4,891 results
Search Results
2. Isolation, Identification, and Selection of Bacteria With Proof-of-Concept for Bioaugmentation of Whitewater From Wood-Free Paper Mills
- Author
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Nada Verdel, Tomaž Rijavec, Iaroslav Rybkin, Anja Erzin, Žiga Velišček, Albin Pintar, and Aleš Lapanje
- Subjects
Microbiology (medical) ,Bioaugmentation ,biology ,principal component analysis ,Papermaking ,Aeromonas, azo dye, bioaugmentation, principal component analysis, environmental microbiology, whitewater ,biology.organism_classification ,Pulp and paper industry ,Isolation (microbiology) ,Microbiology ,Polyvinyl alcohol ,QR1-502 ,chemistry.chemical_compound ,Aeromonas ,Microbial ecology ,chemistry ,environmental microbiology ,Dissolved organic carbon ,azo dye ,whitewater ,bioaugmentation ,Bacteria ,Original Research - Abstract
In the wood-free paper industry, whitewater is usually a mixture of additives for paper production. We are currently lacking an efficient, cost-effective purification technology for their removal. In closed whitewater cycles the additives accumulate, causing adverse production problems, such as the formation of slime and pitch. The aim of our study was to find an effective bio-based strategy for whitewater treatment using a selection of indigenous bacterial isolates. We first obtained a large collection of bacterial isolates and then tested them individually by simple plate and spectrophotometric methods for their ability to degrade the papermaking additives, i.e., carbohydrates, resin acids, alkyl ketene dimers, polyvinyl alcohol, latex, and azo and fluorescent dyes. We examined correlation between carbon source use, genera, and inoculum source of isolates using two multivariate methods: principal component analysis and FreeViz projection. Of the 318 bacterial isolates, we selected a consortium of four strains (Xanthomonadales bacterium sp. CST37-CF, Sphingomonas sp. BLA14-CF, Cellulosimicrobium sp. AKD4-BF and Aeromonas sp. RES19-BTP) that degrade the entire spectrum of tested additives by means of dissolved organic carbon measurements. A proof-of-concept study on a pilot scale was then performed by immobilizing the artificial consortium of the four strains and inserting them into a 33-liter, tubular flow-through reactor with a retention time of < 15 h. The consortium caused an 88% reduction in the COD of the whitewater, even after 21 days., GREENER H2020
- Published
- 2021
3. Quantitative contributions of bacteria and of Deinococcus geothermalis to deposits and slimes in paper industry.
- Author
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Peltola, Minna, Öqvist, Charlotta Kanto, Ekman, Jaakko, Kosonen, Mirva, Jokela, Sanna, Kolari, Marko, Korhonen, Päivi, and Salkinoja-Salonen, Mirja
- Subjects
- *
PAPER industry , *BIOFILMS , *PAPER product manufacturing , *MICROBIAL aggregation , *PROKARYOTES , *FOULING , *PAPER mills , *PULP mills , *MICROBIAL ecology - Abstract
Deinococcus geothermalis has frequently been isolated from pink colored deposits of paper industry processes. Laboratory studies have shown that D. geothermalis is capable of forming on nonliving surfaces patchy biofilms that are resistant to adverse agents such as extreme pH, desiccation, solubilising detergents and biocides. This study was done to quantitatively assess the role of D. geothermalis as a biofouler in paper industry. Colored deposits were collected from 24 European and North American paper and board machines and the densities of the bacterial 16S rRNA genes and those of the red slime producers D. geothermalis and Meiothermus spp. were measured by QPCR (quantitative real time PCR). D. geothermalis was found at nine machines, usually from splash area deposits, but its contribution was minor, 0.001–1%, to the total bacterial burden of 8.3 to log 10.5 log units per gram wet-weight of the deposits. When D. geothermalis was found in a measurable quantity, Meiothermus spp. also was found, often in bulk quantity (7–100% of the total bacteria). The data are in line with the properties of D. geothermalis known from laboratory biofilm studies, indicating this species is a pioneer coloniser of machine surfaces and may help other bacteria to adhere and grown into biofilms, rather than competing with them. [ABSTRACT FROM AUTHOR]
- Published
- 2008
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4. SchlossLab/Sovacool_OptiFit_mSphere_2022: OptiFit paper 1.0.0
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Sovacool, Kelly L., Westcott, Sarah L., M. Brodie Mumphrey, Dotson, Gabrielle A., and Schloss, Patrick D.
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amplicon sequencing ,microbiome ,bioinformatics ,microbial ecology ,algorithms - Abstract
The paper accompanying the OptiFit algorithm is now out in mSphere! https://journals.asm.org/doi/10.1128/msphere.00916-21 Assigning amplicon sequences to operational taxonomic units (OTUs) is an important step in characterizing microbial communities across large data sets. A notable difference betweende novoclustering and database-dependent reference clustering methods is that OTU assignments fromde novomethods may change when new sequences are added. However, one may wish to incorporate new samples to previously clustered data sets without clustering all sequences again, such as when comparing across data sets or deploying machine learning models. Existing reference-based methods produce consistent OTUs but only consider the similarity of each query sequence to a single reference sequence in an OTU, resulting in assignments that are worse than those generated byde novomethods. To provide an efficient method to fit sequences to existing OTUs, we developed the OptiFit algorithm. Inspired by thede novoOptiClust algorithm, OptiFit considers the similarity of all pairs of reference and query sequences to produce OTUs of the best possible quality. We tested OptiFit using four data sets with two strategies: (i) clustering to a reference database and (ii) splitting the data set into a reference and query set, clustering the references using OptiClust, and then clustering the queries to the references. The result is an improved implementation of reference-based clustering. OptiFit produces OTUs of a quality similar to that of OptiClust at faster speeds when using the split data set strategy. OptiFit provides a suitable option for users requiring consistent OTU assignments at the same quality as afforded byde novoclustering methods.
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- 2022
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5. New techniques for studying competition by Rhizobia and for assessing nitrogen fixation in the field
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Wilson, Kate J., Peoples, Mark B., Jefferson, Richard A., Ladha, J. K., editor, and Peoples, M. B., editor
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- 1995
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6. Methods for microbial autecology in the soil rhizosphere
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Schmidt, Edwin L., Keister, Donald L., editor, and Cregan, Perry B., editor
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- 1991
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7. Coliform Bacteria and Nitrogen Fixation in Pulp and Paper Mill Effluent Treatment Systems
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Frederick Archibald, Brian T. Driscoll, Francis Gauthier, and Josh D. Neufeld
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Paper ,Microorganism ,engineering.material ,Biology ,complex mixtures ,Waste Disposal, Fluid ,Applied Microbiology and Biotechnology ,Microbial Ecology ,Microbiology ,Bioreactors ,Enterobacteriaceae ,Klebsiella ,Nitrogen Fixation ,Effluent ,Ecosystem ,DNA Primers ,Base Sequence ,Ecology ,business.industry ,Pulp (paper) ,technology, industry, and agriculture ,food and beverages ,Paper mill ,Pulp and paper industry ,Coliform bacteria ,Biodegradation, Environmental ,Activated sludge ,Genes, Bacterial ,Nitrogen fixation ,engineering ,Water Microbiology ,business ,Food Science ,Biotechnology ,Waste disposal - Abstract
The majority of pulp and paper mills now biotreat their combined effluents using activated sludge. On the assumption that their wood-based effluents have negligible fixed N, and that activated-sludge microorganisms will not fix significant N, these mills routinely spend large amounts adding ammonia or urea to their aeration tanks (bioreactors) to permit normal biomass growth. N 2 fixation in seven Eastern Canadian pulp and paper mill effluent treatment systems was analyzed using acetylene reduction assays, quantitative nitrogenase ( nifH ) gene probing, and bacterial isolations. In situ N 2 fixation was undetectable in all seven bioreactors but was present in six associated primary clarifiers. One primary clarifier was studied in greater detail. Approximately 50% of all culturable cells in the clarifier contained nifH , of which >90% were Klebsiella strains. All primary-clarifier coliform bacteria growing on MacConkey agar were identified as klebsiellas, and all those probed contained nifH . In contrast, analysis of 48 random coliform isolates from other mill water system locations showed that only 24 (50%) possessed the nifH gene, and only 13 (27%) showed inducible N 2 -fixing activity. Thus, all the pulp and paper mill primary clarifiers tested appeared to be sites of active N 2 fixation (0.87 to 4.90 mg of N liter −1 day −1 ) and a microbial community strongly biased toward this activity. This may also explain why coliform bacteria, especially klebsiellas, are indigenous in pulp and paper mill water systems.
- Published
- 2000
8. Feature Papers in Ecology 2022 and the Remarkable Journal's Advancements.
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Arévalo, José Ramón
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ANIMAL-plant relationships ,AQUATIC ecology ,AGRICULTURE ,BIOGEOCHEMICAL cycles ,PLANT ecology ,COWPEA ,MICROBIAL ecology - Abstract
Similarly, it is clear that, when viewed from the perspective of agricultural protection, plant physiology, or ecological restoration, microbial ecology plays a pivotal role in understanding ecological processes. In this case, we obtained an interesting collection of papers from different fields, such as animal ecology, focusing on the impact of agricultural activities on nocturnal mammals and small mammals [[1]]; plant-animal interactions [[3]]; wild felid diversity [[5]]; ecological microbiology from different perspectives [[6], [8], [10]]; aquatic ecology [[11]]; and plant ecology [[13]]. Plant-animal interactions can be considered a fundamental area within ecology, while the description of plant communities and biogeochemical processes significantly contribute to our understanding of ecological functioning. [Extracted from the article]
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- 2023
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9. Cellulolytic potential and filter paper activity of fungi isolated from ancients manuscripts from the Medina of Fez
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Soumya Elabed, Fatimazahra El Bergadi, Iraqui Mohammed, Faouzi Laachari, and Saad Koraichi Ibnsouda
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biology ,Aspergillus oryzae ,Microbial ecology ,Mucor racemosus ,Hypocrea ,Mycology ,Botany ,Aspergillus niger ,Schizophyllum commune ,Penicillium chrysogenum ,biology.organism_classification ,Applied Microbiology and Biotechnology - Abstract
The content of libraries in Fez is an important historical testimony and a treasure of knowledge of several civilizations. Unfortunately, this cultural heritage has suffered deterioration caused by many factors, including microbial deterioration specifically by cellulolytic fungi. The aim of our study was the identification and characterization of the microflora that damage historical manuscripts books from an old library of the Medina of Fez. A total of 31 filamentous fungi were isolated from deteriorated paper of ancient books. Nine of these isolates were screened positive for the ability to degrade carboxymethylcellulose (CMC). The ability of the nine isolates to produce filter paper activity (FPUase) in liquid media as well as the effect of temperature and pH were also studied. According to the molecular identification, the most frequent species were Penicillium chrysogenum, Aspergillus niger, Aspergillus oryzae and Mucor racemosus, and other less frequent, such as Hypocrea lixii, Aspergillus melleus and Schizophyllum commune were also present. Also, the effect of fungal contamination in paper artificially attacked for 18 months at 25 °C was examined. The fungal strains were able to degrade filter paper to varying degrees.
- Published
- 2013
10. University of British Columbia Reports Findings in Campylobacter jejuni (An Integrated Paper Microfluidic Device Based on Isothermal Amplification for Simple Sample-to-Answer Detection of Campylobacter jejuni).
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CAMPYLOBACTER jejuni ,MICROFLUIDIC devices ,CHICKEN as food ,FOODBORNE diseases ,GRAM-negative bacteria ,MICROBIAL ecology - Published
- 2023
11. Production of cryoprotectant extracellular polysaccharide substances (EPS) by the marine psychrophilic bacteriumColwellia psychrerythraeastrain 34H under extreme conditionsThis article is one of a selection of papers in the Special Issue on Polar and Alpine Microbiology
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Jody W. Deming, Shelly D. Carpenter, and Joseph G. MarxJ.G. Marx
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Growth medium ,Strain (chemistry) ,Immunology ,Hydrostatic pressure ,General Medicine ,Biology ,Applied Microbiology and Biotechnology ,Microbiology ,Salinity ,chemistry.chemical_compound ,chemistry ,Microbial ecology ,Genetics ,Extracellular ,Extreme environment ,Food science ,Psychrophile ,Molecular Biology - Abstract
Extracellular polysaccharide substances (EPS) play critical roles in microbial ecology, including the colonization of extreme environments in the ocean, from sea ice to the deep sea. After first developing a sugar-free growth medium, we examined the relative effects of temperature, pressure, and salinity on EPS production (on a per cell basis) by the obligately marine and psychrophilic γ-proteobacterium, Colwellia psychrerythraea strain 34H. Over growth-permissive temperatures of ~10 to –4 °C, EPS production did not change, but from –8 to –14 °C when samples froze, EPS production rose dramatically. Similarly, at growth-permissive hydrostatic pressures of 1–200 atm (1 atm = 101.325 kPa) (at –1 and 8 °C), EPS production was unchanged, but at higher pressures of 400 and 600 atm EPS production rose markedly. In salinity tests at 10‰–100‰ (and –1 and 5 °C), EPS production increased at the freshest salinity tested. Extreme environmental conditions thus appear to stimulate EPS production by this strain. Furthermore, strain 34H recovered best from deep-freezing to –80 °C (not found for Earthly environments) if first supplemented with a preparation of its own EPS, rather than other cryoprotectants like glycerol, suggesting EPS production as both a survival strategy and source of compounds with potentially novel properties for biotechnological and other applications.
- Published
- 2009
12. Prediction, enrichment and isolation identify a responsive, competitive community of cellulolytic microorganisms from a municipal landfill.
- Author
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Co, Rebecca and Hug, Laura A
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LANDFILLS ,TRICHODERMA reesei ,WASTE paper ,HAZARDOUS waste sites ,CELLULOLYTIC bacteria ,MICROBIAL ecology ,LEACHATE - Abstract
Landfills are engineered, heterogeneously contaminated sites containing large reservoirs of paper waste. Cellulose degradation is an important process within landfill microbial ecology, and these anoxic, saturated environments are prime locations for discovery of cellulases that may offer improvements on industrial cellulose degradation efforts. We sampled leachate from three locations within a municipal landfill, a leachate collection cistern, and groundwater from an adjacent aquifer to identify cellulolytic populations and their associated cellulases. Metagenomic sequencing identified wide-spread and taxonomically diverse cellulolytic potential, with a notable scarcity of predicted exocellulases. 16S rRNA amplicon sequencing detected nine landfill microorganisms enriched in a customized leachate medium amended with microcrystalline cellulose or common paper stocks. Paper-enrichment cultures showed competition dynamics in response to the specific composition (lignin: hemi-cellulose: cellulose) of the different paper stocks. From leachate biomass, four novel cellulolytic bacteria were isolated, including two with the capacity for cellulolysis at industrially relevant temperatures. None of the isolates demonstrated exocellulase activity, consistent with the metagenome-based predictions. However, there was very little overlap between metagenome-derived predicted cellulolytic organisms, organisms enriched on paper sources, or the isolates, suggesting the landfill cellulolytic community is at low abundance but able to rapidly respond to introduced substrates. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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13. Niche differentiation of ammonia-oxidising archaea (AOA) and bacteria (AOB) in response to paper and pulp mill effluent
- Author
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Bradley D. Eyre, Michael J. Keough, B. N. Holmes, JP Keane, Stanley Suresh Robert, Guy C. J. Abell, John K. Volkman, and DJ Ross
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Archaeal Proteins ,Molecular Sequence Data ,Microbial metabolism ,Soil Science ,Industrial Waste ,Real-Time Polymerase Chain Reaction ,Tasmania ,Microbial ecology ,Bacterial Proteins ,Rivers ,RNA, Ribosomal, 16S ,Effluent ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,Ecology ,biology ,Bacteria ,Outfall ,Biogeochemistry ,Sediment ,Sequence Analysis, DNA ,biology.organism_classification ,Archaea ,Biota ,Microcosm ,Oxidoreductases ,Water Pollutants, Chemical - Abstract
Sediment organic loading has been shown to affect estuarine nitrification and denitrification, resulting in changes to sediment biogeochemistry and nutrient fluxes detrimental to estuarine health. This study examined the effects of organic loading on nutrient fluxes and microbial communities in sediments receiving effluent from a paper and pulp mill (PPM) by applying microcosm studies and molecular microbial ecology techniques. Three sites near the PPM outfall were compared to three control sites, one upstream and two downstream of the outfall. The control sites showed coupled nitrification–denitrification with minimal ammonia release from the sediment. In contrast, the impacted sites were characterised by nitrate uptake and substantial ammonia efflux from the sediments, consistent with a decoupling of nitrification and denitrification. Analysis of gene diversity demonstrated that the composition of nitrifier communities was not significantly different at the impacted sites compared to the control sites; however, analysis of gene abundance indicated that whilst there was no difference in total bacteria, total archaea or ammonia-oxidising archaea (AOA) abundance between the control and impacted sites, there was a significant reduction in ammonia-oxidising bacteria (AOB) at the impacted sites. The results of this study demonstrate an effect of organic loading on estuarine sediment biogeochemistry and highlight an apparent niche differentiation between AOA and AOB.
- Published
- 2013
14. Deep subsurface microbiology: a guide to the research topic papers
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Virginia P. Edgcomb, Andreas P Teske, Axel Schippers, and Jennifer F. Biddle
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Total organic carbon ,Microbiology (medical) ,Biogeochemical cycle ,geography ,subsurface microbiology ,geography.geographical_feature_category ,Geomicrobiology ,Editorial Article ,lcsh:QR1-502 ,Biosphere ,Aquifer ,oceanic crust ,methanogenesis ,Biology ,Carbon sequestration ,biology.organism_classification ,Microbiology ,lcsh:Microbiology ,Microbial ecology ,uncultured microbes ,sulfate reduction ,marine sediments ,Archaea - Abstract
Deep subsurface microbiology is a rising field in geomicrobiology, environmental microbiology and microbial ecology that focuses on the molecular detection and quantification, cultivation, biogeographic examination, and distribution of bacteria, archaea, and eukarya that permeate the subsurface biosphere. The deep biosphere includes a variety of subsurface habitats, such as terrestrial deep aquifer systems or mines, deeply buried hydrocarbon reservoirs, marine sediments and the basaltic ocean crust. The deep subsurface biosphere abounds with uncultured, only recently discovered and—at best—incompletely understood microbial populations. So far, microbial cells and DNA remain detectable at sediment depths of more than 1 km and life appears limited mostly by heat in the deep subsurface. Severe energy limitation, either as electron acceptor or donor shortage, and scarcity of microbially degradable organic carbon sources are among the evolutionary pressures that may shape the genomic and physiological repertoire of the deep subsurface biosphere. Its biogeochemical importance in long-term carbon sequestration, subsurface elemental cycling and crustal aging, is a major focus of current research at the interface of microbiology, geochemistry, and biosphere/geosphere evolution. The papers of this Frontiers e-volume bear evidence of the rapid advances in deep subsurface microbiology.
- Published
- 2013
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15. VarChat: the generative AI assistant for the interpretation of human genomic variations.
- Author
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Paoli, Federica De, Berardelli, Silvia, Limongelli, Ivan, Rizzo, Ettore, and Zucca, Susanna
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GENERATIVE artificial intelligence ,SCIENTIFIC literature ,PROFESSIONAL ethics ,GENETIC variation ,RESEARCH personnel ,MICROBIAL ecology - Abstract
Motivation In the modern era of genomic research, the scientific community is witnessing an explosive growth in the volume of published findings. While this abundance of data offers invaluable insights, it also places a pressing responsibility on genetic professionals and researchers to stay informed about the latest findings and their clinical significance. Genomic variant interpretation is currently facing a challenge in identifying the most up-to-date and relevant scientific papers, while also extracting meaningful information to accelerate the process from clinical assessment to reporting. Computer-aided literature search and summarization can play a pivotal role in this context. By synthesizing complex genomic findings into concise, interpretable summaries, this approach facilitates the translation of extensive genomic datasets into clinically relevant insights. Results To bridge this gap, we present VarChat (varchat.engenome.com), an innovative tool based on generative AI, developed to find and summarize the fragmented scientific literature associated with genomic variants into brief yet informative texts. VarChat provides users with a concise description of specific genetic variants, detailing their impact on related proteins and possible effects on human health. In addition, VarChat offers direct links to related scientific trustable sources, and encourages deeper research. Availability and implementation varchat.engenome.com. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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16. SYNOPSES OF PAPERS OF MICROBIOLOGICAL INTEREST: SYMPOSIUM: MICROBIAL ECOLOGY IN MIXED POPULATIONS
- Author
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Rosamund J. Williams
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Microbiology (medical) ,Microbial ecology ,Ecology ,General Medicine ,Biology ,Microbiology - Published
- 1991
17. Processes in Microbial Ecology. By David L. Kirchman. Oxford and New York: Oxford University Press. $49.95 (paper). xiii + 312 p.; ill.; index. ISBN: 978-0-19-958692-9. 2012
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J. Vaun McArthur
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Index (economics) ,Microbial ecology ,Anthropology ,General Agricultural and Biological Sciences ,Geology - Published
- 2013
18. I, Microbiologist: A Discovery-Based Course in Microbial Ecology and Molecular Evolution. By Erin R. Sanders and Jeffrey H. Miller; with contributions by, Craig Herbold, Krystle Ziebell, and Karen Flummerfelt. Washington (DC): ASM Press. $79.95 (paper). xxx + 438 p.; ill.; index. ISBN: 978-1-55581-470-0. 2010
- Author
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Chet S. Fornari
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Index (economics) ,biology ,Microbial ecology ,Anthropology ,Philosophy ,Miller ,Environmental ethics ,General Agricultural and Biological Sciences ,biology.organism_classification - Published
- 2012
19. Investigations into the application of a process for the determination of microbial activity in biofilms.
- Author
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Holtmann, D. and Sell, D.
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BIOFILMS ,MICROBIAL aggregation ,MICROBIAL ecology ,WASTE paper ,WASTE products - Abstract
The formation of biofilms in a waste paper medium was studied in a pilot plant by analysing the redox potential in the biofilm. Miniaturised redox electrodes were applied at the reactor wall/biofilm phase boundary. With this measurement set-up, it was possible to demonstrate the effectiveness of biocides and thus to avoid under- and over-doses with these agents. The redox signals measured were correlated with reference methods, such as colony-forming units and dehydrogenase activity. [ABSTRACT FROM AUTHOR]
- Published
- 2001
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20. Retracted: Recent Development in the Methods of Studying Microbial Diversity
- Author
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Ansari, Mohd Ikram, Malik, Abdul, Malik, Abdul, editor, Grohmann, Elisabeth, editor, and Alves, Madalena, editor
- Published
- 2013
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21. Microbial Ecology of the Soil and Plant Growth. By Pierre Davet. Enfield (New Hampshire): Science Publishers. $55.00 (paper). xv + 392 p; ill.; index. ISBN: 1‐57808‐180‐7 (hc); 1‐57808‐303‐6 (pb). [Translation of the French Edition, INRA, Paris, 1996.] 2004
- Author
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Clive A. Edwards
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Plant growth ,Geography ,Index (economics) ,Microbial ecology ,Environmental ethics ,Forestry ,General Agricultural and Biological Sciences - Published
- 2006
22. Strategies and Challenges of Microbiota Regulation in Baijiu Brewing.
- Author
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Zhang, Pengpeng, Liu, Yanbo, Li, Haideng, Hui, Ming, and Pan, Chunmei
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BREWING ,FERMENTED foods ,MICROBIAL ecology ,RAW materials ,QUALITY assurance - Abstract
The traditional Chinese Baijiu brewing process utilizes natural inoculation and open fermentation. The microbial composition and abundance in the microecology of Baijiu brewing often exhibit unstable characteristics, which directly results in fluctuations in Baijiu quality. The microbiota plays a crucial role in determining the quality of Baijiu. Analyzing the driving effect of technology and raw materials on microorganisms. Elucidating the source of core microorganisms and interactions between microorganisms, and finally utilizing single or multiple microorganisms to regulate and intensify the Baijiu fermentation process is an important way to achieve high efficiency and stability in the production of Baijiu. This paper provides a systematic review of the composition and sources of microbiota at different brewing stages. It also analyzes the relationship between raw materials, brewing processes, and brewing microbiota, as well as the steps involved in the implementation of brewing microbiota regulation strategies. In addition, this paper considers the feasibility of using Baijiu flavor as a guide for Baijiu brewing regulation by synthesizing the microbiota, and the challenges involved. This paper is a guide for flavor regulation and quality assurance of Baijiu and also suggests new research directions for regulatory strategies for other fermented foods. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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23. Technical Note: Could benzalkonium chloride be a suitable alternative to mercuric chloride for preservation of seawater samples?
- Author
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Gloël, J., Robinson, C., Tilstone, G. H., Tarran, G., and Kaiser, J.
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BENZALKONIUM chloride ,MERCURIC chloride ,SEA water analysis ,WATER sampling ,MICROBIAL ecology - Abstract
Instrumental equipment unsuitable or unavailable for fieldwork as well as lack of ship space can necessitate the preservation of seawater samples prior to analysis in a shore-based laboratory. Mercuric chloride (HgCl
2 ) is routinely used for such preservation, but its handling and subsequent disposal incur significant risks and expense. Benzalkonium chloride (BAC) has been used previously for freshwater samples. Here, we assess BAC as a less hazardous alternative microbial inhibitor for marine samples prior to the measurement of oxygen-to-argon (O2 =Ar) ratios, as used for the determination of plankton net community production. BAC at a concentration of 50mgdm-3 inhibited microbial activity for at least three days in seawater with chlorophyll a (Chl a) concentrations up to 1mgm-3 , possibly longer when Chl a concentrations were lower. BAC concentrations of 100 and 200mgdm-3 were no more effective than 50mgdm-3 . With fewer risks to human health and the environment, and no requirement for expensive waste disposal, BAC could be a viable alternative to HgCl2 for short-term preservation of seawater samples, but is not a replacement for HgCl2 in the case of oxygen triple isotope analysis, which requires storage over weeks to months. In any event, further tests on a case-by-case basis should be undertaken if use of BAC was considered, since its inhibitory activity may depend on concentration and composition of the microbial community. [ABSTRACT FROM AUTHOR]- Published
- 2015
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24. Optimization of bioprocess of Schleiferilactobacillus harbinensis Ca12 and its viability in frozen Brazilian berries (Açai, Euterpe oleracea Mart.)
- Author
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Mérilie Gagnon, Carolina Alves Petit Couto, Priscilla Oliveira Gil, Paulo Afonso Granjeiro, Heloísa Carneiro Colares, Juliana Teixeira de Magalhães, Gabriele Moreira Guimarães, Stephanie Lourrani Evangelista Neves Santos, Denis Roy, Flávio Guimarães da Fonseca, Tuânia Natacha Lopes Silva, Daniel Bonoto Gonçalves, and Iracema Luisa Quintino de Carvalho
- Subjects
Antioxidant ,Euterpe ,Food Handling ,medicine.medical_treatment ,Biology ,engineering.material ,Microbiology ,Antioxidants ,law.invention ,Probiotic ,Microbial ecology ,Functional food ,law ,Freezing ,Media Technology ,medicine ,Food microbiology ,Food science ,Bioprocess ,Microbial Viability ,Pulp (paper) ,Lactobacillus ,Fruit ,Food Microbiology - Research Paper ,engineering ,Beneficial organism - Abstract
Amazonian palm berries (açaí, Euterpe oleracea Mart.) are fruits with high nutritional value and antioxidant activity and have aroused the interest of consumers, popularizing fruit pulps enriched with probiotics. Amazonian palm berries (açaí, Euterpe oleracea Mart.) are fruits with high nutritional potential, providing a source of carbohydrates, fibers, proteins, lipids, vitamins, and minerals. Furthermore, açai provides several health benefits, including antioxidant activity. Nutritionally enhanced foods have aroused the interest of consumers, popularizing fruit pulps enriched with probiotics. Probiotics are dietary supplements consisting of live, beneficial microorganisms in the host which improve the intestinal microbiota. The objective of this study was to isolate, identify, and characterize the probiotic potential of an isolated Schleiferilactobacillus harbinensis strain (dubbed Ca12) and provide an optimized bioprocess for its production, using the complete factorial and central rotational compound design to supplement the frozen açai pulp. The isolated strain S. harbinensis Ca12 presented adequate resistance to gastric juice and bile salts, microbial activity against different Candida strains, self-aggregation and coaggregation properties, high adhesion in HT-29 cells, and 35% inhibition of Salmonella in HT-29 cells. When optimized, the cellular biomass production of the S. harbinensis Ca12 strain was approximately 600% higher than the unsupplemented whey, with a production of 3.6 × 1010 CFU mL(−1). The S. harbinensis Ca12 strain’s viability in the creamy and traditional frozen açai pulp was shown to be stable for up to 6 months at 20 °C. The impact of this study involved for the first time the S. harbinensis Ca12 described in the Brazilian cocoa pulp with activity against Candida albicans of clinical importance, creating the potential of a new functional food with important benefits to human health as prevention for candidiasis. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42770-021-00559-3.
- Published
- 2021
25. Trends in Seagrass Research and Conservation in Malaysian Waters.
- Author
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Kamal, Abu Hena Mustafa, Abdulla-Al-Asif, Idris, Mohd Hanafi, Bhuiyan, Md Khurshid Alam, and Rahman, A. F. M. Arifur
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SEAGRASS restoration ,WATER conservation ,SEAGRASSES ,BOTANY ,POSIDONIA ,CARBON sequestration ,HABITATS ,REMOTE sensing ,MICROBIAL ecology - Abstract
The seagrass ecosystems found in the marine and coastal areas, with substantial economic and ecological services and span all over the globe excluding the Antarctic region. The Coral Triangle and Southeast Asia are recognized as a worldwide hotspot of seagrass species and habitats, encompassing 10-21 species of seagrass in every nation, although the study, understanding, and quantity of publications on seagrass ecosystems are rather limited in the region, including Malaysia. Malaysia contains 18 seagrass species from three families, which occupy 16.8 km² of coastal area, where the study and discovery of seagrass species and meadows began in 1904 with the report of Beccari. All of the published papers reviewed reported on Malaysian seagrassrelated research, which was divided into nine topic groups: biology and distribution, carbon sequestration, fauna, remote sensing, impact and pollution genetic study, restoration, microbiological investigation, and others. The extensive study of the seagrass ecosystem began in 1993, and we have identified 183 published papers from Scopus, 141 publications from Web of Science, and 42 from Google Scholar. However, the average trend of the number of publications from 1993 to 1999 was 0.71 ± 0.36, while from 2000 to 2022 was 7.70 ± 1.16 followed by the average trend of the yearly number of publications was 6.78 ± 1.08. The highest number of publications was found on faunal categories (43.17%), followed by biology and distribution (21.85%). The number of articles that were published on Malaysian seagrass meadows each year has been discovered to be rising, which indicates that the trends in seagrass study and publishing were progressively garnering the attention of researchers, academics, and the government. However, to better understand the sustainable ecology and ecosystem services provided by seagrass habitats, an emphasis on certain research niches, such as the genetic study of flora and fauna in seagrass meadows, microbial ecology, and restoration as well as conservation of seagrass species might be helpful. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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26. Metaproteomics: an emerging tool for the identification of proteins from extreme environments
- Author
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Nudrat Ehsan, Salma Mukhtar, Kauser A. Malik, Kashif Maseh, and Samina Mehnaz
- Subjects
Microbial ecology ,Metagenomics ,Microbial diversity ,fungi ,Metaproteomics ,Environmental science ,Extreme environment ,Identification (biology) ,Biochemical engineering ,complex mixtures ,Paper manufacturing ,Organic molecules - Abstract
Microbial communities from extreme environments, such as saline, arid, hot, cold, acidic, or alkaline are especially important because they have special genetic and physiological modifications to function properly under extreme environments. They possess extremozymes and other biomolecules that can be used in various industrial processes, e.g., pharmaceuticals, paper manufacturing, degradation of complex organic molecules, biofuel production and food industries. With the advent of new sequencing technologies and ‘omics’ approaches, such as metagenomics, metatranscriptomics and metaproteomics, new windows have been opened to study the microbial ecology and functional microbial communities from extreme environments. Recently, metaproteomic analysis has been extensively used to explore the functional microbial communities from various extreme environments around the globe. In this review, we have focused on the microbial diversity analysis, identification of novel proteins, and enzymes from extreme environments, through metaproteomic approaches.
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- 2021
27. Unseen Weapons: Bacterial Extracellular Vesicles and the Spread of Antibiotic Resistance in Aquatic Environments.
- Author
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Barathan, Muttiah, Ng, Sook-Luan, Lokanathan, Yogeswaran, Ng, Min Hwei, and Law, Jia Xian
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EXTRACELLULAR vesicles ,DRUG resistance in bacteria ,SUSTAINABILITY ,HORIZONTAL gene transfer ,SUSTAINABLE aquaculture ,BIOFILMS ,ECOSYSTEMS - Abstract
This paper sheds light on the alarming issue of antibiotic resistance (ABR) in aquatic environments, exploring its detrimental effects on ecosystems and public health. It examines the multifaceted role of antibiotic use in aquaculture, agricultural runoff, and industrial waste in fostering the development and dissemination of resistant bacteria. The intricate interplay between various environmental factors, horizontal gene transfer, and bacterial extracellular vesicles (BEVs) in accelerating the spread of ABR is comprehensively discussed. Various BEVs carrying resistance genes like blaCTX-M, tetA, floR, and sul/I, as well as their contribution to the dominance of multidrug-resistant bacteria, are highlighted. The potential of BEVs as both a threat and a tool in combating ABR is explored, with promising strategies like targeted antimicrobial delivery systems and probiotic-derived EVs holding significant promise. This paper underscores the urgency of understanding the intricate interplay between BEVs and ABR in aquatic environments. By unraveling these unseen weapons, we pave the way for developing effective strategies to mitigate the spread of ABR, advocating for a multidisciplinary approach that includes stringent regulations, enhanced wastewater treatment, and the adoption of sustainable practices in aquaculture. [ABSTRACT FROM AUTHOR]
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- 2024
- Full Text
- View/download PDF
28. Biodiversity and succession of lactic microbiota involved in Brazilian buffalo mozzarella cheese production
- Author
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Luana Faria Silva, Juliano De Dea Lindner, Tássila Nakata Sunakozawa, Daniel Mathias Fuzette Amaral, Tiago Casella, Ana Lúcia Barretto Penna, Mara Corrêa Lelles Nogueira, Universidade Estadual Paulista (UNESP), Universidade Federal de Santa Catarina (UFSC), and FAMERP - São José Do Rio Preto Medical School
- Subjects
Cheese biodiversity ,Buffaloes ,medicine.disease_cause ,Microbiology ,chemistry.chemical_compound ,Microbial ecology ,Cheese ,Leuconostoc citreum ,RNA, Ribosomal, 16S ,Media Technology ,medicine ,Animals ,Food microbiology ,Food science ,biology ,Microbiota ,Raw milk ,food and beverages ,Autochthonous bacteria ,Biodiversity ,biology.organism_classification ,Random Amplified Polymorphic DNA Technique ,Lactic acid ,Milk ,chemistry ,Leuconostoc mesenteroides ,Food Microbiology - Research Paper ,Food Microbiology ,Restriction fragment length polymorphism ,Lactic acid bacteria identification ,Bacteria - Abstract
Made available in DSpace on 2022-05-01T09:47:14Z (GMT). No. of bitstreams: 0 Previous issue date: 2022-03-01 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) The biodiversity and succession of lactic acid bacteria (LAB) involved in the production and storage of Brazilian buffalo mozzarella cheese were evaluated. The isolates were characterized by Gram staining and catalase test, by the ability to grow at different conditions: temperatures, pH, concentrations of NaCl, and production of CO2 from glucose. The biodiversity and succession of 152 LAB isolated during cheese production were evaluated by 16S rRNA gene sequencing, Random Amplified Polymorphic DNA (RAPD-PCR), and Restriction Fragment Length Polymorphism (RFLP-PCR) techniques. Most of the strains grow well at 30 °C and are tolerant to 6.5% of NaCl, and in general, the best pH for growing was 9.6. Leuconostoc mesenteroides, Lacticaseibacillus casei, Limosilactobacillus fermentum, and Enterococcus sp. were prevalent and present in almost all steps of production. The LAB strains are typically found in the traditional Italian cheese, except the Leuconostoc citreum species. Sixty clusters were obtained by RAPD-PCR with 85% of similarity (114 isolates) while most of the LAB was clustered with 100% of similarity by the RFLP-PCR technique. The applied techniques enabled a valuable elucidation of the LAB biodiversity and succession, contributing to a better understanding of the specific microbial cultures with a technological aptitude of this cheese. Food Engineering and Technology Department UNESP - São Paulo State University, Rua Cristóvão Colombo, 2265, SP Food Science and Technology Department UFSC - Federal University of Santa Catarina, SC Center for Microorganisms Investigation FAMERP - São José Do Rio Preto Medical School, SP Food Engineering and Technology Department UNESP - São Paulo State University, Rua Cristóvão Colombo, 2265, SP FAPESP: 2008/56667-5 FAPESP: 2011/11922-0
- Published
- 2021
29. Research progress on the correlation between intestinal flora and colorectal cancer.
- Author
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Xinyu Wang, Qian Zhang, Rongxuan Xu, Xiaofeng Li, and Zhijun Hong
- Subjects
COLORECTAL cancer ,HUMAN body ,MEDICAL screening ,BOTANY ,MICROBIAL ecology - Abstract
Colorectal cancer (CRC) is one of themost common gastrointestinalmalignancies in the world. With the rapid pace of life and changes in diet structure, the incidence and mortality of CRC increase year by year posing a serious threat to human health. As the most complex and largest microecosystem in the human body, intestinal microecology is closely related to CRC. It is an important factor that affects and participates in the occurrence and development of CRC. Advances in nextgeneration sequencing technology and metagenomics have provided new insights into the ecology of gut microbes. It also helps to link intestinal flora with CRC, and the relationship between intestinal flora and CRC can be continuously understood from different levels. This paper summarizes the relationship between intestinal flora and CRC and its potential role in the diagnosis of CRC providing evidence for early screening and treatment of CRC. [ABSTRACT FROM AUTHOR]
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- 2024
- Full Text
- View/download PDF
30. AFITbin: a metagenomic contig binning method using aggregate l-mer frequency based on initial and terminal nucleotides.
- Author
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Darabi, Amin, Sobhani, Sayeh, Aghdam, Rosa, and Eslahchi, Changiz
- Subjects
BIOTIC communities ,METAGENOMICS ,NUCLEOTIDES ,MATRIX decomposition ,MICROBIAL communities ,MICROBIAL ecology - Abstract
Background: Using next-generation sequencing technologies, scientists can sequence complex microbial communities directly from the environment. Significant insights into the structure, diversity, and ecology of microbial communities have resulted from the study of metagenomics. The assembly of reads into longer contigs, which are then binned into groups of contigs that correspond to different species in the metagenomic sample, is a crucial step in the analysis of metagenomics. It is necessary to organize these contigs into operational taxonomic units (OTUs) for further taxonomic profiling and functional analysis. For binning, which is synonymous with the clustering of OTUs, the tetra-nucleotide frequency (TNF) is typically utilized as a compositional feature for each OTU. Results: In this paper, we present AFIT, a new l-mer statistic vector for each contig, and AFITBin, a novel method for metagenomic binning based on AFIT and a matrix factorization method. To evaluate the performance of the AFIT vector, the t-SNE algorithm is used to compare species clustering based on AFIT and TNF information. In addition, the efficacy of AFITBin is demonstrated on both simulated and real datasets in comparison to state-of-the-art binning methods such as MetaBAT 2, MaxBin 2.0, CONCOT, MetaCon, SolidBin, BusyBee Web, and MetaBinner. To further analyze the performance of the purposed AFIT vector, we compare the barcodes of the AFIT vector and the TNF vector. Conclusion: The results demonstrate that AFITBin shows superior performance in taxonomic identification compared to existing methods, leveraging the AFIT vector for improved results in metagenomic binning. This approach holds promise for advancing the analysis of metagenomic data, providing more reliable insights into microbial community composition and function. Availability: A python package is available at: https://github.com/SayehSobhani/AFITBin. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
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31. Past‐President address: My journey in microbial ecology—footprints in the sand, island hopping, supply chains, and technology bridges.
- Author
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Langlois, Gaytha A.
- Subjects
- *
MICROBIAL ecology , *SUPPLY chains , *SAND , *ISLANDS , *RESEARCH personnel , *ECOLOGICAL impact - Abstract
This paper highlights and honors the connectivity among protistan researchers, using my own research journey as a backdrop, with attention to the supply chain of ideas, supporters, and other influencers who helped to shape and guide my career by sharing their ideas, protocols, skills, and enthusiasm. In looking back at the journey, the supply chain in my career has also included changes in the conceptual framework for my research studies, converging with a continuous flow of ideas and support from colleagues and mentors. To illustrate the complex map of ideas and supporters, this paper will examine technological advances, paradigm shifts in ecological constructs, geographical considerations, breakthroughs in peritrich biology, and the importance of an integrated perspective as we navigate the changing realities of today's scientific challenges. [ABSTRACT FROM AUTHOR]
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- 2024
- Full Text
- View/download PDF
32. Commensalism and syntrophy in the chemostat: a unifying graphical approach.
- Author
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Sari, Tewfik
- Subjects
COMMENSALISM ,SYNTROPHISM ,CHEMOSTAT ,MICROBIAL ecology ,SUBSTRATES (Materials science) ,DILUTION - Abstract
The aim of this paper is to show that Tilman’s graphical method for the study of competition between two species for two resources can be advantageously used for the study of commensalism or syntrophy models, where a first species produces the substrate necessary for the growth of the second species. The growth functions of the species considered are general and include both inhibition by the other substrate and inhibition by the species’ limiting substrate, when it is at a high concentration. Because of their importance in microbial ecology, models of commensalism and syntrophy, with or without self-inhibition, have been the subject of numerous studies in the literature. We obtain a unified presentation of a large number of these results from the literature. The mathematical model considered is a differential system in four dimensions. We give a new result of local stability of the positive equilibrium, which has only been obtained in the literature in the case where the removal rates of the species are identical to the dilution rate and the study of stability can be reduced to that of a system in two dimensions. We describe the operating diagram of the system: this is the bifurcation diagram which gives the asymptotic behavior of the system when the operating parameters are varied, i.e., the dilution rate and the substrate inlet concentrations. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
33. Exopolysaccharides from microalgae: production, characterization, optimization and techno-economic assessment
- Author
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Benan İnan, Mustafa Tahsin Yilmaz, Didem Özçimen, Ibrahim Isildak, Sedef Kaptan Usul, and Anıl Tevfik Koçer
- Subjects
Chlorella minutissima ,Growth medium ,Chlorella sorokiniana ,biology ,Nitrogen ,Context (language use) ,Biorefinery ,biology.organism_classification ,Microbiology ,Carbon ,Culture Media ,Industrial Microbiology ,chemistry.chemical_compound ,Microbial ecology ,chemistry ,Polysaccharides ,Microalgae ,Media Technology ,Botryococcus braunii ,Biomass ,Biotechnology and Industrial Microbiology - Research Paper ,Food science ,Bioprocess - Abstract
Microalgae cultivation for exopolysaccharide production has getting more attention as a result of their high hydrocarbon biosynthesis skill. The aim of this study is to examine the exopolysaccharide production potential of different species of microalgae. In this context, exopolysaccharides were produced from Chlorella minutissima, Chlorella sorokiniana and Botryococcus braunii microalgae and the effects of carbon and nitrogen content in the growth medium and illumination time on exopolysaccharide production were analyzed statistically using Box-Behnken experimental design. In addition, techno-economic assessment of exopolysaccharide production were also performed by using the most productive microalgae and optimum conditions determined in this study. As a result of the experiments, it was seen that C. minutissima, C. sorokiniana and B. braunii produced 0.245 ± 0.0025 g/L, 0.163 ± 0.0016 g/L and 0.117 ± 0.0007 g/L exopolysaccharide, respectively. Statistically, it was observed that there was an inverse relationship between the exopolysaccharide production and investigated parameters such as illumination period and carbon and nitrogen amounts of culture mediums. The techno-economic assessment comprising microalgal exopolysaccharide (EPS) bioprocess was carried out, and it showed that the system can be considered economically viable, yet can be improved with biorefinery approach.
- Published
- 2021
34. Anaerobic 3-methylhopanoid production by an acidophilic photosynthetic purple bacterium
- Author
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M. N. Parenteau, Linda L. Jahnke, Michael T. Madigan, Megan L. Kempher, Paula V. Welander, and Marisa H. Mayer
- Subjects
Hopanoids ,Aerobic bacteria ,Photosynthesis ,Biochemistry ,Microbiology ,Anoxygenic phototrophs ,Microbial ecology ,RNA, Ribosomal, 16S ,Botany ,Genetics ,Anaerobiosis ,Molecular Biology ,Phylogeny ,Original Paper ,Base Composition ,biology ,Phototroph ,Chemistry ,Rhodopila globiformis ,General Medicine ,Sequence Analysis, DNA ,biology.organism_classification ,Anoxic waters ,Warm thermal springs ,Acetobacteraceae ,Anaerobic exercise ,Bacteria - Abstract
Bacterial lipids are well-preserved in ancient rocks and certain ones have been used as indicators of specific bacterial metabolisms or environmental conditions existing at the time of rock deposition. Here we show that an anaerobic bacterium produces 3-methylhopanoids, pentacyclic lipids previously detected only in aerobic bacteria and widely used as biomarkers for methane-oxidizing bacteria. Both Rhodopila globiformis, a phototrophic purple nonsulfur bacterium isolated from an acidic warm spring in Yellowstone, and a newly isolated Rhodopila species from a geochemically similar spring in Lassen Volcanic National Park (USA), synthesized 3-methylhopanoids and a suite of related hopanoids and contained the genes encoding the necessary biosynthetic enzymes. Our results show that 3-methylhopanoids can be produced under anoxic conditions and challenges the use of 3-methylhopanoids as biomarkers of oxic conditions in ancient rocks and as prima facie evidence that methanotrophic bacteria were active when the rocks were deposited.
- Published
- 2021
35. Biofilm formation by strains of Burkholderia cenocepacia lineages IIIA and IIIB and B. gladioli pv. alliicola associated with onion bacterial scale rot
- Author
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Marco Aurélio Siqueira da Gama, Emanuel Feitosa de Assunção, Leandro da Silva Velez, Elineide Barbosa de Souza, Pedro Silva, and Lucas Nascimento dos Santos
- Subjects
Burkholderia cenocepacia ,biology ,Bacterial and Fungal Pathogenesis - Research Paper ,Biofilm ,food and beverages ,Swarming motility ,biochemical phenomena, metabolism, and nutrition ,biology.organism_classification ,Microbiology ,Burkholderia cepacia complex ,Burkholderia ,Microbial ecology ,Biofilms ,Mycology ,Onions ,Microscopy, Electron, Scanning ,Media Technology ,Brazil ,Bacteria ,Plant Diseases - Abstract
The Burkholderia genus has high ecological and nutritional versatility, having species capable of causing diseases in animals, humans, and plants. During chronic infections in humans, biofilm formation is a characteristic often associated with strains from different species of this genus. However, there is still no information on the formation of biofilms by plant pathogenic strains of B. cenocepacia (Bce) lineages IIIA and IIIB and B. gladioli pv. alliicola (Bga), which are associated with onion bacterial scale rot in the semi-arid region of northeast Brazil. In this study, we performed an in vitro characterization of biofilm formation ability in different culture media by the phytopathogenic strains of Bce and Bga and investigated its relationship with swarming motility. Our results indicated the existence of an intraspecific variation in biofilm formation capacity in vitro by these bacteria and the existence of a negative correlation between swarming motility and biofilm formation for strains of Bce lineage IIIB. In addition, histopathological analyses performed using optical microscopy and scanning electron microscopy revealed the formation of biofilm in vivo by Bce strains in onion tissues.
- Published
- 2021
36. Microbial communities associated with honey bees in Brazil and in the United States
- Author
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Carlos A. Rosa, Jay D. Evans, Jeffery S. Pettis, Esther Margarida Alves Ferreira Bastos, Denise de Oliveira Scoaris, Frederic Mendes Hughes, and Milton Adolfo Silveira
- Subjects
Bacteria ,Firmicutes ,Microbiota ,fungi ,Beta diversity ,Zoology ,Honey bee ,Bees ,Biology ,Bacterial Physiological Phenomena ,biology.organism_classification ,Microbiology ,United States ,Microbial ecology ,Yeasts ,Mycology ,Lactobacillus ,Debaryomyces hansenii ,Media Technology ,Animals ,Pollen ,Nestedness ,Education in Microbiology - Research Paper ,Symbiosis ,Brazil - Abstract
Honey bee colony losses worldwide call for a more in-depth understanding of the pathogenic and mutualistic components of the honey bee microbiota and their relation with the environment. In this descriptive study, we characterized the yeast and bacterial communities that arise from six substrates associated with honey bees: corbicular pollen, beebread, hive debris, intestinal contents, body surface of nurses and forager bees, comparing two different landscapes, Minas Gerais, Brazil and Maryland, United States. The sampling of five hives in Brazil and four in the USA yielded 217 yeast and 284 bacterial isolates. Whereas the yeast community, accounted for 47 species from 29 genera, was dominated in Brazil by Aureobasidium sp. and Candida orthopsilosis, the major yeast recovered from the USA was Debaryomyces hansenii. The bacterial community was more diverse, encompassing 65 species distributed across 31 genera. Overall, most isolates belonged to Firmicutes, genus Bacillus. Among LAB, species from Lactobacillus were the most prevalent. Cluster analysis evidenced high structuration of the microbial communities, with two distinguished microbial groups between Brazil and the United States. In general, the higher difference among sites and substrates were dependents on the turnover effect (~ 93% of the beta diversity), with a more pronounced effect of nestedness (~ 28%) observed from Brazil microbiota change. The relative abundance of yeasts and bacteria also showed the dissimilarity of the microbial communities between both environments. These results provide a comprehensive view of microorganisms associated with A. mellifera, highlighting the importance of the environment in the establishment of the microbiota associated with honey bees. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42770-021-00539-7.
- Published
- 2021
37. Prediction, enrichment and isolation identify a responsive, competitive community of cellulolytic microorganisms from a municipal landfill
- Author
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Rebecca Co and Laura A. Hug
- Subjects
0301 basic medicine ,Microorganism ,030106 microbiology ,Biomass ,Cellulase ,Applied Microbiology and Biotechnology ,Microbiology ,Enrichment culture ,03 medical and health sciences ,chemistry.chemical_compound ,Microbial ecology ,RNA, Ribosomal, 16S ,Leachate ,Cellulose ,2. Zero hunger ,Bacteria ,Ecology ,biology ,Pulp and paper industry ,Waste Disposal Facilities ,030104 developmental biology ,chemistry ,Metagenomics ,biology.protein ,Metagenome - Abstract
Landfills are engineered, heterogeneously contaminated sites containing large reservoirs of paper waste. Cellulose degradation is an important process within landfill microbial ecology, and these anoxic, saturated environments are prime locations for discovery of cellulases that may offer improvements on industrial cellulose degradation efforts. We sampled leachate from three locations within a municipal landfill, a leachate collection cistern, and groundwater from an adjacent aquifer to identify cellulolytic populations and their associated cellulases. Metagenomic sequencing identified wide-spread and taxonomically diverse cellulolytic potential, with a notable scarcity of predicted exocellulases. 16S rRNA amplicon sequencing detected nine landfill microorganisms enriched in a customized leachate medium amended with microcrystalline cellulose or common paper stocks. Paper-enrichment cultures showed competition dynamics in response to the specific composition (lignin: hemi-cellulose: cellulose) of the different paper stocks. From leachate biomass, four novel cellulolytic bacteria were isolated, including two with the capacity for cellulolysis at industrially relevant temperatures. None of the isolates demonstrated exocellulase activity, consistent with the metagenome-based predictions. However, there was very little overlap between metagenome-derived predicted cellulolytic organisms, organisms enriched on paper sources, or the isolates, suggesting the landfill cellulolytic community is at low abundance but able to rapidly respond to introduced substrates.
- Published
- 2021
38. Dynamics of microbial contaminants is driven by selection during ethanol production
- Author
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Patrícia S. Costa, Andréa M. A. Nascimento, Gustavo Augusto Lacorte, Maria Silveira Costa, Luciano Lopes Queiroz, Alcilene de Abreu Pereira, and Marcelo P. Ávila
- Subjects
Raw material ,Microbiology ,Industrial Microbiology ,03 medical and health sciences ,Microbial ecology ,RNA, Ribosomal, 16S ,Yeasts ,Lactobacillus ,Media Technology ,Dominance (ecology) ,Ethanol fuel ,Food science ,030304 developmental biology ,0303 health sciences ,Bacteria ,Ethanol ,biology ,030306 microbiology ,Microbiota ,biology.organism_classification ,Pulp and paper industry ,Yeast ,Saccharum ,Fermentation ,Food Microbiology - Research Paper ,Microbial Interactions ,Species richness ,Brazil - Abstract
Brazil is the second largest ethanol producer in the world and largest using sugarcane feedstock. Bacteria contamination is one of the most important issues faced by ethanol producers that seek to increase production efficiency. Each step of production is a selection event due to the environmental and biological changes that occur. Therefore, we evaluated the influence of the selection arising from the ethanol production process on diversity and composition of bacteria. Our objectives were to test two hypotheses, (1) that species richness will decrease during the production process and (2) that lactic acid bacteria will become dominant with the advance of ethanol production. Bacterial community assemblage was accessed using 16S rRNA gene sequencing from 19 sequential samples. Temperature is of great importance in shaping microbial communities. Species richness increased between the decanter and must steps of the process. Low Simpson index values were recorded at the fermentation step, indicating a high dominance of Lactobacillus. Interactions between Lactobacillus and yeast may be impairing the efficiency of industrial ethanol production. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s42770-019-00147-6) contains supplementary material, which is available to authorized users.
- Published
- 2019
39. Rhizobia and endophytic bacteria isolated from rainforest fragments within an iron ore mining site of the Eastern Brazilian Amazon
- Author
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Fatima Maria de Souza Moreira, José Oswaldo Siqueira, Marco Aurélio Carbone Carneiro, Raquel Milagros Rodríguez-Rodríguez, Amanda Azarias Guimarães, and Jordana Luísa de Castro
- Subjects
Rainforest ,Iron ,Microbiology ,Bradyrhizobium ,Mining ,Rhizobia ,Soil ,03 medical and health sciences ,Paenibacillus ,Microbial ecology ,Mycology ,Botany ,Endophytes ,Media Technology ,Symbiosis ,Phylogeny ,Environmental Microbiology - Research Paper ,030304 developmental biology ,Macroptilium atropurpureum ,0303 health sciences ,Bacteria ,biology ,030306 microbiology ,Pantoea ,Edaphic ,biology.organism_classification ,Root Nodules, Plant ,Brazil ,Rhizobium - Abstract
The aim of the present study was to isolate and evaluate the diversity of rhizobial and endophytic bacterial strains from undisturbed native rainforests within an iron ore mining site of the Serra Norte de Carajás in the Eastern Brazilian Amazon region to assess their biotechnological utility in reclamation of areas. Experiments were conducted to capture strains from samples of the soil of these forests at the sites Arenito II, Noroeste II, and Sul IV using Macroptilium atropurpureum and Mimosa acutistipula var. ferrea as trap host plants. Only M. atropurpureum nodulated, and the different bacterial strains were isolated from its nodules. There was no difference in the number of nodules among the areas, but the Arenito II bacterial community was the most efficient, indicated by the aboveground biomass production and suitable shoot mass/root mass ratio. Fifty-two (52) bacterial isolates were obtained, distributed in five groups, including nodulating and endophytic bacteria: 32 from Arenito II, 12 from Noroeste II, and 8 from Sul IV. The nodulating Bradyrhizobium genus was common to the three areas, whereas Paraburkholderia was found only in Arenito II. The nodD1 gene was amplified in all the strains of both nodulating genera. Strains of the nodulating genus Methylobacterium were also isolated from the three areas; however, they did not nodulate the host of origin, and their nodD1 gene was not amplified. Endophytic strains were also isolated from the genera Paenibacillus, Pantoea, and Leifsonia in Arenito II, Leifsonia in Noroeste I, and Paenibacillus in Sul IV. The greater nodulation and rhizobial and endophytic bacterial diversity observed in Arenito II were probably due to the more suitable edaphic properties of the area. The isolated strains were incorporated in the collection of the Department of Soil Science of UFLA and will be investigated in relation to their symbiotic characteristics with native host plants, as well as their ability to perform other biological processes. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42770-021-00524-0.
- Published
- 2021
40. Broad diversity of bacteria degrading 17ß-estradiol-3-sulfate isolated from river sediment and biofilm at a wastewater treatment plant discharge
- Author
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Marilena Palmisano, Susanne Kern, Fabio Rezzonico, Tamara Mainetti, Theo H. M. Smits, and Blaž Stres
- Subjects
Geologic Sediments ,Identification ,Microorganism ,010501 environmental sciences ,Enrichment cultures ,01 natural sciences ,Biochemistry ,Microbiology ,Enrichment culture ,Water Purification ,03 medical and health sciences ,Microbial ecology ,Genetics ,Conjugated estrogens ,Molecular Biology ,Effluent ,030304 developmental biology ,0105 earth and related environmental sciences ,Original Paper ,0303 health sciences ,Bacteria ,Estradiol ,Aquatic ecosystem ,Biofilm ,Biodiversity ,General Medicine ,Microbial population biology ,579: Mikrobiologie ,Biofilms ,Environmental chemistry ,Environmental science ,Sewage treatment ,Water Pollutants, Chemical - Abstract
Erworben im Rahmen der Schweizer Nationallizenzen (http://www.nationallizenzen.ch), Conjugated estrogens, such as 17β-estradiol-3-sulfate (E2-3S), can be released into aquatic environments through wastewater treatment plants (WWTP). There, they are microbiologically degraded into free estrogens, which can have harmful effects on aquatic wildlife. Here, the degradation of E2-3S in environmental samples taken upstream, downstream and at the effluent of a WWTP was assessed. Sediment and biofilm samples were enriched for E2-3S-degrading microorganisms, yielding a broad diversity of bacterial isolates, including known and novel degraders of estrogens. Since E2-3S-degrading bacteria were also isolated in the sample upstream of the WWTP, the WWTP does not influence the ability of the microbial community to degrade E2-3S.
- Published
- 2021
41. Plant growth–promoting traits of yeasts isolated from the tank bromeliad Vriesea minarum L.B. Smith and the effectiveness of Carlosrosaea vrieseae for promoting bromeliad growth
- Author
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Carlos A. Rosa, Vera Lúcia dos Santos, Alessandra A. Resende, Ana Raquel O. Santos, José P. Lemos-Filho, Fátima de Cássia Oliveira Gomes, Andréa Rodrigues Marques, and Alexandre A. Duarte
- Subjects
Bromeliaceae ,Siderophore ,Biofertilizer ,Siderophores ,Microbiology ,Phosphates ,03 medical and health sciences ,chemistry.chemical_compound ,Microbial ecology ,Botany ,Media Technology ,Environmental Microbiology - Research Paper ,030304 developmental biology ,0303 health sciences ,Indoleacetic Acids ,biology ,030306 microbiology ,Basidiomycota ,food and beverages ,biology.organism_classification ,Phosphate ,Yeast ,chemistry ,Seedling ,Indole-3-acetic acid - Abstract
Yeasts can play important roles in promoting plant growth; however, little information is available in this regard for yeasts in water of bromeliad tanks. Here, we characterize the ability of 79 yeast isolates from tank bromeliad Vriesea minarum, an endangered species, to solubilize phosphate, secrete siderophores, and synthesize indole-3-acetic acid (IAA). The results showed that 67.8% of all assayed yeast isolates mobilized inorganic phosphate; 40.0% secreted siderophores; and 89.9% synthetized IAA and IAA-like compounds. Among the species studied, Carlosrosaea vrieseae UFMG-CM-Y6724 is highlighted for producing IAA (76.1 μg mL(−1)) and siderophores, and solubilizing phosphate. In addition, evaluation of the effects of filtrate containing IAA-like compounds produced by the C. vrieseae on the development and photosynthetic performance of V. minarum seedlings found it to improve seedling growth equal to that of commercial IAA. These results demonstrate that C. vrieseae can produce compounds with great potential for future use as biofertilizer agents.
- Published
- 2021
42. Community structure of environmental microorganisms associated with COVID-19 affected patients
- Author
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Xingshuo Hu, Han Xia, Lixin Xie, Hujie Huang, Guoxin Mo, Jie Yang, Jing Zhu, Pei Zhang, and Weihua Zhang
- Subjects
Face shield ,Veterinary medicine ,business.product_category ,Metagenomic next-generation sequencing (mNGS) ,Microorganism ,Immunology ,Plant Science ,medicine.disease_cause ,03 medical and health sciences ,0302 clinical medicine ,Microbial ecology ,Abundance (ecology) ,medicine ,Immunology and Allergy ,030212 general & internal medicine ,Microbiome ,Aerosol ,030304 developmental biology ,Original Paper ,0303 health sciences ,Environmental microbiology ,biology ,COVID-19 ,Acinetobacter ,biology.organism_classification ,Hospital microbiome ,Metagenomics ,business ,Staphylococcus - Abstract
To clarify the characteristics and distribution of hospital environmental microbiome associated with confirmed COVID-19 patients. Environmental samples with varying degrees of contamination which were associated with confirmed COVID-19 patients were collected, including 13 aerosol samples collected near eight patients in different wards, five swabs from one patient’s skin and his personal belongings, and two swabs from the surface of positive pressure respiratory protective hood and the face shield from a physician who had close contact with one patient. Metagenomic next-generation sequencing (mNGS) was used to analyze the composition of the microbiome. One of the aerosol samples (near patient 4) was detected positive for COVID-19, and others were all negative. The environmental samples collected in different wards possessed protean compositions and community structures, the dominant genera including Pseudomonas, Corynebacterium, Neisseria, Staphylococcus, Acinetobacter, and Cutibacterium. Top 10 of genera accounted for more than 76.72%. Genera abundance and proportion of human microbes and pathogens radiated outward from the patient, while the percentage of environmental microbes increased. The abundance of the pathogenic microorganism of medical supplies is significantly higher than other surface samples. The microbial compositions of the aerosol collected samples nearby the patients were mostly similar to those from the surfaces of the patient's skin and personal belongings, but the abundance varied greatly. The positive rate of COVID-19 RNA detected from aerosol around patients in general wards was quite low. The ward environment was predominantly inhabited by species closely related to admitted patients. The spread of hospital microorganisms via aerosol was influenced by the patients’ activity.
- Published
- 2021
43. Variation of salinity and nitrogen concentration affects the pentacyclic triterpenoid inventory of the haloalkaliphilic aerobic methanotrophic bacterium Methylotuvimicrobium alcaliphilum
- Author
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Andreas Kappler, Jörn Peckmann, Alexmar Cordova-Gonzalez, and Daniel Birgel
- Subjects
Salinity ,Nitrogen ,Tetrahymanol ,chemistry.chemical_element ,Nitrate ,Microbiology ,Methane ,03 medical and health sciences ,chemistry.chemical_compound ,Nutrient ,Microbial ecology ,Bacteriohopanepolyols ,Pentacyclic triterpenoids ,030304 developmental biology ,Original Paper ,0303 health sciences ,biology ,030306 microbiology ,Temperature ,General Medicine ,biology.organism_classification ,Triterpenes ,Hopanoids ,chemistry ,Environmental chemistry ,Molecular Medicine ,Aerobic methanotrophs ,Bacteria - Abstract
The occurrence and activity of aerobic methanotrophs are influenced by environmental conditions, including pH, temperature, salinity, methane and oxygen concentrations, and nutrient availability. Aerobic methanotrophs synthesize a variety of lipids important for cell functions. However, culture-based experiments studying the influence of environmental parameters on lipid production by aerobic methanotrophs are scarce. Such information is crucial to interpret lipid patterns of methanotrophic bacteria in the environment. In this study, the alkaliphilic strain Methylotuvimicrobium alcaliphilum was cultivated under different salinities and different nitrate concentrations to assess the effect of changing conditions on the inventory of pentacyclic triterpenoids. The results indicate that hopanoid abundance is enhanced at lower salinity and higher nitrate concentration. The production of most pentacyclic triterpenoids was favored at low salinity, especially for aminotriol. Interestingly, 3-methyl-aminotetrol and tetrahymanol were favored at higher salinity. Bacteriohopanepolyols (BHPs), particularly aminotriol and 3-methyl-aminotriol, increased considerably at higher nitrate concentrations. Four novel N-containing BHPs—aminodiol, 3-methyl-aminodiol, and isomers of aminotriol and 3-methyl-aminotriol—were identified. This study highlights the significance of environmental factors for bacterial lipid production and documents the need for cultivation studies under variable conditions to utilize the full potential of the biomarker concept. Supplementary Information The online version contains supplementary material available at 10.1007/s00792-021-01228-x.
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- 2021
44. A Distinct, Flocculent, Acidogenic Microbial Community Accompanies Methanogenic Granules in Anaerobic Digesters
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Umer Zeeshan Ijaz, Anna Christine Trego, Gavin Collins, Piet N.L. Lens, and Simon Mills
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Microbiology (medical) ,anaerobic digestion ,Acidogenesis ,Physiology ,Streptococcaceae ,Microbiology ,biofilm ,anaerobic granules ,Bacterial Adhesion ,Water Purification ,Granulation ,Bacteria, Anaerobic ,Bioreactors ,Microbial ecology ,Genetics ,Bioreactor ,community succession ,16S rRNA ,General Immunology and Microbiology ,Ecology ,Sewage ,Chemistry ,Microbiota ,Granule (cell biology) ,Biofilm ,Flocculation ,Cell Biology ,Pulp and paper industry ,QR1-502 ,Anaerobic digestion ,Infectious Diseases ,Microbial population biology ,methanogenic granules ,acidogenic ,Biofilms ,Methane ,Research Article - Abstract
The formation of dense, well-settling methanogenic granules is essential for the operation of high-rate, up-flow anaerobic bioreactors used for wastewater treatment. Granule formation (granulation) mechanisms have been previously proposed, but an ecological understanding of granule formation is still lacking. Additionally, much of the current research on granulation only examines the start-up phase of bioreactor operation, rather than monitoring the fate of established granules and how new granules emerge over time. This paper, therefore, attempts to provide an insight into the microbial ecology of granule formation outside the start-up phase of bioreactor operation and develop an ecological granulation model. The microbial communities of granules actively undergoing growth, breakage, and reformation were examined, and an ecological granulation model was proposed. A distinct pregranular microbial community, with a high proportion of acidogenic organisms, such as the Streptococcaceae, was identified and suggested to have a role in initiating granulation by providing simpler substrates for the methanogenic and syntrophic communities which developed during granule growth. After initial granule formation, deterministic influences on microbial community assembly increased with granule size and indicated that microbial community succession was influenced by granule growth, leading to the formation of a stepwise ecological model for granulation. IMPORTANCE Complex microbial communities in engineered environments can aggregate to form surface-attached biofilms. Others form suspended biofilms, such as methanogenic granules. The formation of dense, methanogenic granules underpins the performance of high-rate, anaerobic bioreactors in industrial wastewater treatment. Granule formation (granulation) has been well studied from a physico-chemical perspective, but the ecological basis is poorly understood. We identified a distinct, flocculent, microbial community, which was present alongside granules, comprising primary consumers likely key in providing simpler substrates to granules. This flocculent community is understudied in anaerobic digestion and may initiate, or perpetuate, granule formation. We propose that it may be possible to influence bioreactor performance (e.g., to regulate volatile fatty acid concentrations) by manipulating this community. The patterns of microbial community diversity and assembly revealed by the study indicate that cycles of granule growth and breakage lead to overall diversification of the bioreactor meta-community, with implications for bioreactor process stability.
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- 2021
45. Microbial ecology of submerged marine caves and holes characterized by high levels of hydrogen sulphide
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Canganella, Francesco, Bianconi, Giovanna, Kato, Chiaki, Gonzalez, Juan, Amils, Ricardo, editor, Ellis-Evans, Cynan, editor, and Hinghofer-Szalkay, Helmut, editor
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- 2007
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46. Comparing models of microbial-substrate interactions and their response to warming.
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Sihi, D., Gerber, S., Inglett, P. W., and Inglett, K. S.
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MICROBIAL ecology ,GLOBAL warming ,CARBON sequestration ,MICROBIAL respiration ,FINITE square well - Abstract
Recent developments in modelling soil organic carbon decomposition include the explicit incorporation of enzyme and microbial dynamics. A characteristic of these models is a positive feedback between substrate and consumers which is absent in traditional first order decay models. Under sufficient large substrate, this new feedback allows an unconstrained growth of microbial biomass. A second phenomenon incorporated in the microbial decomposition models is decreased carbon use efficiency (CUE) with increasing temperature. Here, first we analyse microbial decomposition models by parameterising changes in CUE based on the differentiation between growth and maintenance respiration. We then explore mechanisms that curb unrestricted microbial growth by including finite potential sites where enzymes can bind and by allowing microbial scavenging for enzymes. Finally, we propose a model where enzyme synthesis is associated with a respiratory cost and microbial population adjusts enzyme production in order to optimise their growth. When applying a step increase in temperature, we find fast responses that reflect adjustments to enzyme dynamics and maintenance respiration, a short-term adjustment in microbial growth, and the long-term change in carbon storage. We find that mechanisms that prevent unrestricted microbial growth lead to a similar response to warming as traditional first order decomposition models. [ABSTRACT FROM AUTHOR]
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- 2015
- Full Text
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47. Combined characterization of a new member of Marivita cryptomonadis strain LZ-15-2 isolated from cultivable phycosphere microbiota of highly toxic HAB dinoflagellate Alexandrium catenella LZT09
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Zhang Xiaoling, Zhiwei Jiang, Qiao Yang, Xin Zhou, Xi Yang, and Xiao-Ai Zhang
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Alexandrium catenella ,Harmful Algal Bloom ,Microbiology ,03 medical and health sciences ,Microbial ecology ,Media Technology ,medicine ,Rhodobacteraceae ,Paralytic shellfish poisoning ,Phylogeny ,Environmental Microbiology - Research Paper ,030304 developmental biology ,Comparative genomics ,Genetics ,0303 health sciences ,biology ,Phylogenetic tree ,030306 microbiology ,Microbiota ,Strain (biology) ,Dinoflagellate ,biology.organism_classification ,16S ribosomal RNA ,medicine.disease ,Bacterial Typing Techniques ,Dinoflagellida ,Genome, Bacterial - Abstract
During our conveying the microbial structures of phycosphere microbiota (PM) derived from diverse marine harmful algal bloom (HAB) dinoflagellates, a new rod-sharped, white-colored cultivable bacterial strain, designated as LZ-15-2, was isolated from the PM of highly toxic Alexandrium catenella LZT09. Phylogenetic analysis of 16S rRNA gene sequence indicated that strain LZ-15-2 belonged to the genus Marivita within the family Rhodobacteraceae, and demonstrated the highest gene similarity of 99.2% to M. cryptomonadis CL-SK44(T), and less than 98.65% with other type strains of Marivita. Phylogenomic calculations on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the new isolate and M. cryptomonadis CL-SK44(T) were 99.86% and 99.88%, respectively. Genomic comparison of strain LZ-15-2 with available genomes of Marivita species further verified its taxonomic position within the genus of Marivita. Moreover, comparative genomics analysis showed a proximal similarity of strain LZ-15-2 with M. cryptomonadis CL-SK44(T), and it also revealed an open pan-genome status based on constructed gene accumulation curves among Marivita members with 9,361 and 1,712 genes for the pan- and core-genome analysis, respectively. Based on combined polyphasic taxonomic characteristics, strain LZ-15-2 represents a new member of M. cryptomonadis, and proposed as a potential candidate for further exploration of the detailed mechanisms governing the dynamic cross-kingdom algae–bacteria interactions (ABI) between PM and their algal host LZT09. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42770-021-00463-w.
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- 2021
48. Impacts of replanting American ginseng on fungal assembly and abundance in response to disease outbreaks
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Chunjie Tian, Chunling Chang, Jingjing Chang, Lei Tian, Xiujun Li, Li Ji, Jianfeng Zhang, and Fahad Nasir
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0106 biological sciences ,Panax ,complex mixtures ,01 natural sciences ,Biochemistry ,Microbiology ,Disease Outbreaks ,Soil ,03 medical and health sciences ,Ginseng ,Microbial ecology ,Genetics ,Wilcoxina ,Old ginseng field ,Continuous cropping ,Molecular Biology ,American ginseng ,Soil Microbiology ,Plant Diseases ,030304 developmental biology ,Original Paper ,0303 health sciences ,biology ,Armillaria ,Soil organic matter ,Fungal community ,Fungi ,food and beverages ,High-Throughput Nucleotide Sequencing ,Outbreak ,General Medicine ,Alternaria ,biology.organism_classification ,Agronomy ,Pathogens ,Mycobiome ,010606 plant biology & botany - Abstract
Soil physicochemical properties and fungal communities are pivotal factors for continuous cropping of American ginseng (Panax quinquefoliumL.). However, the response of soil physicochemical properties and fungal communities to replant disease of American ginseng has not yet been studied. High-throughput sequencing and soil physicochemical analyses were undertaken to investigate the difference of soil fungal communities and environmental driver factors in new and old ginseng fields; the extent of replant disease in old ginseng fields closely related to changes in soil properties and fungal communities was also determined. Results indicated that fungal communities in an old ginseng field were more sensitive to the soil environment than those in a new ginseng field, and fungal communities were mainly driven by soil organic matter (SOM), soil available phosphorus (AP), and available potassium (AK). Notably, healthy ginseng plants in new and old ginseng fields may influence fungal communities by actively recruiting potential disease suppressive fungal agents such asAmphinema,Cladophialophora,Cadophora,Mortierella,andWilcoxina. When these key groups and members were depleted, suppressive agents in the soil possibly declined, increasing the abundance of pathogens. Soil used to grow American ginseng in the old ginseng field contained a variety of fungal pathogens, includingAlternaria,Armillaria,Aphanoascus,Aspergillus,Setophoma,andRhexocercosporidium. Additionally, micro-ecological factors affecting disease outbreaks in the old ginseng field included a strengthening in competition relationships, a weakening in cooperation relationships, and a change of trophic strategies among fungal communities.
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- 2021
49. Benzoyl ester formation in Aspergillus ustus by hijacking the polyketide acyl intermediates with alcohols
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Shu-Ming Li and Liujuan Zheng
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Stereochemistry ,Biosynthesis ,01 natural sciences ,Biochemistry ,Microbiology ,03 medical and health sciences ,Polyketide ,chemistry.chemical_compound ,Aspergillus ustus ,Microbial ecology ,Genetics ,Molecular Biology ,Original Paper ,0303 health sciences ,010405 organic chemistry ,030306 microbiology ,organic chemicals ,Benzoyl esters ,Esters ,General Medicine ,Methylation ,0104 chemical sciences ,Aspergillus ,chemistry ,Polyketides ,Alcohols ,Alcohols feeding - Abstract
Accumulation of two benzoyl esters in Aspergillus ustus after feeding with alcohols was reported 30 years ago. To the best of our knowledge, the biosynthesis for these esters has not been elucidated prior to this study. Here, we demonstrate that these compounds are artifical products of the phenethyl polyketide ustethylin A biosynthestic pathway. In addition, four aditional benzoyl esters with different methylation levels were also isolated and identified as shunt products. Feeding experiments provided evidence that the enzyme-bound polyketide acyl intermediates are hijacked by externally fed MeOH or EtOH, leading to the formation of the benzoyl esters. Graphic abstract
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- 2021
50. Taxonomic and functional analyses reveal existence of virulence and antibiotic resistance genes in beach sand bacterial populations
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Timothy Sibanda and Selvarajan Ramganesh
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Bacteroidia ,Antibiotic resistance ,Firmicutes ,Zoology ,Biochemistry ,Microbiology ,Bathing Beaches ,Actinobacteria ,South Africa ,03 medical and health sciences ,chemistry.chemical_compound ,Microbial ecology ,Sand ,Metals, Heavy ,Drug Resistance, Bacterial ,Gammaproteobacteria ,Genetics ,Humans ,Gemmatimonadetes ,Child ,Molecular Biology ,Soil Microbiology ,030304 developmental biology ,Original Paper ,Public health ,0303 health sciences ,Bacteria ,Virulence ,biology ,030306 microbiology ,Microbiota ,High-Throughput Nucleotide Sequencing ,Bacteroidetes ,Bacterial Infections ,General Medicine ,biology.organism_classification ,Anti-Bacterial Agents ,chemistry ,Recreation ,Aerobactin ,Beach sand ,Water Microbiology ,Environmental Monitoring - Abstract
Coastal sands are important natural recreational facilities that have become hotspots for tourism and economic development. However, these sands harbour diverse microbial assemblages that play a critical role in the balance between public health and ecology. In this study, targeted high-throughput sequencing analysis was used to identify sand-borne bacterial populations at four public beaches in Durban. The effect of heavy metal in shaping the distribution of bacterial metacommunities was determined using canonical correspondence analysis (CCA), while the functional gene profiles were predicted using PICRUSt2 analysis. Sequences matching those of the bacterial phylum Proteobacteria were the most abundant in all samples, followed by those of the phyla Firmicutes, Actinobacteria, Bacteroidetes, and Gemmatimonadetes. Genus-level taxonomic analysis showed the presence of 1163 bacterial genera in all samples combined. The distribution of bacterial communities was shaped by heavy metal concentrations, with the distribution of Flavobacteria, Bacteroidia, and Deltaproteobacteria influenced by Pb and Zn, while B and Cr influenced the distribution of Clostridia and Gammaproteobacteria, respectively. Identified antibiotic resistance genes included the peptidoglycan biosynthesis gene II, III, IV, and V, as well as the polymyxin resistance gene, while the virulence genes included the sitA, fimB, aerobactin synthase, and pilL gene. Our findings demonstrate that beach sand-borne bacteria are reservoirs of virulence and antibiotic resistance genes. Contamination of beach sands with heavy metals selects for both heavy metal resistance and antibiotic resistance in beach sand bacterial communities. Children and immunocompromised people engaging in recreational activities on beaches may be exposed to higher risk of infection.
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- 2021
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