Summary
In situ detection of microorganisms by fluorescence in situ hybridization (FISH) is a powerful tool for environmental microbiology, but analyses can be hampered by low rRNA content in target ...organisms, especially in oligotrophic environments. Here, we present a non‐enzymatic, hybridization chain reaction (HCR)‐based signal amplified in situ whole‐cell detection technique (in situ DNA‐HCR). The components of the amplification buffer were optimized to polymerize DNA amplifier probes for in situ DNA‐HCR. In situ hybridization of initiator probes followed by signal amplification via HCR produced bright signals with high specificity and probe permeation into cells. The detection rates for Bacteria in a seawater sample and Archaea in anaerobic sludge samples were comparable with or greater than those obtained by catalyzed reporter deposition (CARD)‐FISH or standard FISH. Detection of multiple organisms (Bacteria, Archaea and Methanosaetaceae) in an anaerobic sludge sample was achieved by simultaneous in situ DNA‐HCR. In summary, in situ DNA‐HCR is a simple and easy technique for detecting single microbial cells and enhancing understanding of the ecology and behaviour of environmental microorganisms in situ.
Water quality parameters influence the abundance of pathogenic bacteria. The genera Aeromonas, Arcobacter, Klebsiella, and Mycobacterium are among the representative pathogenic bacteria identified in ...wastewater. However, information on the correlations between water quality and the abundance of these bacteria, as well as their reduction rate in existing wastewater treatment facilities (WTFs), is lacking. Hence, this study aimed to determine the abundance and reduction rates of these bacterial groups in WTFs. Sixty-eight samples (34 influent and 34 non-disinfected, treated, effluent samples) were collected from nine WTFs in Japan and Thailand. 16S rRNA gene amplicon sequencing analysis revealed the presence of Aeromonas, Arcobacter, and Mycobacterium in all influent wastewater and treated effluent samples. Quantitative real-time polymerase chain reaction (qPCR) was used to quantify the abundance of Aeromonas, Arcobacter, Klebsiella pneumoniae species complex (KpSC), and Mycobacterium. The geometric mean abundances of Aeromonas, Arcobacter, KpSC, and Mycobacterium in the influent wastewater were 1.2 x 10.sup.4 -2.4 x 10.sup.5, 1.0 x 10.sup.5 -4.5 x 10.sup.6, 3.6 x 10.sup.2 -4.3 x 10.sup.4, and 6.9 x 10.sup.3 -5.5 x 10.sup.4 cells mL.sup.-1, respectively, and their average log reduction values were 0.77-2.57, 1.00-3.06, 1.35-3.11, and -0.67-1.57, respectively. Spearman's rank correlation coefficients indicated significant positive or negative correlations between the abundances of the potentially pathogenic bacterial groups and Escherichia coli as well as water quality parameters, namely, chemical/biochemical oxygen demand, total nitrogen, nitrate-nitrogen, nitrite-nitrogen, ammonium-nitrogen, suspended solids, volatile suspended solids, and oxidation-reduction potential. This study provides valuable information on the development and appropriate management of WTFs to produce safe, hygienic water.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
A data set containing more than 6 years (February 2009 to present) of radiance spectra for carbon dioxide (CO2) and methane (CH4) observations has been acquired by the Greenhouse gases Observing ...SATellite (GOSAT, available at http://data.gosat.nies.go.jp/GosatUserInterfaceGateway/guig/GuigPage/open.do), nicknamed “Ibuki”, Thermal And Near infrared Sensor for carbon Observation Fourier Transform Spectrometer (TANSO-FTS). This paper provides updates on the performance of the satellite and TANSO-FTS sensor and describes important changes to the data product, which has recently been made available to users. With these changes the typical accuracy of retrieved column-averaged dry air mole fractions of CO2 and CH4 (XCO2 and XCH4, respectively) are 2 ppm or 0.5 % and 13 ppb or 0.7 %, respectively. Three major anomalies of the satellite system affecting TANSO-FTS are reported: a failure of one of the two solar paddles in May 2014, a switch to the secondary pointing system in January 2015, and most recently a cryocooler shutdown and restart in August 2015. The Level 1A (L1A) (raw interferogram) and the Level 1B (L1B) (radiance spectra) of version V201 described here have long-term uniform quality and provide consistent retrieval accuracy even after the satellite system anomalies. In addition, we discuss the unique observation abilities of GOSAT made possible by an agile pointing mechanism, which allows for optimization of global sampling patterns.
Anaerobic oxidation of methane (AOM) in marine sediments is an important global methane sink, but the physiological characteristics of AOM-associated microorganisms remain poorly understood. Here we ...report the cultivation of an AOM microbial community from deep-sea methane-seep sediment using a continuous-flow bioreactor with polyurethane sponges, called the down-flow hanging sponge (DHS) bioreactor. We anaerobically incubated deep-sea methane-seep sediment collected from the Nankai Trough, Japan, for 2,013 days in the bioreactor at 10°C. Following incubation, an active AOM activity was confirmed by a tracer experiment using 13C-labeled methane. Phylogenetic analyses demonstrated that phylogenetically diverse Archaea and Bacteria grew in the bioreactor. After 2,013 days of incubation, the predominant archaeal components were anaerobic methanotroph (ANME)-2a, Deep-Sea Archaeal Group, and Marine Benthic Group-D, and Gammaproteobacteria was the dominant bacterial lineage. Fluorescence in situ hybridization analysis showed that ANME-1 and -2a, and most ANME-2c cells occurred without close physical interaction with potential bacterial partners. Our data demonstrate that the DHS bioreactor system is a useful system for cultivating fastidious methane-seep-associated sedimentary microorganisms.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Denitrifying anaerobic methane oxidizing (DAMO) microorganisms were enriched from paddy field soils using continuous-flow and batch cultures fed with nitrate or nitrite as a sole electron acceptor. ...After several months of cultivation, the continuous-flow cultures using nitrite showed remarkable simultaneous methane oxidation and nitrite reduction and DAMO bacteria belonging to phylum NC10 were enriched. A maximum volumetric nitrite consumption rate of 70.4±3.4 mg-N·L(-1)·day(-1) was achieved with very short hydraulic retention time of 2.1 hour. In the culture, about 68% of total microbial cells were bacteria and no archaeal cells were detected by fluorescence in situ hybridization. In the nitrate-fed continuous-flow cultures, 58% of total microbial cells were bacteria while archaeal cells accounted for 7% of total cell numbers. Phylogenetic analysis of pmoA gene sequence showed that enriched DAMO bacteria in the continuous-flow cultivation had over 98% sequence similarity to DAMO bacteria in the inoculum. In contrast, for batch culture, the enriched pmoA gene sequences had 89-91% sequence similarity to DAMO bacteria in the inoculum. These results indicate that electron acceptor and cultivation method strongly affect the microbial community structures of DAMO consortia.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
•Many people still drink unpurified water, containing Escherichia coli, in rural areas.•Ingestion of this water causes many potentially deadly diseases such as diarrhea.•We tested a combined water ...purification system and monitored E. coli concentration.•The DHS-SSF system could reduce the diarrheal infection risk by up to 99.5%.•The DHS-SSF system can provide 30 people with sufficient water (50 L each per day).
Worldwide, many people still drink unpurified water, putting them at risk of contracting waterborne diseases such as diarrhea. In this study, an interview survey was conducted to evaluate the infection risk from the current water supply in rural areas in Kenya. According to the interview, the residents living in areas with no public water supply drink water from various sources such as surface water, spring water, dug well, rainwater, tap water, and water sold by nearby non-governmental organizations. Further, most of the respondents usually drink unpurified water, which generated a high infection risk value of 0.77 owing to inadequate water storage management. A new self-sustaining water purification process, which is a combination of a down-flow hanging sponge (DHS) reactor kind of biological trickling filter and a slow sand filter (SSF) with a 500 W solar was installed in an area with no public electricity and water supply. The DHS-SSF system efficiently decreased the total organic carbon, color, and turbidity by over 80% after the two-week operation, and the treated water could be used for household water. In addition, a survey for infection risk evaluation was conducted to determine the utility of the DHS-SSF system. However, drinking water supplied by the DHS-SSF system could reduce the infection risk of diarrhea by up to 99.5%. This result indicates that the DHS-SSF system could be an appropriate water purification system in no public water supply area.
Catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) with rRNA-targeted oligonucleotide probes has significantly improved the identification of microorganisms in various ...environmental samples. However, one of the major constraints of CARD-FISH is the low probe penetration due to the high molecular weight of the horseradish peroxidase (HRP) label. Recently, this limitation has been overcome by a novel signal amplification approach termed in situ DNA-hybridization chain reaction (in situ DNA-HCR). In this study, we present an improved and accelerated in situ DNA-HCR protocol (quickHCR-FISH) with increased signal intensity, which was approximately 2 times higher than that of standard in situ DNA-HCR. In addition, the amplification time was only 15min for the extension of amplifier probes from the initiator probe compared to 2h in the original protocol. The quickHCR-FISH was successfully tested for the quantification of marine bacteria with low rRNA contents in both seawater and sediment samples. It was possible to detect the same number of marine bacteria with quickHCR-FISH compared to CARD-FISH within only 3h. Thus, this newly developed protocol could be an attractive alternative to CARD-FISH for the detection and visualization of microorganisms in their environmental context.
Spatial and temporal variability of atmospheric water vapor (H2O) is extremely high, and therefore it is difficult to accurately evaluate the measurement precision of H2O data by a simple comparison ...between the data derived from two different instruments. We determined the measurement precisions of column-averaged dry-air mole fractions of H2O (XH2O) retrieved independently from spectral radiances in the thermal infrared (TIR) and the short-wavelength infrared (SWIR) regions measured using a Thermal And Near-infrared Sensor for carbon Observation-Fourier Transform Spectrometer (TANSO-FTS) onboard the Greenhouse gases Observing SATellite (GOSAT), by an intercomparison between the two TANSO-FTS XH2O data products and the ground-based FTS XH2O data. Furthermore, the spatial variability of XH2O was also estimated in the intercomparison process. Mutually coincident XH2O data above land for the period ranging from April 2009 to May 2014 were intercompared with different spatial coincidence criteria. We found that the precisions of the TANSO-FTS TIR and TANSO-FTS SWIR XH2O were 7.3%-7.7% and 3.5%-4.5%, respectively, and that the spatial variability of XH2O was 6.7% within a radius of 50 km and 18.5% within a radius of 200 km. These results demonstrate that, in order to accurately evaluate the measurement precision of XH2O, it is necessary to set more rigorous spatial coincidence criteria or to take into account the spatial variability of XH2O as derived in the present study.
A network of 10 southern hemisphere tropical and subtropical stations, designated the Southern Hemisphere Additional Ozonesondes (SHADOZ) project and established from operational sites, provided over ...1000 ozone profiles during the period 1998–2000. Balloon‐borne electrochemical concentration cell (ECC) ozonesondes, combined with standard radiosondes for pressure, temperature, and relative humidity measurements, collected profiles in the troposphere and lower to midstratosphere at: Ascension Island; Nairobi, Kenya; Irene, South Africa; Réunion Island; Watukosek, Java; Fiji; Tahiti; American Samoa; San Cristóbal, Galapagos; and Natal, Brazil. The archived data are available at: 〈http://croc.gsfc.nasa.gov/shadoz〉.1 In this paper, uncertainties and accuracies within the SHADOZ ozone data set are evaluated by analyzing: (1) imprecisions in profiles and in methods of extrapolating ozone above balloon burst; (2) comparisons of column‐integrated total ozone from sondes with total ozone from the Earth‐Probe/Total Ozone Mapping Spectrometer (TOMS) satellite and ground‐based instruments; and (3) possible biases from station to station due to variations in ozonesonde characteristics. The key results are the following: (1) Ozonesonde precision is 5%. (2) Integrated total ozone column amounts from the sondes are usually to within 5% of independent measurements from ground‐based instruments at five SHADOZ sites and overpass measurements from the TOMS satellite (version 7 data). (3) Systematic variations in TOMS‐sonde offsets and in ground‐based‐sonde offsets from station to station reflect biases in sonde technique as well as in satellite retrieval. Discrepancies are present in both stratospheric and tropospheric ozone. (4) There is evidence for a zonal wave‐one pattern in total and tropospheric ozone, but not in stratospheric ozone.
Performance of a wastewater treatment system utilizing a sulfur-redox reaction of microbes was investigated using a pilot-scale reactor that was fed with actual sewage. The system consisted of an ...up-flow anaerobic sludge blanket (UASB) reactor and a down-flow hanging sponge (DHS) reactor with a recirculation line. Consequently, the total COD
Cr (465
±
147
mg
L
−1; total BOD of 207
±
68
mg
L
−1) at the influent was reduced (70
±
14
mg
L
−1; total BOD of 9
±
2
mg
L
−1) at the DHS effluent under the conditions of an overall hydraulic retention time of 12
h, a recirculation ratio of 2, and a low-sewage temperature of 7.0
±
2.8
°C. A microbial analysis revealed that sulfate-reducing bacteria contributed to the degradation of organic matter in the UASB reactor even in low temperatures. The utilized sulfur-redox reaction is applicable for low-strength wastewater treatment under low-temperature conditions.
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