scholarly journals Photodynamic Inactivation reduces the diversity and changes the composition of bacterial and fungal communities associated with leaf surfaces

2021 ◽  
Author(s):  
Robert R. Junker ◽  
Lisa-Maria Ohler ◽  
Christoph Hamminger ◽  
Kristjan Plaetzer
Keyword(s):  
Plant Pathogens ◽  
Control Strategies ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Fungal Communities ◽  
Target Cells ◽  
Rrna Gene ◽  
Photodynamic Inactivation ◽  
Photodynamic Treatment ◽  
Leaf Surfaces

Plant surfaces are colonized by a myriad of microorganisms including mutualistic strains and pathogens. Particularly in agricultural systems applications are required that protect the plants against pathogens without negative side effects on the environment and humans. Photodynamic Inactivation (PDI) has been demonstrated to be a promising approach to efficiently fight plant pathogens. Based on its mechanism of action, the light-induced and photosensitizer-mediated overproduction of reactive oxygen species in target cells, PDI is likely to generally inactivates microorganisms on plants irrespective of their pathogenicity. In order to prove this hypothesis we used next-generation 16S rRNA gene amplicon sequencing to characterize the bacterial and fungal communities associated with leaf surfaces of Arabidopsis thaliana before and after the photodynamic treatment using the chlorine e6 derivative B17-0024 as photoactive compound and showed that this treatment reduced the microbial richness and altered the microbial community composition. These findings may help to develop effective pathogen-control strategies and may also stimulate research on plant-microbe interactions exploiting the potential of PDI.

scholarly journals Do initial concentration and activated sludge seasonality affect pharmaceutical biotransformation rate constants?

2021 ◽  
Author(s):  
Tamara J. H. M. van Bergen ◽  
Ana B. Rios-Miguel ◽  
Tom M. Nolte ◽  
Ad M. J. Ragas ◽  
Rosalie van Zelm ◽  
...  
Keyword(s):  
Microbial Community ◽  
Activated Sludge ◽  
Community Composition ◽  
Rate Constants ◽  
Wastewater Treatment Plants ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Initial Concentration ◽  
Different Seasons

Abstract Pharmaceuticals find their way to the aquatic environment via wastewater treatment plants (WWTPs). Biotransformation plays an important role in mitigating environmental risks; however, a mechanistic understanding of involved processes is limited. The aim of this study was to evaluate potential relationships between first-order biotransformation rate constants (kb) of nine pharmaceuticals and initial concentration of the selected compounds, and sampling season of the used activated sludge inocula. Four-day bottle experiments were performed with activated sludge from WWTP Groesbeek (The Netherlands) of two different seasons, summer and winter, spiked with two environmentally relevant concentrations (3 and 30 nM) of pharmaceuticals. Concentrations of the compounds were measured by LC–MS/MS, microbial community composition was assessed by 16S rRNA gene amplicon sequencing, and kb values were calculated. The biodegradable pharmaceuticals were acetaminophen, metformin, metoprolol, terbutaline, and phenazone (ranked from high to low biotransformation rates). Carbamazepine, diatrizoic acid, diclofenac, and fluoxetine were not converted. Summer and winter inocula did not show significant differences in microbial community composition, but resulted in a slightly different kb for some pharmaceuticals. Likely microbial activity was responsible instead of community composition. In the same inoculum, different kb values were measured, depending on initial concentration. In general, biodegradable compounds had a higher kb when the initial concentration was higher. This demonstrates that Michealis-Menten kinetic theory has shortcomings for some pharmaceuticals at low, environmentally relevant concentrations and that the pharmaceutical concentration should be taken into account when measuring the kb in order to reliably predict the fate of pharmaceuticals in the WWTP. Key points • Biotransformation and sorption of pharmaceuticals were assessed in activated sludge. • Higher initial concentrations resulted in higher biotransformation rate constants for biodegradable pharmaceuticals. • Summer and winter inocula produced slightly different biotransformation rate constants although microbial community composition did not significantly change. Graphical abstract

scholarly journals pH and Phosphate Induced Shifts in Carbon Flow and Microbial Community during Thermophilic Anaerobic Digestion

2020 ◽  
Vol 8 (2) ◽  
pp. 286
Author(s):  
Nina Lackner ◽  
Andreas O. Wagner ◽  
Rudolf Markt ◽  
Paul Illmer
Keyword(s):  
Microbial Community ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Carbon Flow ◽  
Rrna Gene ◽  
Organic Substrates ◽  
Ch4 Production ◽  
Ph Conditions ◽  
Ph Range ◽  
In The Beginning

pH is a central environmental factor influencing CH4 production from organic substrates, as every member of the complex microbial community has specific pH requirements. Here, we show how varying pH conditions (5.0–8.5, phosphate buffered) and the application of a phosphate buffer per se induce shifts in the microbial community composition and the carbon flow during nine weeks of thermophilic batch digestion. Beside monitoring the methane production as well as volatile fatty acid concentrations, amplicon sequencing of the 16S rRNA gene was conducted. The presence of 100 mM phosphate resulted in reduced CH4 production during the initial phase of the incubation, which was characterized by a shift in the dominant methanogenic genera from a mixed Methanosarcina and Methanoculleus to a pure Methanoculleus system. In buffered samples, acetate strongly accumulated in the beginning of the batch digestion and subsequently served as a substrate for methanogens. Methanogenesis was permanently inhibited at pH values ≤5.5, with the maximum CH4 production occurring at pH 7.5. Adaptations of the microbial community to the pH variations included shifts in the archaeal and bacterial composition, as less competitive organisms with a broad pH range were able to occupy metabolic niches at unfavorable pH conditions.

scholarly journals Identifying the abundant and active microorganisms common to full-scale anaerobic digesters

2017 ◽  
Author(s):  
Rasmus H. Kirkegaard ◽  
Simon J. McIlroy ◽  
Jannie M. Kristensen ◽  
Marta Nierychlo ◽  
Søren M. Karst ◽  
...  
Keyword(s):  
Microbial Community ◽  
Anaerobic Digestion ◽  
Wastewater Treatment Plants ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Full Scale ◽  
Rrna Gene ◽  
Anaerobic Digesters ◽  
Abundant Otus ◽  
Source Of Information

AbstractAnaerobic digestion is widely applied to treat organic waste at wastewater treatment plants. Characterisation of the underlying microbiology represents a source of information to develop strategies for improved operation. To this end, we investigated the microbial community composition of thirty-two full-scale digesters over a six-year period using 16S rRNA gene amplicon sequencing. Sampling of the sludge fed into these systems revealed that several of the most abundant populations were likely inactive and immigrating with the influent. This observation indicates that a failure to consider immigration will interfere with correlation analysis and give an inaccurate picture of the active microbial community. Furthermore, several abundant OTUs could not be classified to genus level with commonly applied taxonomies, making inference of their function unreliable. As such, the existing MiDAS taxonomy was updated to include these abundant phylotypes. The communities of individual plants surveyed were remarkably similar – with only 300 OTUs representing 80% of the total reads across all plants, and 15% of these identified as likely inactive immigrating microbes. By identifying the abundant and active taxa in anaerobic digestion, this study paves the way for targeted characterisation of the process important organisms towards an in-depth understanding of the microbial ecology of these biotechnologically important systems.

scholarly journals Ultrahigh-Throughput Multiplexing and Sequencing of >500-Base-Pair Amplicon Regions on the Illumina HiSeq 2500 Platform

mSystems ◽  
2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Johanna B. Holm ◽  
Michael S. Humphrys ◽  
Courtney K. Robinson ◽  
Matthew L. Settles ◽  
Sandra Ott ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Sequence Data ◽  
Microbial Community Composition ◽  
Pcr Amplification ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Illumina Hiseq ◽  
Illumina Miseq Platform ◽  
Miseq Platform

ABSTRACT Amplification, sequencing, and analysis of the 16S rRNA gene affords characterization of microbial community composition. As this tool has become more popular and amplicon-sequencing applications have grown in the total number of samples, growth in sample multiplexing is becoming necessary while maintaining high sequence quality and sequencing depth. Here, modifications to the Illumina HiSeq 2500 platform are described which produce greater multiplexing capabilities and 300-bp paired-end reads of higher quality than those produced by the current Illumina MiSeq platform. To improve the feasibility and flexibility of this method, a 2-step PCR amplification protocol is also described that allows for targeting of different amplicon regions, and enhances amplification success from samples with low bacterial bioburden. IMPORTANCE Amplicon sequencing has become a popular and widespread tool for surveying microbial communities. Lower overall costs associated with high-throughput sequencing have made it a widely adopted approach, especially for projects that necessitate sample multiplexing to eliminate batch effect and reduced time to acquire data. The method for amplicon sequencing on the Illumina HiSeq 2500 platform described here provides improved multiplexing capabilities while simultaneously producing greater quality sequence data and lower per-sample cost relative to those of the Illumina MiSeq platform without sacrificing amplicon length. To make this method more flexible for various amplicon-targeted regions as well as improve amplification from low-biomass samples, we also present and validate a 2-step PCR library preparation method.

scholarly journals Microbiota Associated with Sclerotia of Soilborne Fungal Pathogens – A Novel Source of Biocontrol Agents Producing Bioactive Volatiles

2019 ◽  
Vol 3 (2) ◽  
pp. 125-136 ◽  
Author(s):  
Pascal Mülner ◽  
Alessandro Bergna ◽  
Philipp Wagner ◽  
Dženana Sarajlić ◽  
Barbara Gstöttenmayr ◽  
...  
Keyword(s):  
Fungal Pathogens ◽  
Plant Pathogens ◽  
Control Strategies ◽  
Antagonistic Activity ◽  
Biocontrol Agents ◽  
High Yield ◽  
Rrna Gene ◽  
Strain Collection ◽  
Antifungal Volatiles ◽  
Differential Imaging

Soilborne plant pathogens are an increasing problem in modern agriculture, and their ability to survive long periods in soil as persistent sclerotia makes control and treatment particularly challenging. To develop new control strategies, we explored bacteria associated with sclerotia of Sclerotinia sclerotiorum and Rhizoctonia solani, two soilborne fungi causing high yield losses. We combined different methodological approaches to get insights into the indigenous microbiota of sclerotia, to compare it to bacterial communities of the surrounding environment, and to identify novel biocontrol agents and antifungal volatiles. Analysis of 16S rRNA gene fragment amplicons revealed significant compositional differences in the bacterial microbiomes of Rhizoctonia sclerotia, the unaffected tuber surface and surrounding soil. Moreover, distinctive bacterial lineages were associated with specific sample types. Flavobacteriaceae and Caulobacteraceae were primarily found in unaffected areas, while Phyllobacteriaceae and Bradyrhizobiaceae were associated with sclerotia of R. solani. In parallel, we studied a strain collection isolated from sclerotia of the pathogens for emission of bioactive volatile compounds. Isolates of Bacillus, Pseudomonas, and Buttiauxella exhibited high antagonistic activity toward both soilborne pathogens and were shown to produce novel, not yet described volatiles. Differential imaging showed that volatiles emitted by the antagonists altered the melanized sclerotia surface of S. sclerotiorum. Interestingly, combinations of bacterial antagonists increased inhibition of mycelial growth up to 60% when compared with single isolates. Our study showed that fungal survival structures are associated with a specific microbiome, which is also a reservoir for new biocontrol agents.

Community Structure and Co-Occurrence Network Analysis of Bacteria and Fungi in Wheat Fields vs Fruit Orchards

2021 ◽  
Author(s):  
Xinyu Cui ◽  
Huan He ◽  
Fengxiao Zhu ◽  
Xiaobo Liu ◽  
You Ma ◽  
...  
Keyword(s):  
Community Structure ◽  
Amplicon Sequencing ◽  
Yangtze River Delta ◽  
Vital Role ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Network Analyses ◽  
Planting Methods ◽  
Bacteria And Fungi ◽  
Occurrence Patterns

Abstract Soil microorganisms play a vital role in biogeochemical processes and nutrient turnover in agricultural ecosystems. However, the information on how the structure and co-occurrence patterns of microbial communities respond to the change of planting methods is still limited. In this study, a total of 34 soil samples were collected from 17 different fields of two planting types (wheat and orchards) along the Taige Canal in Yangtze River Delta. The distribution and diversity of bacterial and fungal communities in soil were determined using amplicon sequencing targeting the 16S rRNA gene and ITS gene, respectively. The dominated bacteria were Proteobacteria, Acidobacteriota, Actinobacteriota, Chloroflexi, Bacteroidota, and Firmicutes. The relative abundance of Actinobacteriota and Firmicutes was higher in the orchards, while Chloroflexi and Nitrospirota were more abundant in wheat fields. Ascomycota, Mortierellomycota, and Basidiomycota were the predominant fungi in both types of soils. The diversity of bacterial and fungal communities was greater in the wheat fields than in the orchards. The statistical analyses showed that pH was the main factor shaping the community structure. Moreover, high co-occurrence patterns of bacteria and fungi were confirmed in both wheat fields and orchards. Network analyses showed that both the wheat fields and orchards occurred modular structure, which mainly contained nodes of Acidobacteriota, Chloroflexi, Gemmatimonadota, Nitrospirota and Ascomycota. In summary, our work showed the co-occurrence network and the convergence/divergence of microbial community structure in wheat fields and orchards, giving a comprehensive understanding of the microbe-microbe interaction during planting methods changes.

scholarly journals Assessing Microbial Communities Related to Mercury Transformations in Contaminated Streambank Soils

2021 ◽  
Vol 232 (1) ◽  
Author(s):  
Yazeed Abdelmageed ◽  
Carrie Miller ◽  
Carrie Sanders ◽  
Timothy Egbo ◽  
Alexander Johs ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Contaminated Soils ◽  
Microbial Community Composition ◽  
Inorganic Mercury ◽  
Amplicon Sequencing ◽  
Soil Samples ◽  
Rrna Gene ◽  
Enrichment Cultures ◽  
Relative Abundances

AbstractIn nature, the bioaccumulative potent neurotoxin methylmercury (MeHg) is produced from inorganic mercury (Hg) predominantly by anaerobic microorganisms. Hg-contaminated soils are a potential source of MeHg due to microbial activity. We examine streambank soils collected from the contaminated East Fork Poplar Creek (EFPC) in Tennessee, USA, where seasonal variations in MeHg levels have been observed throughout the year, suggesting active microbial Hg methylation. In this study, we characterized the microbial community in contaminated bank soil samples collected from two locations over a period of one year and compared the results to soil samples from an uncontaminated reference site with similar geochemistry (n = 12). Microbial community composition and diversity were assessed by 16S rRNA gene amplicon sequencing. Furthermore, to isolate potential methylators from soils, enrichment cultures were prepared using selective media. A set of three clade-specific primers targeting the gene hgcA were used to detect Hg methylators among the δ-Proteobacteria in EFPC bank soils across all seasons. Two families among the δ-Proteobacteria that have been previously associated with Hg methylation, Geobacteraceae and Syntrophobacteraceae, were found to be predominant with relative abundances of 0.13% and 4.0%, respectively. However, in soil enrichment cultures, Firmicutes were predominant among families associated with Hg methylation. Specifically, Clostridiaceae and Peptococcaceae and their genera Clostridium and Desulfosporosinus were among the ten most abundant genera with relative abundances of 2.6% and 1.7%, respectively. These results offer insights into the role of microbial communities on Hg transformation processes in contaminated bank soils in EFPC. Identifying the biogeochemical drivers of MeHg production is critical for future remediation efforts.

scholarly journals Impact of inter- and intra-individual variation, sample storage and sampling fraction on human stool microbial community profiles

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6172 ◽  
Author(s):  
Yun Kit Yeoh ◽  
Zigui Chen ◽  
Mamie Hui ◽  
Martin C.S. Wong ◽  
Wendy C.S. Ho ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Individual Variation ◽  
Large Scale ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Relative Effect ◽  
Individual Variability ◽  
Rrna Gene ◽  
Sample Collection

Stools are commonly used as proxies for studying human gut microbial communities as sample collection is straightforward, cheap and non-invasive. In large-scale human population surveys, however, sample integrity becomes an issue as it is not logistically feasible for researchers to personally collect stools from every participant. Instead, participants are usually given guidelines on sample packaging and storage, and asked to deliver their stools to a centralised facility. Here, we tested a number of delivery conditions (temperature, duration and addition of preservative medium) and assessed their effects on stool microbial community composition using 16S rRNA gene amplicon sequencing. The largest source of variability in stool community composition was attributable to inter-individual differences regardless of delivery condition. Although the relative effect of delivery condition on community composition was small compared to inter-individual variability (1.6% vs. 60.5%, permutational multivariate analysis of variance [PERMANOVA]) and temporal variation within subjects over 10 weeks (5.2%), shifts in microbial taxa associated with delivery conditions were non-systematic and subject-specific. These findings indicated that it is not possible to model or accurately predict shifts in stool community composition associated with sampling logistics. Based on our findings, we recommend delivery of fresh, preservative-free stool samples to laboratories within 2 hr either at ambient or chilled temperatures to minimise perturbations to microbial community composition. In addition, subsamples from different fractions of the same stool displayed a small (3.3% vs. 72.6% inter-individual variation, PERMANOVA) but significant effect on community composition. Collection of larger sample volumes for homogenisation is recommended.

scholarly journals On giant shoulders: How a seamount affects the microbial community composition of seawater and sponges

2020 ◽  
Author(s):  
Kathrin Busch ◽  
Ulrike Hanz ◽  
Furu Mienis ◽  
Benjamin Müller ◽  
Andre Franke ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Dissolved Inorganic Carbon ◽  
Environmental Gradients ◽  
Microbial Community Composition ◽  
Geographic Location ◽  
Environmental Parameters ◽  
Amplicon Sequencing ◽  
The Arctic ◽  
Rrna Gene

Abstract. Seamounts represent ideal systems to study the influence and interdependency of environmental gradients at a single geographic location. These topographic features represent a prominent habitat for various forms of life, including microbiota and macrobiota, spanning benthic as well as pelagic organisms. While it is known that seamounts are globally abundant structures, it still remains unclear how and to which extend the complexity of the seafloor is intertwined with the local oceanographic mosaic, biogeochemistry and microbiology of a seamount ecosystem. Along these lines, the present study aimed to explore whether and to which extend seamounts can have an imprint on the microbial community composition of seawater and of sessile benthic invertebrates, sponges. For our high-resolution sampling approach of microbial diversity (16S rRNA gene Amplicon sequencing) along with measurements of inorganic nutrients and other biogeochemical parameters, we focused on the Schulz Bank seamount ecosystem, a sponge ground ecosystem which is located on the Arctic Mid-Ocean Ridge. Seawater samples were collected at two sampling depths (mid-water: MW, and near-bed water: BW) from a total of 19 sampling sites. With a clustering approach we defined microbial micro-habitats within the pelagic realm at Schulz Bank, which were mapped onto the seamount's topography, and related to various environmental parameters (such as suspended particulate matter (SPM), dissolved inorganic carbon (DIC), silicate (SiO4−), phosphate (PO43−), ammonia (NH4+), nitrate (NO32−), nitrite (NO2

scholarly journals Ultra-high throughput multiplexing and sequencing of >500 bp amplicon regions on the Illumina HiSeq 2500 platform

2018 ◽  
Author(s):  
Johanna B. Holm ◽  
Michael S. Humphrys ◽  
Courtney K. Robinson ◽  
Matthew L. Settles ◽  
Sandra Ott ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Sequence Data ◽  
Microbial Community Composition ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Illumina Hiseq ◽  
Illumina Miseq Platform ◽  
Miseq Platform

AbstractAmplification, sequencing and analysis of the 16S rRNA gene affords characterization of microbial community composition. As this tool has become more popular and amplicon-sequencing applications have grown in the total number of samples, growth in sample multiplexing is becoming necessary while maintaining high sequence quality and sequencing depth. Here, modifications to the Illumina HiSeq 2500 platform are described which produce greater multiplexing capabilities and 300 bp paired-end reads of higher quality than produced by the current Illumina MiSeq platform. To improve the feasibility and flexibility of this method, a 2-Step PCR amplification protocol is also described that allows for targeting of different amplicon regions, thus improving amplification success from low bacterial bioburden samples.ImportanceAmplicon sequencing has become a popular and widespread tool for surveying microbial communities. Lower overall costs associated with high throughput sequencing have made it a widely-adopted approach, especially for projects which necessitate sample multiplexing to eliminate batch effect and reduced time to acquire data. The method for amplicon sequencing on the Illumina HiSeq 2500 platform described here provides improved multiplexing capabilities while simultaneously producing greater quality sequence data and lower per sample cost relative to the Illumina MiSeq platform, without sacrificing amplicon length. To make this method more flexible to various amplicon targeted regions as well as improve amplification from low biomass samples, we also present and validate a 2-Step PCR library preparation method.

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