scholarly journals Soil prokaryotes associated with decreasing pathogen density during anaerobic soil disinfestation

2019 ◽  
Author(s):  
Chol Gyu Lee ◽  
Eriko Kunitomo ◽  
Toshiya Iida ◽  
Kazuhiro Nakaho ◽  
Moriya Ohkuma
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Community Analysis ◽  
Soil Disinfestation ◽  
Chain Reactions ◽  
Anaerobic Soil Disinfestation ◽  
Polymerase Chain Reactions ◽  
Operational Taxonomic Units ◽  
The Relationship

AbstractAnaerobic soil disinfestation (ASD) is a chemical-independent method that can reduce pathogens. Although soil microbes play essential roles in ASD, the relationship between the microbial community structure and disinfestation efficiency remains unclear. To this end, we investigated changes in the microbial community and pathogen density during a period of ASD under field conditions for 14 days in a greenhouse using three different substrates. Soil samples were collected at 0, 3, 7, and 14 days after ASD treatment. The pathogen densities were analyzed by real-time polymerase chain reactions, prokaryotic community analysis was conducted using unidirectional pyrosequencing, and the factors related to pathogen density were statistically analyzed. The pathogen density rapidly decreased by >90% at 3 days after treatment and then slowly decreased until day 14, but the rate of decrease differed among the substrates. The microbial communities became altered after 3 days and recovered to their original state on day 14. The dipyridyl reaction, microbial diversity, richness, and community structure were not correlated with pathogen density. The most negatively correlated operational taxonomic units with pathogen density were Clostridia and Bacilli, both belonging to Firmicutes. These results suggested that the growth of specific microbes, but not the changes in microbial community structure, might be important for ASD disinfestation efficiency.

scholarly journals Microbial community structure and the relationship with soil carbon and nitrogen in an original Korean pine forest of Changbai Mountain, China

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Minghui Liu ◽  
Xin Sui ◽  
Yanbo Hu ◽  
Fujuan Feng
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Organic Carbon ◽  
Microbial Community Structure ◽  
Soil Microbes ◽  
Mixed Forest ◽  
Korean Pine ◽  
Soil Microbial ◽  
The Relationship ◽  
Main Factor

Abstract Background The broad-leaved Korean pine mixed forest is an important and typical component of a global temperate forest. Soil microbes are the main driver of biogeochemical cycling in this forest ecosystem and have complex interactions with carbon (C) and nitrogen (N) components in the soil. Results We investigated the vertical soil microbial community structure in a primary Korean pine-broadleaved mixed forest in Changbai Mountain (from 699 to 1177 m) and analyzed the relationship between the microbial community and both C and N components in the soil. The results showed that the total phospholipid fatty acid (PLFA) of soil microbes and Gram-negative bacteria (G-), Gram-positive bacteria (G+), fungi (F), arbuscular mycorrhizal fungi (AMF), and Actinomycetes varied significantly (p < 0.05) at different sites (elevations). The ratio of fungal PLFAs to bacterial PLFAs (F/B) was higher at site H1, and H2. The relationship between microbial community composition and geographic distance did not show a distance-decay pattern. The coefficients of variation for bacteria were maximum among different sites (elevations). Total soil organic carbon (TOC), total nitrogen (TN), soil water content (W), and the ratio of breast-height basal area of coniferous trees to that of broad-leaved tree species (RBA) were the main contributors to the variation observed in each subgroup of microbial PLFAs. The structure equation model showed that TOC had a significant direct effect on bacterial biomass and an indirect effect upon bacterial and fungal biomass via soil readily oxidized organic carbon (ROC). No significant relationship was observed between soil N fraction and the biomass of fungi and bacteria. Conclusion The total PLFAs (tPLFA) and PLFAs of soil microbes, including G-, G+, F, AMF, and Actinomycetes, were significantly affected by elevation. Bacteria were more sensitive to changes in elevation than other microbes. Environmental heterogeneity was the main factor affecting the geographical distribution pattern of microbial community structure. TOC, TN, W and RBA were the main driving factors for the change in soil microbial biomass. C fraction was the main factor affecting the biomass of fungi and bacteria and ROC was one of the main sources of the microbial-derived C pool.

scholarly journals Evaluation of DESS as a storage medium for microbial community analysis

2018 ◽  
Author(s):  
Kevin M Lee ◽  
Madison Adams ◽  
Jonathan L Klassen
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Ecology ◽  
Microbial Community Structure ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Ant Colonies ◽  
And Storage ◽  
Phosphate Buffered Saline

Microbial ecology research requires sampling strategies that accurately represent the microbial community under study. These communities must typically be transported from the collection location to the laboratory and then stored until they can be processed. However, there is a lack of consensus on how best to preserve microbial communities during transport and storage. Here, we evaluated DESS (Dimethyl sulfoxide, Ethylenediamine tetraacetic acid, Saturated Salt) solution as a broadly applicable preservative for microbial ecology experiments. We stored fungus gardens grown by the ant Trachymyrmex septentrionalis in DESS, 15% glycerol, and phosphate buffered saline (PBS) to test the ability of these preservatives to maintain the structure of fungus garden microbial communities. Variation in microbial community structure due to differences in preservative type was minimal when compared to variation between ant colonies. Additionally, DESS preserved the structure of a defined mock community more faithfully than either 15% glycerol or PBS. DESS is inexpensive, easy to transport, and effective in preserving microbial community structure. We therefore conclude that DESS is a valuable preservative for use in microbial ecology research.

Effect of pH on the Microbial Community Structure of SBBR Autotrophic Nitrogen Removal Process

2011 ◽  
Vol 378-379 ◽  
pp. 428-432
Author(s):  
Yu Qin ◽  
Jing Song Guo ◽  
Fang Fang
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Nitrogen Removal ◽  
Microbial Community Structure ◽  
Anaerobic Bacteria ◽  
Biofilm Reactor ◽  
Active Sludge ◽  
Removal Process ◽  
The Relationship ◽  
Autotrophic Nitrogen Removal

PCR-DGGE was applied to analyze the relationship between pH and the microbial community structure of Sequence Batch Biofilm Reactor (SBBR) autotrophic nitrogen removal process. The reactor was possessed of a high nitrogen removal efficiency at pH=8.0 where the similarity of microbial community structure between active sludge and biofilm samples was the lowest about 84.6% and the richness of bacterial community was the most abundant in biofilm compared with other pH conditions. pH=7.0 was good for the microbes in active sludge but unfavorable for anaerobic bacteria. At pH=9.0, the effects were presented with both bacterial activities and microbial community structure and when pH=6.0 the amount of microbial types dramatically dropped

scholarly journals Evaluation of DESS as a storage medium for microbial community analysis

2018 ◽  
Author(s):  
Kevin M Lee ◽  
Madison Adams ◽  
Jonathan L Klassen
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Ecology ◽  
Microbial Community Structure ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Ant Colonies ◽  
And Storage ◽  
Phosphate Buffered Saline

Microbial ecology research requires sampling strategies that accurately represent the microbial community under study. These communities must typically be transported from the collection location to the laboratory and then stored until they can be processed. However, there is a lack of consensus on how best to preserve microbial communities during transport and storage. Here, we evaluated DESS (Dimethyl sulfoxide, Ethylenediamine tetraacetic acid, Saturated Salt) solution as a broadly applicable preservative for microbial ecology experiments. We stored fungus gardens grown by the ant Trachymyrmex septentrionalis in DESS, 15% glycerol, and phosphate buffered saline (PBS) to test the ability of these preservatives to maintain the structure of fungus garden microbial communities. Variation in microbial community structure due to differences in preservative type was minimal when compared to variation between ant colonies. Additionally, DESS preserved the structure of a defined mock community more faithfully than either 15% glycerol or PBS. DESS is inexpensive, easy to transport, and effective in preserving microbial community structure. We therefore conclude that DESS is a valuable preservative for use in microbial ecology research.

scholarly journals A full-scale survey of sludge landfill: sludge properties, leachate characteristics and microbial community structure

2019 ◽  
Vol 80 (6) ◽  
pp. 1185-1195 ◽  
Author(s):  
Xiaodan Zhao ◽  
Jiazhe Yang ◽  
Chengqin Tu ◽  
Zhen Zhou ◽  
Wei Wu ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Community Analysis ◽  
Organic Content ◽  
Full Scale ◽  
Waste Landfill ◽  
Leachate Characteristics ◽  
Main Pathway ◽  
Sludge Properties

Abstract In this study, a full-scale survey was conducted of a sludge landfill that had been sealed for 10 years to investigate sludge properties, leachate characteristics and microbial community structure. Vertical distribution of sludge and leachate pollutants in the landfill site showed that the sludge and soluble pollutants in the leachate were both distributed almost evenly even after long-term anaerobic digestion, and higher concentrations of soluble pollutants and richness of microbial community were observed at the middle layer. Compared to dewatered excess sludge generated from the activated sludge process before landfill, landfill sludge had a much lower organic content (28.1%), smaller particle size and worse dewaterability. Compared to municipal waste landfill, sludge landfill generated leachate with a lower concentration of organic substances, and comparable concentrations of nitrogenous and phosphorus pollutants. Bacterial community analysis by Illumina MiSeq sequencing showed that Proteobacteria, Firmicutes, Chloroflexi, Actinobacteria and Bacteroidetes were the major phyla, and some new genera (Methylocystaceae, Mariniphaga and Aminicenantes) were enriched in the sludge landfill. Archaeal community analysis showed that aceticlastic methanogenesis by Methanosaeta and Methanosarcina was the main pathway for methane production in the sludge landfill, in contrast to waste landfill with hydrogenotrophic methanogenesis as the main pathway.

scholarly journals Comparison of prokaryotic communities among fields exhibiting different disinfestation effects by anaerobic soil disinfestation

2019 ◽  
Author(s):  
Chol Gyu Lee ◽  
Toshiya Iida ◽  
Eriko Matsuda ◽  
Kayo Yoshida ◽  
Masato Kawabe ◽  
...  
Keyword(s):  
Microbial Community ◽  
Next Generation Sequencing ◽  
Soil Health ◽  
Aerobic Bacteria ◽  
Soil Environment ◽  
Soil Disinfestation ◽  
Anaerobic Soil Disinfestation ◽  
Operational Taxonomic Units ◽  
Generation Sequencing ◽  
Tomato Bacterial Wilt

AbstractAnaerobic soil disinfestation (ASD) is a chemical-independent fumigation method used for reducing the abundance of pathogens at soil depths of <40 cm. However, its disinfestation efficiency is unstable under field conditions. The microbial community reflects the soil environment and is a good indicator of soil health. Therefore, soil with a good disinfestation efficiency may have a unique microbial community. The aim of the present study was to compare the prokaryotic communities among soils obtained from 17 geographically different greenhouses that experienced tomato bacterial wilt but exhibited different disinfestation efficiencies after ASD treatment with the same substrate. In the present study, soil prokaryotic communities in the field, which indicate difference in disinfestation effects after ASD treatment among several fields, were compared using next-generation sequencing. The prokaryotic communities in the fields showing different disinfestation effects were roughly separated into sampling fields. The relative abundances of Betaproteobacteria and Clostridia were significantly increased in well-disinfested fields. Overall, 25 operational taxonomic units (OTUs) were specifically increased in various well-disinfested soils and 18 OTUs belonged to phylogenetically diversified Clostridia. Other OTUs belonged to aerobic bacteria and were not previously detected in sample collected from ASD-treated fields. The results showed that the changes to the prokaryotic communities did not affect ASD efficiency, whereas changes in the abundance of specific microbes in the community were related to disinfestation.

scholarly journals Theoretical and Simulation-Based Investigation of the Relationship between Sequencing Effort, Microbial Community Richness, and Diversity in Binning Metagenome-Assembled Genomes

mSystems ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Taylor M. Royalty ◽  
Andrew D. Steen
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Genome Size ◽  
Relative Abundance ◽  
Microbial Community Structure ◽  
Data Sets ◽  
Short Read ◽  
Coupon Collector ◽  
Simulation Based ◽  
The Relationship

ABSTRACT We applied theoretical and simulation-based approaches to characterize how microbial community structure influences the amount of sequencing effort to reconstruct metagenomes that are assembled from short-read sequences. First, a coupon collector equation was proposed as an analytical model for predicting sequencing effort as a function of microbial community structure. Characterization was performed by varying community structure properties such as richness, evenness, and genome size. Simulations demonstrated that while community richness and evenness influenced the sequencing effort required to sequence a community metagenome to exhaustion, the effort necessary to sequence an individual genome to a target fraction of exhaustion depended only on the relative abundance of the genome and its genome size. A second analysis evaluated the quantity, completion, and contamination of metagenome-assembled genomes (MAGs) as a function of sequencing effort on four preexisting sequence read data sets from different environments. These data sets were subsampled to various degrees of completeness to simulate the effect of sequencing effort on MAG retrieval. Modeling suggested that sequencing efforts beyond what is typical in published experiments (1 to 10 Gbp) would generate diminishing returns in terms of MAG binning. A software tool, Genome Relative Abundance to Sequencing Effort (GRASE), was created to assist investigators to further explore this relationship. Reevaluation of the relationship between sequencing effort and binning success in the context of genome relative abundance, as opposed to base pairs, provides a constraint on sequencing experiments based on the relative abundance of microbes in an environment rather than arbitrary levels of sequencing effort. IMPORTANCE Short-read sequencing with Illumina sequencing technology provides an accurate, high-throughput method for characterizing the metabolic potential of microbial communities. Short-read sequences can be assembled and binned into metagenome-assembled genomes, thus shedding light on the function of microbial ecosystems that are important for health, agriculture, and Earth system processes. The work presented here provides an analytical framework for selecting sequencing effort as a function of genome relative abundance. As such, experimental goals in metagenome-assembled genome creation projects can select sequencing effort based on the rarest target genome as a constrained threshold. We hope that the results presented here, as well as GRASE, will be valuable to researchers planning sequencing experiments.

scholarly journals Relating Anaerobic Digestion Microbial Community and Process Function : Supplementary Issue: Water Microbiology

2015 ◽  
Vol 8s2 ◽  
pp. MBI.S33593 ◽  
Author(s):  
Kaushik Venkiteshwaran ◽  
Benjamin Bocher ◽  
James Maki ◽  
Daniel Zitomer
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Anaerobic Digestion ◽  
Microbial Community Structure ◽  
Hydrolysis Rate ◽  
Methane Production Rate ◽  
And Function ◽  
Key Microorganisms ◽  
The Relationship ◽  
Made In

Anaerobic digestion (AD) involves a consortium of microorganisms that convert substrates into biogas containing methane for renewable energy. The technology has suffered from the perception of being periodically unstable due to limited understanding of the relationship between microbial community structure and function. The emphasis of this review is to describe microbial communities in digesters and quantitative and qualitative relationships between community structure and digester function. Progress has been made in the past few decades to identify key microorganisms influencing AD. Yet, more work is required to realize robust, quantitative relationships between microbial community structure and functions such as methane production rate and resilience after perturbations. Other promising areas of research for improved AD may include methods to increase/control (1) hydrolysis rate, (2) direct interspecies electron transfer to methanogens, (3) community structure–function relationships of methanogens, (4) methanogenesis via acetate oxidation, and (5) bioaugmentation to study community–activity relationships or improve engineered bioprocesses.

Sign in / Sign up

Export Citation Format

Share Document