Detection of living bacterial cells in clay - bentonite 

Author(s):  
Veronika Hlavackova ◽  
Katerina Cerna ◽  
Lenka Kejzlarova ◽  
Deepa Bartak ◽  
Rojina Shestra ◽  
...  

<p>Bentonite is a swelling clay, consisting mainly of montmorillonire,  being planned to be used as a backfill material in the nuclear waste repository. It contains indigenous microbial populations that can negatively influence the long-term safety of the geological repository due to their metabolic activity (canister corrosion, illitization of bentonite, gas production, degradation of cementitious materials). However, reliable detection of microorganisms in clayish material is generally very difficult. Although the compactness of bentonite will undoubtedly limit the microbial activity, in the extremely long-time frame of repository lifetime this condition can fail. It is thus crucial to understand the potential of the naturally present microbial community in bentonite to compromise the safety of repository, if not limited by the compactness. Higher metabolic activity can be mainly expected at the interfaces or in the places with a lower density of bentonite.</p><p>Here we present an optimized cell extraction method enabling direct estimation of bacterial density and viability in bentonite. Indigenous bacterial cells were extracted from bentonite suspensions by an improved step-wise protocol and their viability was detected using live/dead staining and epifluorescence microscopy. We used dispersant (2.5 mM natrium pyrophosphate-based solution or 1% methanol) to partially disintegrate the bentonite and detach the vital and dead microbial cells from its surface. The dispersed material was subsequently stepwise centrifuged over two high-density media (sucrose and Histodenz) to remove most of the heavy bentonite particles while keeping the light bentonite particles and cells in the final extract. We were able to detect and enumerate the cells concentrated at the surface of the light bentonite particles, which served as a sieve to retain all free cells during centrifugation.    </p><p>Different extraction procedures were tested and their efficiency was estimated by comparing live/dead ratios of resulting extracts and was also proved by implementing both NGS and quantitative PCR. The results show that most of the microbial genera present in the original suspension are also present in extracts but as proved by Deseq2 analysis some genera tend to settle down with heavier bentonite particles during the first centrifugation step.</p><p>To conclude, we present a protocol for extraction and detection of metabolically active cells in clayish material – bentonite. The quality of the extraction procedure was estimated both by a combination of fluorescent microscopy and genetic methods. The protocol was successfully tested on different bentonite types showing general applicability of this approach for clay materials.</p>

Author(s):  
О.В. Шамова ◽  
М.С. Жаркова ◽  
П.М. Копейкин ◽  
Д.С. Орлов ◽  
Е.А. Корнева

Антимикробные пептиды (АМП) системы врожденного иммунитета - соединения, играющие важную роль в патогенезе инфекционных заболеваний, так как обладают свойством инактивировать широкий спектр патогенных бактерий, обеспечивая противомикробную защиту живых организмов. В настоящее время АМП рассматриваются как потенциальные соединения-корректоры инфекционной патологии, вызываемой антибиотикорезистентными бактериями (АБР). Цель данной работы состояла в изученим механизмов антибактериального действия трех пептидов, принадлежащих к семейству бактенецинов - ChBac3.4, ChBac5 и mini-ChBac7.5Nb. Эти химически синтезированные пептиды являются аналогами природных пролин-богатых АМП, обнаруженных в лейкоцитах домашней козы Capra hircus и проявляющих высокую антимикробную активность, в том числе и в отношении грамотрицательных АБР. Методы. Минимальные ингибирующие и минимальные бактерицидные концентрации пептидов (МИК и МБК) определяли методом серийных разведений в жидкой питательной среде с последующим высевом на плотную питательную среду. Эффекты пептидов на проницаемость цитоплазматической мембраны бактерий для хромогенного маркера исследовали с использованием генетически модифицированного штамма Escherichia coli ML35p. Действие бактенецинов на метаболическую активность бактерий изучали с применением маркера резазурина. Результаты. Показано, что все исследованные пептиды проявляют высокую антимикробную активность в отношении Escherichia coli ML35p и антибиотикоустойчивых штаммов Escherichia coli ESBL и Acinetobacter baumannii in vitro, но их действие на бактериальные клетки разное. Использован комплекс методик, позволяющих наблюдать в режиме реального времени динамику действия бактенецинов в различных концентрациях (включая их МИК и МБК) на барьерную функцию цитоплазматической мембраны и на интенсивность метаболизма бактериальных клеток, что дало возможность выявить различия в характере воздействия бактенецинов, отличающихся по структуре молекулы, на исследуемые микроорганизмы. Установлено, что действие каждого из трех исследованных бактенецинов в бактерицидных концентрациях отличается по эффективности нарушения целостности бактериальных мембран и в скорости подавления метаболизма клеток. Заключение. Полученная информация дополнит существующие фундаментальные представления о механизмах действия пролин-богатых пептидов врожденного иммунитета, а также послужит основой для биотехнологических исследований, направленных на разработку на базе этих соединений новых антибиотических препаратов для коррекции инфекционных заболеваний, вызываемых АБР и являющимися причинами тяжелых внутрибольничных инфекций. Antimicrobial peptides (AMPs) of the innate immunity are compounds that play an important role in pathogenesis of infectious diseases due to their ability to inactivate a broad array of pathogenic bacteria, thereby providing anti-microbial host defense. AMPs are currently considered promising compounds for treatment of infectious diseases caused by antibiotic-resistant bacteria. The aim of this study was to investigate molecular mechanisms of the antibacterial action of three peptides from the bactenecin family, ChBac3.4, ChBac5, and mini-ChBac7.5Nb. These chemically synthesized peptides are analogues of natural proline-rich AMPs previously discovered by the authors of the present study in leukocytes of the domestic goat, Capra hircus. These peptides exhibit a high antimicrobial activity, in particular, against antibiotic-resistant gram-negative bacteria. Methods. Minimum inhibitory and minimum bactericidal concentrations of the peptides (MIC and MBC) were determined using the broth microdilution assay followed by subculturing on agar plates. Effects of the AMPs on bacterial cytoplasmic membrane permeability for a chromogenic marker were explored using a genetically modified strain, Escherichia coli ML35p. The effect of bactenecins on bacterial metabolic activity was studied using a resazurin marker. Results. All the studied peptides showed a high in vitro antimicrobial activity against Escherichia coli ML35p and antibiotic-resistant strains, Escherichia coli ESBL and Acinetobacter baumannii, but differed in features of their action on bacterial cells. The used combination of techniques allowed the real-time monitoring of effects of bactenecin at different concentrations (including their MIC and MBC) on the cell membrane barrier function and metabolic activity of bacteria. The differences in effects of these three structurally different bactenecins on the studied microorganisms implied that these peptides at bactericidal concentrations differed in their capability for disintegrating bacterial cell membranes and rate of inhibiting bacterial metabolism. Conclusion. The obtained information will supplement the existing basic concepts on mechanisms involved in effects of proline-rich peptides of the innate immunity. This information will also stimulate biotechnological research aimed at development of new antibiotics for treatment of infectious diseases, such as severe in-hospital infections, caused by antibiotic-resistant strains.


2018 ◽  
Author(s):  
Arnaldo Negron ◽  
Natasha DeLeon-Rodriguez ◽  
Samantha M. Waters ◽  
Luke D. Ziemba ◽  
Bruce Anderson ◽  
...  

Abstract. The abundance and speciation of primary biological aerosol particles (PBAP) is important for understanding their impacts on human health, cloud formation and ecosystems. Towards this, we have developed a protocol for quantifying PBAP collected from large volumes of air with a portable wet-walled cyclone bioaerosol sampler. A flow cytometry (FCM) protocol was then developed to quantify and characterize the PBAP populations from the sampler, which were confirmed against epifluorescence microscopy. The sampling system and FCM analysis were used to study PBAP in Atlanta, GA over a two-month period and showed clearly defined populations of DNA-containing particles: Low Nucleic Acid-content particles (bioLNA), High Nucleic Acid-content particles (HNA) being fungal spores and pollen. We find that daily-average springtime PBAP concentration (1 to 5 μm diameter) ranged between 1.4 × 104 and 1.1 × 105 m−3. The BioLNA population dominated PBAP during dry days (72 ± 18 %); HNA dominated the PBAP during humid days and following rain events, where HNA (e.g., wet-ejected fungal spores) comprised up to 92 % of the PBAP number. Concurrent measurements with a Wideband Integrated Bioaerosol Sensor (WIBS-4A) showed that FBAP and total FCM counts are similar; HNA (from FCM) significantly correlated with ABC type FBAP concentrations throughout the sampling period (and for the same particle size range, 1–5 μm diameter). However, the FCM bioLNA population, possibly containing bacterial cells, did not correlate to any FBAP type. The lack of correlation of any WIBS FBAP type with the bioLNA suggest bacterial cells may be more difficult to detect with autofluorescence than previously thought. Ιdentification of bacterial cells even in the FCM (bioLNA population) is challenging, given that the fluorescence level of stained cells at times may be comparable to that seen from abiotic particles. HNA and ABC displayed highest concentration on a humid and warm day after a rain event (4/14), suggesting that both populations correspond to wet-ejected fungal spores. Overall, information from both instruments combined reveals a highly dynamic airborne bioaerosol community over Atlanta, with a considerable presence of fungal spores during humid days, and a bioLNA population dominating bioaerosol community during dry days.


2005 ◽  
Vol 45 (1) ◽  
pp. 13
Author(s):  
A.J. McDiarmid ◽  
P.T. Bingaman ◽  
S.T. Bingham ◽  
B. Kirk-Burnnand ◽  
D.P. Gilbert ◽  
...  

The John Brookes gas field was discovered by the drilling of John Brookes–1 in October 1998 and appraisal drilling was completed in 2003. The field is located about 40 km northwest of Barrow Island on the North West Shelf, offshore West Australia. The John Brookes structure is a large (>90 km2) anticline with >100 m closure mapped at the base of the regional seal. Recoverable sales gas in the John Brookes reservoir is about 1 Tcf.Joint venture approval to fast track the development was gained in January 2004 with a target of first gas production in June 2005. The short development time frame required parallel workflows and use of a flexible/low cost development approach proven by Apache in the area.The John Brookes development is sized for off-take rates up to 240 TJ/d of sales gas with the development costing A$229 million. The initial development will consist of three production wells tied into an unmanned, minimal facility wellhead platform. The platform will be connected to the existing East Spar gas processing facilities on Varanus Island by an 18-inch multi-phase trunkline. Increasing the output of the existing East Spar facility and installation of a new gas sweetening facility are required. From Varanus Island, the gas will be exported to the mainland by existing sales gas pipelines. Condensate will be exported from Varanus Island by tanker.


2010 ◽  
Vol 76 (15) ◽  
pp. 5088-5096 ◽  
Author(s):  
Mohiuddin M. Taimur Khan ◽  
Barry H. Pyle ◽  
Anne K. Camper

ABSTRACT An issue of critical concern in microbiology is the ability to detect viable but nonculturable (VBNC) and viable-culturable (VC) cells by methods other than existing approaches. Culture methods are selective and underestimate the real population, and other options (direct viable count and the double-staining method using epifluorescence microscopy and inhibitory substance-influenced molecular methods) are also biased and time-consuming. A rapid approach that reduces selectivity, decreases bias from sample storage and incubation, and reduces assay time is needed. Flow cytometry is a sensitive analytical technique that can rapidly monitor physiological states of bacteria. This report outlines a method to optimize staining protocols and the flow cytometer (FCM) instrument settings for the enumeration of VBNC and VC bacterial cells within 70 min. Experiments were performed using the FCM to quantify VBNC and VC Escherichia coli O157:H7, Pseudomonas aeruginosa, Pseudomonas syringae, and Salmonella enterica serovar Typhimurium cells after staining with different fluorescent probes: SYTO 9, SYTO 13, SYTO 17, SYTO 40, and propidium iodide (PI). The FCM data were compared with those for specific standard nutrient agar to enumerate the number of cells in different states. By comparing results from cultures at late log phase, 1 to 64% of cells were nonculturable, 40 to 98% were culturable, and 0.7 to 4.5% had damaged cell membranes and were therefore theoretically dead. Data obtained using four different Gram-negative bacteria exposed to heat and stained with PI also illustrate the usefulness of the approach for the rapid and unbiased detection of dead versus live organisms.


2017 ◽  
Author(s):  
Michael Weigert ◽  
Rolf Kümmerli

AbstractBacteria secrete a variety of compounds important for nutrient scavenging, competition mediation and infection establishment. While there is a general consensus that secreted compounds can be shared and therefore have social consequences for the bacterial collective, we know little about the physical limits of such bacterial social interactions. Here, we address this issue by studying the sharing of iron-scavenging siderophores between surface-attached microcolonies of the bacterium Pseudomonas aeruginosa. Using single-cell fluorescent microscopy, we show that siderophores, secreted by producers, quickly reach non-producers within a range of 100 μm, and significantly boost their fitness. Producers in turn respond to variation in sharing efficiency by adjusting their pyoverdine investment levels. These social effects wane with larger cell-to-cell distances and on hard surfaces. Thus, our findings reveal the boundaries of compound sharing, and show that sharing is particularly relevant between nearby yet physically separated bacteria on soft surfaces, matching realistic natural conditions such as those encountered in soft tissue infections.


Nanomaterials ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 778 ◽  
Author(s):  
Vishma Pratap Sur ◽  
Aninda Mazumdar ◽  
Amirmansoor Ashrafi ◽  
Atripan Mukherjee ◽  
Vedran Milosavljevic ◽  
...  

In this study, the titanium–gadolinium quantum dots (TGQDs) were novel, first of its type to be synthesized, and fully characterized to date. Multiple physical characterization includes scanning electron microscopy (SEM), scanning electrochemical microscope (SCEM), x-ray fluorescence, spectrophotometry, and dynamic light scattering were carried out. The obtained results confirmed appropriate size and shape distributions in addition to processing optical features with high quantum yield. The synthesized TGQD was used as a fluorescent dye for bacterial detection and imaging by fluorescent microscopy and spectrophotometry, where TGQD stained only bacterial cells, but not human cells. The significant antibacterial activities of the TGQDs were found against a highly pathogenic bacterium (Staphylococcus aureus) and its antibiotic resistant strains (vancomycin and methicillin resistant Staphylococcus aureus) using growth curve analysis and determination of minimum inhibitory concentration (MIC) analysis. Live/dead cell imaging assay using phase-contrast microscope was performed for further confirmation of the antibacterial activity. Cell wall disruption and release of cell content was observed to be the prime mode of action with the reduction of cellular oxygen demand (OD).


2020 ◽  
Vol 20 (3) ◽  
pp. 1817-1838 ◽  
Author(s):  
Arnaldo Negron ◽  
Natasha DeLeon-Rodriguez ◽  
Samantha M. Waters ◽  
Luke D. Ziemba ◽  
Bruce Anderson ◽  
...  

Abstract. The abundance and speciation of primary biological aerosol particles (PBAP) is important for understanding their impacts on human health, cloud formation, and ecosystems. Towards this, we have developed a protocol for quantifying PBAP collected from large volumes of air with a portable wet-walled cyclone bioaerosol sampler. A flow cytometry (FCM) protocol was then developed to quantify and characterize the PBAP populations from the sampler, which were confirmed against epifluorescence microscopy. The sampling system and FCM analysis were used to study PBAP in Atlanta, GA, over a 2-month period and showed clearly defined populations of nucleic-acid-containing particles: low nucleic acid-content particles above threshold (LNA-AT) and high nucleic acid-content particles (HNA) likely containing wet-ejected fungal spores and pollen. We find that the daily-average springtime PBAP concentration (1 to 5 µm diameter) ranged between 1.4×104 and 1.1×105 m−3. The LNA-AT population dominated PBAP during dry days (72±18 %); HNA dominated the PBAP during humid days and following rain events, where HNA comprised up to 92 % of the PBAP number. Concurrent measurements with a Wideband Integrated Bioaerosol Sensor (WIBS-4A) showed that fluorescent biological aerosol particles (FBAP) and total FCM counts are similar; HNA (from FCM) moderately correlated with ABC-type FBAP concentrations throughout the sampling period (and for the same particle size range, 1–5 µm diameter). However, the FCM LNA-AT population, possibly containing bacterial cells, did not correlate with any FBAP type. The lack of correlation of any WIBS FBAP type with the LNA-AT suggests that airborne bacterial cells may be more difficult to unambiguously detect with autofluorescence than currently thought. Identification of bacterial cells even in the FCM (LNA-AT population) is challenging, given that the fluorescence level of stained cells at times may be comparable to that seen from abiotic particles. HNA and ABC displayed the highest concentration on a humid and warm day after a rain event (14 April 2015), suggesting that both populations correspond to wet-ejected fungal spores. Overall, information from both instruments combined reveals a highly dynamic airborne bioaerosol community over Atlanta, with a considerable presence of fungal spores during humid days and an LNA-AT population dominating the bioaerosol community during dry days.


2021 ◽  
Author(s):  
Nazia Zaffar ◽  
Erik Ferchau ◽  
Hermann Heilmeier ◽  
Oliver Wiche

<p>Bioharvesting of toxic and valuable elements by growing high biomass crops in the regions with low-grade mining ores and metal-polluted soils is a new concept in the area of mining termed phytomining. The biomass is used in anaerobic digestion to produce biogas and digestate. To the best of our knowledge, there are limited studies on the enrichment and distribution of heavy metals and economically valuable elements in digestate, obtained from mesophilic and thermophilic fermentation conditions. This study conducted a laboratory experiment to recover and enrich toxic elements (Zn, Cd, Pb, As) and economically valuable elements (Ge and rare earth elements REEs) at mesophilic (37⁰C) and thermophilic (55⁰C) conditions. To analyze the distribution of these elements in the liquid and solid-state of digestate a three-step sequential extraction procedure was carried out. Microfiltration (0.2µm) was used to separate elements in the solid and liquid phases. The solid digestate was extracted with ammonium acetate (pH 7) and ammonium acetate (pH 5) to determine exchangeable and acid-soluble elements. As a result, we found that thermophilic conditions significantly enriched Zn (3%), Cd (48%), Pb (25%), As (21%), Ge (40%), and REEs (22%) compared to mesophilic conditions. The following elements were enriched in decreasing order Cd > Ge > Pb > REEs > As > Zn. This enrichment may be due to differences in availability of substrates to microorganisms and higher gas production with increased temperature. The sequential extraction revealed that the concentration of elements in dissolved form was significantly increased in thermophilic conditions. While the concentrations in exchangeable are decreased indicating that previous elements bound on exchangeable sites were removed and transferred in solution. Furthermore, the element concentration in the residue fraction was not affected by temperature. Possibly the release of secondary metabolites from microorganisms triggered by higher temperature improved the solubility of elements which is an important prerequisite for element separation and recovery.</p><p> </p>


2007 ◽  
Vol 74 (2) ◽  
pp. 410-415 ◽  
Author(s):  
Stefanie Mangold ◽  
Kerstin Harneit ◽  
Thore Rohwerder ◽  
Günter Claus ◽  
Wolfgang Sand

ABSTRACT Bioleaching of metal sulfides is an interfacial process comprising the interactions of attached bacterial cells and bacterial extracellular polymeric substances with the surface of a mineral sulfide. Such processes and the associated biofilms can be investigated at high spatial resolution using atomic force microscopy (AFM). Therefore, we visualized biofilms of the meso-acidophilic leaching bacterium Acidithiobacillus ferrooxidans strain A2 on the metal sulfide pyrite with a newly developed combination of AFM with epifluorescence microscopy (EFM). This novel system allowed the imaging of the same sample location with both instruments. The pyrite sample, as fixed on a shuttle stage, was transferred between AFM and EFM devices. By staining the bacterial DNA with a specific fluorescence dye, bacterial cells were labeled and could easily be distinguished from other topographic features occurring in the AFM image. AFM scanning in liquid caused deformation and detachment of cells, but scanning in air had no effect on cell integrity. In summary, we successfully demonstrate that the new microscopic system was applicable for visualizing bioleaching samples. Moreover, the combination of AFM and EFM in general seems to be a powerful tool for investigations of biofilms on opaque materials and will help to advance our knowledge of biological interfacial processes. In principle, the shuttle stage can be transferred to additional instruments, and combinations of AFM and EFM with other surface-analyzing devices can be proposed.


2002 ◽  
Vol 713 ◽  
Author(s):  
Alberto A. Sagüés

ABSTRACTThe proposed high-level nuclear waste repository at Yucca Mountain relies heavily on the corrosion resistance of waste packages (WP) emplaced in tunnels bored through tuffaceous rock for adequate performance during the anticipated 10,000 years regulatory period. Present WP design uses a ∼20-mm-thick outer shell of Alloy 22 as the main corrosion-resistant barrier. The operating conditions may include an initial high-temperature (>96 °C) pulse that will last approximately several hundred to a thousand years. Ti-alloy shields are envisioned to prevent water from directly dripping on the WP. However, recent findings suggest that deliquescent salts and other contaminants on the WP surfaces may cause liquid water to form there, even at high temperatures. Current performance projections predict that during the anticipated regulatory period localized corrosion modes will be unlikely and that the Alloy 22 barrier will degrade primarily by very slow uniform dissolution, essentially under passive surface conditions. A review is presented of the assumptions and experimental findings leading to those projections, as well as a discussion of findings of a recent Workshop on the challenges involved in extrapolating limited information on corrosion behavior over an extremely long service period that extends beyond the time frame of common engineering experience. Potential mechanisms for deterioration of the passive regime that may be encountered under those circumstances are discussed.


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