic digestion efficiency and stability: A Review

2020 ◽  
Vol 9 (1) ◽  
pp. 85-95
Author(s):  
Yumechris Amekan
Keyword(s):  
Microbial Community ◽  
Anaerobic Digestion ◽  
Community Composition ◽  
Energy Recovery ◽  
Volatile Fatty Acids ◽  
Community Dynamics ◽  
Microbial Community Composition ◽  
Microbial Community Dynamics ◽  
Stable Performance ◽  
Microbial Groups

An essential component in sustainable energy development is the production of bioenergy from waste. The most successful bioenergy technology worldwide is anaerobic digestion (AD), which is a microbially-mediated process of organic feedstock conversion into energy-rich compounds (volatile fatty acids (VFA) and biogas) for renewable energy generation. AD is deployed in a range of situations including systems for on-farm energy recovery from animal and plant waste to the processing of food and municipal solid waste (with the additional benefit of land-fill reduction).Anaerobic digesters rely on a diverse microbial community working syntrophycally through a series of interrelated biochemical processes.Each stage in anaerobic digestion is carried out by different microbial groups. Thus, to optimise energy recovery from the AD process, the microbial community must have stable performance over time, balancing the various metabolic functions and taxonomic community composition in digesters. Complicating this balance, it has been found that the presence of ammonia, sulphate, and hydrogen sulphide in substantial concentrations often cause failure in the AD process. Thus, these substances cause adverse shifts in microbial community composition and/or inhibit bacterial growth, that influencing AD performance.  ©2020. CBIORE-IJRED. All rights reserved

scholarly journals Silicon-Rich Soil Amendments Impact Microbial Community Composition and The Composition of Arsm Bearing Microbes

2021 ◽  
Author(s):  
Gretchen E. Dykes ◽  
Matt A. Limmer ◽  
Angelia L Seyfferth
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Calcium Silicate ◽  
Rhizosphere Soil ◽  
Soil Amendments ◽  
Microbial Community Composition ◽  
Methane Flux ◽  
Rice Paddy ◽  
C Storage ◽  
As Species

Abstract Purpose: Arsenic (As) cycling in flooded rice paddies is driven by soil microbes which among other transformations can cause conversion between inorganic and organic As species. Silicon (Si)-rich soil amendments cause increased methylated As species, particularly DMA, in grain likely because they influence the microbial community responsible for As methylation, but the mechanism remains unclear. Methods: To investigate how Si-rich amendments influenced the microbial community, we sequenced the 16S rRNA and arsM genes from rhizosphere soil collected at grain ripening from unamended rice paddy mesocosms or those amended with Si-rich rice husk, charred husk, or calcium silicate, and paired these data with geochemistry and As speciation in grain. Results: We found that Si-amendments influenced the 16S and arsM community composition. Increased C storage from calcium silicate amendment drove differences in the 16S community, whereas low redox from husk amendments drove differences in the arsM community. High grain DMA was not associated with treatment or microbial community, but with low redox.Conclusions: Differences in grain As were observed independent of amendments, and did not correspond to differences in either the 16S or arsM community. Instead, methane flux and redox correlated with differences in grain DMA, implying that methanogen activity and redox are more important factors than community composition in determining grain As speciation. Silicon amendments did not impact grain As, but impacted the microbial community composition, and the subset of arsM-bearing organisms. These findings imply that redox, porewater As, and methanogen activity are likely more important factors than arsM or overall microbial community composition in determining grain DMA levels.

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