scholarly journals Toxicity effects of improved aged refuse on Tagetes patula and rhizosphere microbes

2021 ◽  
Author(s):  
Fen Hou ◽  
Xu Bi ◽  
Ye Yuan ◽  
Xihui Wu ◽  
Junjie Du
Keyword(s):  
Microbial Community ◽  
Stress Responses ◽  
Dynamic Equilibrium ◽  
Physiological Stress ◽  
Microbial Community Composition ◽  
Microbial Community Analysis ◽  
Tagetes Patula ◽  
Contaminant Exposure ◽  
Aged Refuse ◽  
Mass Ratios

In this study, we examined the effects of different mass ratios of aged refuse on Tagetes patula and rhizosphere microbes. The results showed that chlorophyll content and activities of superoxide dismutase, catalase, and peroxidase in leaf tissue increased significantly in plants cultivated in soil:aged refuse mixtures compared with ordinary soil, whereas levels of malondialdehyde and protein carbonyl decreased significantly in soil:aged refuse mixtures. Microbial community analysis revealed that aged refuse is rich in a variety of rhizosphere microbes that contribute to pollutant degradation, although microbial diversity was found to be relatively low. Bacterial genera such as Ferruginibacter, Hymenobacter, unclassified_Gemmataceae, Longimicrobium, Tychonema CCAP 1459-11B, Gemmatirosa, and Rubellimicrobium tended to be enriched to a greater extent in ordinary soil compared with soil:aged refuse mixtures. Correspondingly, bacterial genera such as Emticicia, Caedibacter, Anaerosalibacter, Tumebacillus, Patulibacter, Oceanotoga, Dyadobacter, Chloroflexus, and Acidobacteria bacterium SCN 69-37, Polycyclovorans, tended to be enriched in mixtures with a higher proportion of aged refuse. Functional prediction analysis revealed that rhizosphere microbe functions changed markedly following the addition of aged refuse. These findings indicate that aged refuse may represent a source of environmental stress for plants and modifies the dominant bacterial composition of rhizosphere microbes. The combination of organic or inorganic pollutants, plant physiological stress responses, and rhizosphere microbial community composition may have potential cooperative or dynamic equilibrium relationships. With respect to identifying potential approaches to recycling aged refuse, it will be necessary to focus on selecting optimal mass ratios of aged refuse and ordinary soil to control contaminant exposure.

scholarly journals Resilience of Microbial Communities after Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms

2021 ◽  
Vol 9 (7) ◽  
pp. 1495
Author(s):  
Tim Piel ◽  
Giovanni Sandrini ◽  
Gerard Muyzer ◽  
Corina P. D. Brussaard ◽  
Pieter C. Slot ◽  
...  
Keyword(s):  
Hydrogen Peroxide ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Composition ◽  
Glycoside Hydrolases ◽  
Microbial Community Analysis ◽  
Cyanobacterial Blooms ◽  
Temporary Increase ◽  
Low Concentrations ◽  
Harmful Cyanobacterial Blooms

Applying low concentrations of hydrogen peroxide (H2O2) to lakes is an emerging method to mitigate harmful cyanobacterial blooms. While cyanobacteria are very sensitive to H2O2, little is known about the impacts of these H2O2 treatments on other members of the microbial community. In this study, we investigated changes in microbial community composition during two lake treatments with low H2O2 concentrations (target: 2.5 mg L−1) and in two series of controlled lake incubations. The results show that the H2O2 treatments effectively suppressed the dominant cyanobacteria Aphanizomenon klebahnii, Dolichospermum sp. and, to a lesser extent, Planktothrix agardhii. Microbial community analysis revealed that several Proteobacteria (e.g., Alteromonadales, Pseudomonadales, Rhodobacterales) profited from the treatments, whereas some bacterial taxa declined (e.g., Verrucomicrobia). In particular, the taxa known to be resistant to oxidative stress (e.g., Rheinheimera) strongly increased in relative abundance during the first 24 h after H2O2 addition, but subsequently declined again. Alpha and beta diversity showed a temporary decline but recovered within a few days, demonstrating resilience of the microbial community. The predicted functionality of the microbial community revealed a temporary increase of anti-ROS defenses and glycoside hydrolases but otherwise remained stable throughout the treatments. We conclude that the use of low concentrations of H2O2 to suppress cyanobacterial blooms provides a short-term pulse disturbance but is not detrimental to lake microbial communities and their ecosystem functioning.

scholarly journals Antibiotic resistome and microbial community structure during anaerobic co-digestion of food waste, paper and cardboard

2020 ◽  
Vol 96 (2) ◽  
Author(s):  
Kärt Kanger ◽  
Nigel G H Guilford ◽  
HyunWoo Lee ◽  
Camilla L Nesbø ◽  
Jaak Truu ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Solid State ◽  
Food Waste ◽  
Microbial Community Structure ◽  
Microbial Community Composition ◽  
Microbial Community Analysis ◽  
Waste Paper ◽  
Rrna Gene ◽  
Significant Shift

ABSTRACT Solid organic waste is a significant source of antibiotic resistance genes (ARGs) and effective treatment strategies are urgently required to limit the spread of antimicrobial resistance. Here, we studied ARG diversity and abundance as well as the relationship between antibiotic resistome and microbial community structure within a lab-scale solid-state anaerobic digester treating a mixture of food waste, paper and cardboard. A total of 10 samples from digester feed and digestion products were collected for microbial community analysis including small subunit rRNA gene sequencing, total community metagenome sequencing and high-throughput quantitative PCR. We observed a significant shift in microbial community composition and a reduction in ARG diversity and abundance after 6 weeks of digestion. ARGs were identified in all samples with multidrug resistance being the most abundant ARG type. Thirty-two per cent of ARGs detected in digester feed were located on plasmids indicating potential for horizontal gene transfer. Using metagenomic assembly and binning, we detected potential bacterial hosts of ARGs in digester feed, which included Erwinia, Bifidobacteriaceae, Lactococcus lactis and Lactobacillus. Our results indicate that the process of sequential solid-state anaerobic digestion of food waste, paper and cardboard tested herein provides a significant reduction in the relative abundance of ARGs per 16S rRNA gene.

scholarly journals Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Vanessa L. Brisson ◽  
Jennifer E. Schmidt ◽  
Trent R. Northen ◽  
John P. Vogel ◽  
Amélie C. M. Gaudin
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Microbial Community Analysis ◽  
Agricultural System ◽  
Community Members ◽  
Genetic Groups ◽  
Maize Domestication ◽  
Rhizosphere Microbial Community

Abstract Maize domestication and breeding have resulted in drastic and well documented changes in aboveground traits, but belowground effects on root system functioning and rhizosphere microbial communities remain poorly understood, despite their critical importance for nutrient and water acquisition. We investigated the rhizosphere microbial community composition and structure of ten Zea mays accessions along an evolutionary transect (two teosinte, three inbred maize lines, and five modern maize hybrids) grown in nutrient depleted soil from a low input agricultural system. Microbial community analysis revealed significant differences in community composition between soil compartments (proximal vs. distal rhizosphere) and between plant genetic groups (teosinte, inbred, and modern hybrid). Only a small portion of the microbial community was differentially selected across plant genetic groups: 3.7% of prokaryotic community members and 4.9% of fungal community members were significantly associated with a specific plant genetic group. Indicator species analysis showed the greatest differentiation between modern hybrids and the other two plant genetic groups. Co-occurrence network analysis revealed that microbial co-occurrence patterns of the inbred maize lines’ rhizosphere were significantly more similar to those of the teosintes than to the modern hybrids. Our results suggest that advances in hybrid development significantly impacted rhizosphere microbial communities and network assembly.

scholarly journals Microbial Community Composition Affects Soil Fungistasis

2003 ◽  
Vol 69 (2) ◽  
pp. 835-844 ◽  
Author(s):  
Wietse de Boer ◽  
Patrick Verheggen ◽  
Paulien J. A. Klein Gunnewiek ◽  
George A. Kowalchuk ◽  
Johannes A. van Veen
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Fusarium Culmorum ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Carbon Limitation ◽  
Soil Fungistasis

ABSTRACT Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis. Previous observations have implicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis) or production of antifungal compounds (antibiosis hypothesis). To obtain evidence for either of these hypotheses, we measured soil respiration and microbial numbers (as indicators of nutrient stress) and bacterial community composition (as an indicator of potential differences in the composition of antifungal components) during the development of fungistasis. This was done for two fungistatic dune soils in which fungistasis was initially fully or partly relieved by partial sterilization treatment or nutrient addition. Fungistasis development was measured as restriction of the ability of the fungi Chaetomium globosum, Fusarium culmorum, Fusarium oxysporum, and Trichoderma harzianum to colonize soils. Fungistasis did not always reappear after soil treatments despite intense competition for carbon, suggesting that microbial community composition is important in the development of fungistasis. Both microbial community analysis and in vitro antagonism tests indicated that the presence of pseudomonads might be essential for the development of fungistasis. Overall, the results lend support to the antibiosis hypothesis.

scholarly journals Perspective for Aquaponic Systems: “Omic” Technologies for Microbial Community Analysis

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Perla Munguia-Fragozo ◽  
Oscar Alatorre-Jacome ◽  
Enrique Rico-Garcia ◽  
Irineo Torres-Pacheco ◽  
Andres Cruz-Hernandez ◽  
...  
Keyword(s):  
Microbial Community ◽  
Nutrient Dynamics ◽  
Microbial Community Composition ◽  
Chemical Species ◽  
Community Analysis ◽  
Taxonomic Diversity ◽  
Microbial Community Analysis ◽  
Emergent Properties ◽  
Microbial Profile ◽  
Set Up

Aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. In this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. The nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. In this particular field, the microbial research, the “Omic” technologies will allow a broader scope of studies about a current microbial profile inside aquaponics community, even in those species that currently are unculturable. This approach can also be useful to understand complex interactions of living components in the system. Until now, the analog studies were made to set up the microbial characterization on recirculation aquaculture systems (RAS). However, microbial community composition of aquaponics is still unknown. “Omic” technologies like metagenomic can help to reveal taxonomic diversity. The perspectives are also to begin the first attempts to sketch the functional diversity inside aquaponic systems and its ecological relationships. The knowledge of the emergent properties inside the microbial community, as well as the understanding of the biosynthesis pathways, can derive in future biotechnological applications. Thus, the aim of this review is to show potential applications of current “Omic” tools to characterize the microbial community in aquaponic systems.

scholarly journals Rapid Method for Coextraction of DNA and RNA from Natural Environments for Analysis of Ribosomal DNA- and rRNA-Based Microbial Community Composition

2000 ◽  
Vol 66 (12) ◽  
pp. 5488-5491 ◽  
Author(s):  
Robert I. Griffiths ◽  
Andrew S. Whiteley ◽  
Anthony G. O'Donnell ◽  
Mark J. Bailey
Keyword(s):  
Microbial Community ◽  
Ribosomal Dna ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Microbial Community Composition ◽  
Pcr Amplification ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Natural Environments ◽  
Dna And Rna ◽  
Gradient Gel Electrophoresis

ABSTRACT A rapid protocol for the extraction of total nucleic acids from environmental samples is described. The method facilitates concomitant assessment of microbial 16S rRNA diversity by PCR and reverse transcription-PCR amplification from a single extraction. Denaturing gradient gel electrophoresis microbial community analysis differentiated the active component (rRNA derived) from the total bacterial diversity (ribosomal DNA derived) down the horizons of an established grassland soil.

scholarly journals Biofilms in premise plumbing systems as a double-edged sword: microbial community composition and functional profiling of biofilms in a tropical region

2020 ◽  
Vol 18 (2) ◽  
pp. 172-185
Author(s):  
Ryan De Sotto ◽  
Rena Tang ◽  
Sungwoo Bae
Keyword(s):  
Microbial Community ◽  
Metabolic Pathways ◽  
Microbial Community Composition ◽  
Microbial Community Analysis ◽  
Global Network ◽  
Tropical Region ◽  
Gene Markers ◽  
Premise Plumbing ◽  
Functional Profiling ◽  
Plumbing Systems

Abstract To understand distributions of opportunistic premise plumbing pathogens (OPPPs) and microbial community structures governed by sample location, pipe materials, water temperature, age of property and type of house, 29 biofilm samples obtained from faucets, pipes, and shower heads in different households in Singapore were examined using next-generation sequencing technology. Predictive functional profiling of the biofilm communities was also performed to understand the potential of uncultivated microorganisms in premise plumbing systems and their involvement in various metabolic pathways. Microbial community analysis showed Proteobacteria, Bacteroidetes, Acidobacteria, Nitrospira, and Actinobacteria to be the most abundant phyla across the samples which was found to be significantly different when grouped by age of the properties, location, and the type of house. Meanwhile, opportunistic premise plumbing pathogens such as Mycobacterium, Citrobacter, Pseudomonas, Stenotrophomonas, and Methylobacterium were observed from the samples at 0.5% of the total reads. Functional prediction using 16S gene markers revealed the involvement of the biofilm communities in different metabolic pathways like nitrogen metabolism, biodegradation of xenobiotics, and bacterial secretion implying diverse functionalities that are yet to be studied in this environment. This study serves as a preliminary survey on the microbial communities harboring premise plumbing systems in a tropical region like Singapore. This article has been made Open Access thanks to the generous support of a global network of libraries as part of the Knowledge Unlatched Select initiative.

scholarly journals Analysis of Microbial Communities in Aged Refuse Based on 16S Sequencing

2021 ◽  
Vol 13 (8) ◽  
pp. 4111
Author(s):  
Fen Hou ◽  
Junjie Du ◽  
Ye Yuan ◽  
Xihui Wu ◽  
Sai Zhao
Keyword(s):  
Microbial Community ◽  
Soil Fertility ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Undisturbed Soil ◽  
16S Sequencing ◽  
Bacterial Phyla ◽  
Aged Refuse

Aged refuse is widely considered to have certain soil fertility. 16S rRNA amplicon sequencing is used to investigate the microbial community of aged refuse. The aged refuse is found to contain higher soil fertility elements (total nitrogen, total phosphorus, total potassium, etc.) and higher concentrations of heavy metals (Pb, Cd, Zn, and Hg). Taxonomy based on operational taxonomic units (OTUs) shows that Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes are the main bacterial phyla in the two soils and there is a palpable difference in the microbial community composition between the two groups of samples. The genera Paramaledivibacter, Limnochorda, Marinobacter, Pseudaminobacter, Kocuria, Bdellovibrio, Halomonas, Gillisia, and Membranicola are enriched in the aged refuse. Functional predictive analysis shows that both the control soil and aged refuse have a high abundance of “carbohydrate metabolism” and “amino acid metabolism”, and show differences in the abundance of several metabolism pathways, such as “xenobiotics biodegradation and metabolism” and “lipid metabolism”. Aged refuse and undisturbed soil show significant differences in alpha diversity and microbial community composition. Multiple environmental factors (Hg, TN, Cr, Cd, etc.) significantly impact microorganisms’ abundance (Marinobacter, Halomonas, Blastococcus, etc.). Our study provides valuable knowledge for the ecological restoration of closed landfills.

scholarly journals Effect of Start-Up Strategies and Electrode Materials on Carbon Dioxide Reduction on Biocathodes

2017 ◽  
Vol 84 (4) ◽  
Author(s):  
Soroush Saheb-Alam ◽  
Abhijeet Singh ◽  
Malte Hermansson ◽  
Frank Persson ◽  
Anna Schnürer ◽  
...  
Keyword(s):  
Microbial Community ◽  
Electrode Materials ◽  
Microbial Community Composition ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Cathodic Current ◽  
Content Type ◽  
Term Operation ◽  
Start Up

ABSTRACT The enrichment of CO 2 -reducing microbial biocathodes is challenging. Previous research has shown that a promising approach could be to first enrich bioanodes and then lower the potential so the electrodes are converted into biocathodes. However, the effect of such a transition on the microbial community on the electrode has not been studied. The goal of this study was thus to compare the start-up of biocathodes from preenriched anodes with direct start-up from bare electrodes and to investigate changes in microbial community composition. The effect of three electrode materials on the long-term performance of the biocathodes was also investigated. In this study, preenrichment of acetate-oxidizing bioanodes did not facilitate the start-up of biocathodes. It took about 170 days for the preenriched electrodes to generate substantial cathodic current, compared to 83 days for the bare electrodes. Graphite foil and carbon felt cathodes produced higher current at the beginning of the experiment than did graphite rods. However, all electrodes produced similar current densities at the end of the over 1-year-long study (2.5 A/m 2 ). Methane was the only product detected during operation of the biocathodes. Acetate was the only product detected after inhibition of the methanogens. Microbial community analysis showed that Geobacter sp. dominated the bioanodes. On the biocathodes, the Geobacter sp. was succeeded by Methanobacterium spp., which made up more than 80% of the population. After inhibition of the methanogens, Acetobacterium sp. became dominant on the electrodes (40% relative abundance). The results suggested that bioelectrochemically generated H 2 acted as an electron donor for CO 2 reduction. IMPORTANCE In microbial electrochemical systems, living microorganisms function as catalysts for reactions on the anode and/or the cathode. There is a variety of potential applications, ranging from wastewater treatment and biogas generation to production of chemicals. Systems with biocathodes could be used to reduce CO 2 to methane, acetate, or other high-value chemicals. The technique can be used to convert solar energy to chemicals. However, enriching biocathodes that are capable of CO 2 reduction is more difficult and less studied than enriching bioanodes. The effect of different start-up strategies and electrode materials on the microbial communities that are enriched on biocathodes has not been studied. The purpose of this study was to investigate two different start-up strategies and three different electrode materials for start-up and long-term operation of biocathodes capable of reducing CO 2 to valuable biochemicals.

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