Epifluorescence Microscopy with Image Analysis as a Promising Method for Multispecies Biofilm Quantification

Epifluorescence microscopy with image analysis was evaluated as a biofilm quantification method (i.e., quantification of surface area colonized by biofilms), in comparison with crystal violet (CV) staining. We performed different experiments to generate multispecies biofilms with natural and artificial bacterial assemblages. First, four species were inoculated daily in 16 different sequences to form biofilms (surface colonization, 0.1%-56.6%). Second, a 9-species assemblage was allowed to form biofilms under 10 acylase treatment episodes (33.8%-55.6%). The two methods comparably measured the quantitative variation in biofilms, exhibiting a strong positive relationship (R² ≥ 0.7). Moreover, the two methods exhibited similar levels of variation coefficients. Finally, six synthetic and two natural consortia were allowed to form biofilms for 14 days, and their temporal dynamics were monitored. The two methods were comparable in quantifying four biofilms colonizing ≥18.7% (R² ≥ 0.64), but not for the other biofilms colonizing ≤ 3.7% (R² ≤ 0.25). In addition, the two methods exhibited comparable coefficients of variation in the four biofilms. Microscopy and CV staining comparably measured the quantitative variation of biofilms, exhibiting a strongly positive relationship, although microscopy cannot appropriately quantify the biofilms below the threshold colonization. Microscopy with image analysis is a promising approach for easily and rapidly estimating absolute quantity of multispecies biofilms.

Determination of methanogenesis by nutrient availability via regulating the relative fitness of methanogens in anaerobic digestion

Response of microbial community to nutrient availability in anaerobic digestion (AD) remains elusive. Prokaryotic communities in AD batch cultures with 0, 1, 3, 5, 7, 11, 15, 20, and 25 g/L peptone were monitored using massive parallel sequencing and quantitative PCR over a 34-day experimental period. Methane production displayed a hump-shaped response to the nutrient gradient (peaking at 15 g/L peptone). Moreover, total and acetoclastic methanogens showed hump-shaped responses (both peaking at 11 g/L peptone). However, prokaryotic population increased with nutrient concentration (linear regression, R² = 0.86) while diversity decreased (R² = 0.94), and ordination analysis showed a gradual succession of community structure along the first axis. Network analysis revealed that extent of interspecific interactions (e.g., edge number and clustering coefficient) exhibited a hump-shaped response. The combined results indicate that abundant species became more dominated with increasing nutrient, which can result in a gain or loss of interspecific interaction within the community. Network module analysis showed that one module dominated the network at each nutrient level (comprising 41%-65% of the nodes), indicating that AD community formed a core microbial guild. The most abundant phylotypes, Macellibacteroides and Butyricicoccaceae, were consistently negative with acetoclastic methanogens in the dominant modules. Their predominance at ≥15 g/L peptone can explain the hump-shaped responses of methanogenesis and methanogens. Collectively, methanogenesis and microbial network exhibited hump-shaped responses, although microbial community exhibited monotonic responses. Therefore, nutrient availability can determine the methanogenesis through regulating the relative fitness of methanogens within the community.

[Laparoscopic transchiatal access in Boerhaave syndrome]

Diagnosis of spontaneous rupture of the esophagus (Boerhaave syndrome) followed by purulent mediastinitis and pleural empyema has now been greatly simplified due to CT. The main thing is to suspect this syndrome in a timely manner. Methods of surgical treatment of this disease are still being discussed. We present successful laparoscopic treatment of spontaneous rupture of the esophagus.

Improving the bioavailability of manganese and meat quality of broilers by using hot-melt extrusion nano method

1. Mineral excretion is an issue in the poultry industry. The use of micro minerals in nano form can increase bioavailability and decrease excretion rate. However, information concerning the bioavailability of nano manganese (Mn) in broiler chicks is limited.2. This experiment studied the influences of hot-melt extrusion (HME)-processed manganese sulphate on body weight gain, Mn bioavailability, nutrient digestibility and meat quality in broiler chicks fed a corn-soybean meal-based diet as a starter and grower phase. A total of 700 birds (Ross 308, 1-day-old) were randomly placed in 35 cages (20 birds per cage). The broiler chicks were fed one of seven experimental diets, which consisted of a control (without supplemental Mn), different levels of MnSO₄ (IN-Mn60; 60, 120, and 200 mg/kg), or HME MnSO₄ (HME-Mn; 60, 120, and 200 mg/kg).3. There was an increased serum Mn content in broilers fed diet supplemented with HME-Mn. In the grower phase, increased dietary Mn levels elevated the concentrations in the serum, liver, and tibia. There were increases in the excreta Mn content of broilers fed increasing levels. The supplementation of HME-Mn showed a lower percentage of abdominal fat compared with the IN-Mn treatment diets. Supplementation with HME-Mn decreased intramuscular fat compared with the diets supplemented with IN-Mn. The supplementation of HME-Mn decreased the thiobarbituric acid reactive substances (TBARS) at d 6 of age. The HME-Mn source showed a greater decrease in TBARS compared with the IN-Mn treatment.4. In conclusion, HME processing increased bioavailability and could be used as an environmentally friendly method to facilitate lower levels of Mn in the diet of broiler chickens.

Indigenous Fungivorous Nematodes Affect the Biocontrol Efficacy of Trichoderma harzianum through Reducing the Hyphal Density

Indigenous fungus-feeding nematodes may adversely affect the growth and activity of introduced biocontrol fungi. Alginate pellets of the biocontrol fungus Trichoderma harzianum ThzID1-M3 and sclerotia of the fungal plant pathogen Sclerotinia sclerotiorum were added to nonsterile soil at a soil water potential of -50 or -1,000 kPa. The biomass of ThzID1-M3, nematode populations, and extent of colonization of sclerotia by ThzID1-M3 were monitored over time. The presence of ThzID1-M3 increased the nematode population under both moisture regimes (p < 0.05), and fungivores comprised 69-75% of the nematode population. By day 5, the biomass of ThzID1-M3b and its colonization of sclerotia increased and were strongly correlated (R² = 0.98), followed by a rapid reduction, under both regimes. At -50 kPa (the wetter of the two environments), fungal biomass and colonization by ThzID1-M3 were less, in the period from 5 to 20 days, while fungivores were more abundant. These results indicate that ThzID1-M3 stimulated the population growth of fungivorous nematodes, which in turn, reduced the biocontrol ability of the fungus to mycoparasitize sclerotia. However, colonization incidence reached 100% by day 5 and remained so for the experimental period under both regimes, although hyphal fragments disappeared by day 20. Our results suggest that indigenous fungivores are an important constraint for the biocontrol activity of introduced fungi, and sclerotia can provide spatial refuge for biocontrol fungi from the feeding activity of fungivorous nematodes.

Effects of dispersal on species distribution, abundance, diversity and interaction in a bacterial biofilm metacommunity

AIMS

Dispersal effects on biofilms have not been adequately studied despite their strong potential impacts on biofilm development. We investigated the effects of dispersal on biofilm metacommunity.

METHODS AND RESULTS

A bacterial consortium was allowed to form biofilms on 12 glass beads attached to disposable plates (compartmentalized or not), and biofilms were scrutinized on days 5, 10 and 15 using quantitative PCR and MiSeq sequencing. Biofilm population density was lesser by 2 orders of magnitude on day 5 when dispersal was allowed (p < 0.05). Then, the population rapidly increased by 4.4 orders with dispersal (p < 0.05) but did not change without dispersal. Community analyses revealed that dispersal increased the species diversity at all sampling times (p < 0.05). Dispersal affected the community structure and increased the homogeneity of local communities (p < 0.05). Distance-decay analysis showed that dispersal reduced the dissimilarity among local communities at all distance levels. Furthermore, dispersal reduced the variability of diversity, population and community structure. Network analysis revealed that dispersal increased the clustering coefficient, network density and connectivity.

CONCLUSIONS

Dispersal increased the species diversity, population and interaction and reduced the variability of the diversity, population and structure among local communities.

SIGNIFICANCE AND IMPACT OF STUDY

Our results suggest that dispersal can induce the niche complementarity and mass effects.

Effects of Plants on Metacommunities and Correlation Networks of Soil Microbial Groups in an Ecologically Restored Wetland

Plants may influence different aspects of the belowground microorganisms, including abundance, distribution, and interaction, in wetlands. Microbial communities were scrutinized in a 4-year-old restored wetland ecosystem with 5 distinct sites: a bare-soil site (10 local patches) and sites dominated by Miscanthus, Phragmites, Typha, and Zizania (20 patches per site). Ordination analysis revealed that plant-induced attributes (e.g., organic matter and total carbon and nitrogen) could explain the total environmental variance. Community comparisons showed that all groups (Bacteria, Fungi, Protista, and Metazoa) differed in community structure among the 5 sites (P < 0.05). Comparisons between the community and environmental ordination plots revealed that community structural variation among the sites correlated with the environmental change across all groups (R² ≥ 0.61). This indicates that all groups were primarily influenced by plant detritus. In addition, correlation networks markedly varied in topology and composition among the sites across all groups. There was a strong coupling between the metacommunity and correlation network for both Bacteria and Fungi (R² ≥ 0.58), indicating that the plants determined the spatial covariation patterns of microbial populations. Multi-group networks and group synchrony results revealed that Bacteria, Fungi, and Protista were synchronized with each other (R² ≥ 0.52) as the key founders of the microbial systems, while Metazoa participated in the system only under Miscanthus. Our findings concluded that the plants shaped the communities by controlling the abundance and interaction of their populations.

Spatial Variance of Species Distribution Predicts the Interspecies Interactions within a Microbial Metacommunity

Interspecies interactions have a profound influence on spatial distribution of coexisting microbial species. We explored whether spatial variance of species distribution (SVSD) predicts the degree of interspecies interactions within a microbial metacommunity. Simulations were used to determine the relationships from random, lake, soil, and biofilm metacommunity datasets (1,000 times). All of the bacterial datasets showed a negative correlation between the habitat breadth (inverse to SVSD) and the numbers of total, positive, and negative interspecies interactions (P < 0.05); the only exception was the relationship between habitat breadth and negative interactions in the biofilm dataset. The random dataset had no significant relationships (P > 0.05). We repeated the simulations to determine the degree of correlation and reproducibility (100 times). Habitat breadth was negatively correlated with the total and positive interactions in all of the real datasets (P < 0.05), and the negative relationships persisted across repetitions. Despite variability in the slope of total interactions, the slope values of positive interactions were similar for the real datasets (- 19.9, - 19.2, and - 25.8 for lake, soil, and biofilm, respectively). In conclusion, our results demonstrate the patterns of species interaction-distribution and show that interspecies interactions are positively correlated with the SVSD.

Comparison of five membrane filters to collect bioaerosols for airborne microbiome analysis

AIMS

Recovering DNA of airborne micro-organisms (AM) from air is a challenging task. We compared five membrane filters for bioaerosol sampling-mixed cellulose ester (MCE), polyethersulfone (PES), polyamide (PA), polytetrafluorethylene (PTFE) and polyvinylidene fluoride (PVDF)-based on their bacterial, fungal and eukaryotic DNA recoveries.

METHODS AND RESULTS

Bacterial, fungal and eukaryotic populations were quantified using quantitative PCR. With a bacterial consortium, PTFE exhibited the best recovery efficiency (113%), followed by PA (92%), PES (86%), MCE (48%) and PVDF (1%). When filters were compared with air, PA was used as a control to normalize results from the others. The bacterial, fungal and eukaryotic DNA recovery ratios were markedly greater in PES (9·3, 11·5 and 10·3 respectively) than in the remaining. Eukaryotic MiSeq sequencing revealed that PES recovered a more diverse and considerably richer assemblage (richness ratios, 4·97 vs ≤ 1·16 for PES vs the others). Rank abundance distribution analysis showed that distribution tails were longer (>4 times) in PES, but these did not differ between the remaining and PA. Community comparison showed that PES exhibited a lower variation across trials than the PA, while the remaining did not.

CONCLUSIONS

PES filter markedly outperformed the other filters in quantitative and qualitative recovery of AM.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our findings demonstrated the importance of filter selection for sampling AM.

[Pulmonary insufficiency in acute stroke: risk factors and mechanisms of development]

Various degrees of pulmonary insufficiency (PI) (PaO₂ ≤60 mm Hg, SaO₂ ≤90%) are diagnosed in most of patients with severe acute stroke (AS). Frequency and severity of PI positively correlates with the severity of AS. PI worsens patient's condition, prolongs the hospitalization period, and increases the probability of fatal outcome. Early clinical signs of PI may be undiagnosed due to the severity of stroke and thus not treated. The initiating pathogenic mechanism of PI is stress-related activation of sympathetic nervous system (SNS) and systemic immunosuppression. In severe stroke with mass effect, the rapid and significant increase in intracranial pressure may additionally activate the SNS. Risk factors of PI include older age, previous pulmonary disease, prolonged supine position, respiratory muscle dysfunction, apnea, and concomitant somatic diseases. Decompensation of somatic diseases leads to multiple stage reactions with facilitation of functional and morphologic changes in the pulmonary system, hypoxemia and hypoxia, promotes infectious complications and multiple organ failure and worsens neurological outcome. Diagnosis and treatment of PI in AS decreases mortality and improves rehabilitation prognosis.

Coordinated Metacommunity Assembly and Spatial Distribution of Multiple Microbial Kingdoms within a Lake

Freshwater planktonic communities comprise a tremendous diversity of microorganisms. This study investigated the distribution patterns of microbial kingdoms (bacteria, fungi, protists, and microbial metazoans) within a lake ecosystem. Water samples were collected from 50 sites along the shoreline in a lake during an early eutrophication period, and MiSeq sequencing was performed with different marker genes. Metacommunity analyses revealed a bimodal occupancy-frequency distribution and a Clementsian gradient persisting throughout all microbial kingdoms, suggesting similar regional processes in all kingdoms. Variation partitioning revealed that environmental characteristics, macrophyte/macroinvertebrate composition, space coordinates, and distance-based Moran's eigenvector maps (dbMEM) together could explain up to 29% of the community variances in microbial kingdoms. Kingdom synchrony results showed strong couplings between kingdoms (R² ≥ 0.31), except between Fungi and Metazoa (R² = 0.09). Another variation partitioning revealed that microbial kingdoms could well explain their community variances up to 73%. Interestingly, the kingdom Protista was best synchronized with the other kingdoms. A correlation network showed that positive associations between kingdoms outnumbered the negative ones and that the kingdom Protista acted as a hub among kingdoms. Module analysis showed that network modules included multi-kingdom associations that were prevalent. Our findings suggest that protists coordinate community assembly and distribution of other kingdoms, and inter-kingdom interactions are a key determinant in shaping their community structures in a freshwater lake.

Effects of Quorum Quenching on Biofilm Metacommunity in a Membrane Bioreactor

Quorum quenching (QQ) has received attention for the control of biofilms, e.g., biofilms that cause biofouling in membrane bioreactors (MBRs). Despite the efficacy of QQ on biofouling, it is elusive how QQ influences biofilm formation on membranes. A pilot-scale QQ-MBR and non-QQ-MBR were identically operated for 4 days and 8 days to destructively sample the membranes. QQ prolonged the membrane filterability by 43% with no harmful influence on MBR performance. qPCR showed no effect of QQ on microbial density during either of these time periods. Community comparisons revealed that QQ influenced the bacterial and fungal community structures, and the fungal structure corresponded with the bacterial structure. Metacommunity and spatial analyses showed that QQ induced structural variation rather than compositional variation of bacteria and fungi. Moreover, QQ considerably enhanced the bacterial dispersal across membrane during the early development. As the dispersal enhancement by QQ counteracted the ecological drift, it eliminated the distance-decay relationship, reflecting a neutral theory archetype of metacommunity. Network analyses showed that QQ substantially reduced the amount and magnitude of interactions, e.g., competition and cooperation, for bacteria and fungi, and weakened their network structures, irrespective of time. Additionally, QQ suppressed the growth of specific microbial species (e.g., Acinetobacter), abundant and widespread at the early stage. These findings suggest that QQ influenced the community dynamics at the regional and local levels, correspondingly the ecological selection and dispersal processes, during the biofilm development.

Effects of quorum quenching on temporal succession of activated sludge microbial community in a membrane bioreactor

AIMS

Quorum quenching (QQ) is an attractive strategy for mitigating biofouling in membrane bioreactors (MBRs). However, the effects of QQ on the activated sludge (AS) process have not been adequately evaluated. This study investigated the long-term effects of QQ on a laboratory-scale anoxic-oxic MBR, focusing on AS performance and microbial community.

METHODS AND RESULTS

Anoxic-oxic MBRs with and without QQ were operated for 91 days. QQ did not affect COD and TN removal efficiencies over the experimental period, during which its activity remained >90%. QQ reduced floc size by approximately 8% but had no effect on biomass concentration. AS microbial communities were regularly analysed using massively parallel sequencing. AS bacterial communities were temporally dynamic irrespective of QQ presence, for example, a temporal increase in bacterial diversity and a temporal decay of community similarity. QQ counteracted the temporal change in diversity and the temporal distance-community decay. Community comparison revealed that QQ changed the successional trajectory of the AS community at a late period, because it decelerated temporal changes of specific members, such as Thiothrix and Sphingomonadaceae*. Correlation networks revealed that QQ increased network clustering, complexity and density. The combined results suggest that the tighter microbial association by QQ increased the community resistance.

CONCLUSIONS

QQ can enhance the diversity and stability of the AS community in MBR by counteracting the innate temporal change in community structure.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our findings are useful for the further advancement of QQ-based strategies in engineered microbial environments.

Risk of malignancy in patients with psoriasis: a 15-year nationwide population-based prospective cohort study in Korea

BACKGROUND

The association between psoriasis and risk of malignancy has not been thoroughly evaluated in a large longitudinal cohort of Asian population.

OBJECTIVE

To determine the long-term risk of malignancy in Korean adult patients with psoriasis.

METHODS

We conducted a nationwide population-based prospective cohort study with a 15-year observational period. During the baseline period (1997-2000), total 1 773 786 Korean subjects who received health insurance from the National Health Insurance System were enrolled and 5788 subjects were defined as a psoriasis group. The number of new-onset malignancy was collected during the observational period (2001-2015).

RESULTS

Patients with psoriasis had a higher adjusted hazard ratio (aHR) for development of overall malignancy [aHR 1.08, 95% confidence interval (CI) 1.00-1.18] and gastric cancer (aHR 1.31, 95% CI 1.08-1.58) compared to controls. The risks of non-Hodgkin lymphoma and non-melanoma skin cancer were significantly increased only in patients with psoriasis who received systemic treatments (aHR 2.86, 95% CI 1.07-7.61 and aHR 3.93, 95% CI 1.47-10.47, respectively).

CONCLUSION

Psoriasis is associated with long-term risk for overall malignancy in Koreans, which was primarily driven by the increased risk of gastric cancer.

Abstract OT2-04-02: A phase 3 study of post-lumpectomy radiotherapy to whole breast + regional lymph nodes vs whole breast alone for patients with pN1 breast cancer treated with taxane-based chemotherapy (KROG 1701): Trial in progress

Background

In patients with early stage breast cancer, regional nodal irradiation (RNI) is added to whole breast irradiation (WBI) in order to control microscopic regional disease and to prevent systemic spread of cancer. According to recent randomized trials (MA.20 and EORTC 22922-10925), prophylactic RNI was associated with improvement in disease-free survival (DFS) in the patients with high-risk node negative or pN1 breast cancer. However, systemic agents now known to improve loco-regional control, such as taxane or endocrine therapy, were prescribed to a small percentage of patients in the studies. The benefit of RNI found in the previous studies might be attributed to incorporation of less effective systemic treatments. The impact of prophylactic RNI in pN1 breast cancer should be evaluated in the patients receiving modern systemic treatment. The current study was conducted to compare the effect of post-lumpectomy WBI vs WBI plus RNI on DFS in pN1 breast cancer patients who received adjuvant taxane-based chemotherapy.

Methods

This study is a multicenter, phase 3, randomized controlled non-inferiority trial (NCT03269981). Eligibility criteria are ≥ 20 years female; pathologically proven invasive carcinoma of the breast; one to three positive axillary lymph nodes (pN1) in pathologic specimen; receiving breast-conserving surgery followed by taxane-based chemotherapy; having adjuvant endocrine therapy or anti-HER2 treatment according to molecular subtype of tumor. Patients are randomly assigned in a 1:1 ratio to receive WBI or WBI plus RNI. Patient randomization was stratified by molecular subtype of tumor (i.e. luminal A/luminal B/luminal HER2/HER2-enriched/triple-negative) and methods of axillary management (i.e. sentinel lymph node biopsy/axillary lymph node dissection). The primary outcome is DFS. The secondary outcomes include DFS according to molecular subtype, treatment-related toxicity, and patient's quality of life per EORTC QLQ-C30 and QLQ-BR23. Patients will be followed for survival and disease recurrence for seven years. A total of 1,926 patients are planned to be enrolled, with recruitment initiated in April 2017. As of June 2018, a total of 236 patients were enrolled.

Acknowledgement

This study was supported by a grant from the National R&D Program for Cancer Control, Ministry of Health & Welfare, Republic of Korea (grant number: HA17C0043010018).

Citation Format: Kim H, Park W, Choi DH, Ahn SJ, Kim SS, Kim ES, Lee JH, Lee KC, Kim JH, Lee H-S, Kim JH, Kim MY, Park HJ, Kim K, Song SH, Kwon J, Lee IJ, Kim TH, Kim TG, Chang AR, Cho O, Jeong BK, Ha B, Lee J, Ki Y. A phase 3 study of post-lumpectomy radiotherapy to whole breast + regional lymph nodes vs whole breast alone for patients with pN1 breast cancer treated with taxane-based chemotherapy (KROG 1701): Trial in progress [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr OT2-04-02.

A large-aperture strip-grid beam splitter for partially combined two millimeter-wave diagnostics on Korea Superconducting Tokamak Advanced Research

A large-aperture beam splitter has been developed for simultaneous operation of two millimeter-wave diagnostics employing different probe beams in the frequency and polarization, microwave imaging reflectometer (∼85 GHz X-mode), and collective scattering system (300 GHz O-mode), on the Korea Superconducting Tokamak Advanced Research device. The beam splitter was designed based on a polarizer concept (i.e., grid of metal strips on a thin dielectric sheet), and this can be an optimal solution for these two diagnostics. Fabrication of the strips with uniform sub-millimeter width and spacing on a large dielectric sheet was achieved with an etching technique, and the laboratory test results on the reflection and transmission ratio are in good agreement with design values.

Adverse Effect of the Methanotroph Methylocystis sp. M6 on the Non-Methylotroph Microbacterium sp. NM2

Several non-methylotrophic bacteria have been reported to improve the growth and activity of methanotrophs; however, their interactions remain to be elucidated. We investigated the interaction between Methylocystis sp. M6 and Microbacterium sp. NM2. A batch co-culture experiment showed that NM2 markedly increased the biomass and methane removal of M6. qPCR analysis revealed that NM2 enhanced both the growth and methane-monooxygenase gene expression of M6. A fed-batch experiment showed that co-culture was more efficient in removing methane than M6 alone (28.4 vs. 18.8 μmol·l^-1·d^-1), although the biomass levels were similar. A starvation experiment for 21 days showed that M6 population remained stable while NM2 population decreased by 66% in co-culture, but the results were opposite in pure cultures, indicating that M6 may cross-feed growth substrates from NM2. These results indicate that M6 apparently had no negative effect on NM2 when M6 actively proliferated with methane. Interestingly, a batch experiment involving a dialysis membrane indicates that physical proximity between NM2 and M6 is required for such biomass and methane removal enhancement. Collectively, the observed interaction is beneficial to the methanotroph but adversely affects the non-methylotroph; moreover, it requires physical proximity, suggesting a tight association between methanotrophs and non-methylotrophs in natural environments.

Development of a novel methanotrophic process with the helper micro-organism Hyphomicrobium sp. NM3

AIMS

Microbial consortia can be more efficient at biological processes than single isolates. The purposes of this study were to design and evaluate a synthetic microbial consortium containing the methanotroph Methylocystis sp. M6 and the helper Hyphomicrobium sp. NM3, and develop a novel methanotrophic process for this consortium utilizing a dialysis membrane.

METHODS AND RESULTS

Hyphomicrobium increased the methane-oxidation rate (MOR), biomass and stability at a dilution rate of 0·067 day^-1 in fed-batch co-culture. qRT-PCR showed that Methylocystis population increased gradually with time, whereas Hyphomicrobium population remained stable despite cell washing, confirming synergistic population interaction. At 0·1 day^-1 , spiking of Hyphomicrobium effectively increased the methanotrophic activity, after which Hyphomicrobium population decreased with time, indicating that the consortium is optimal at <0·1 day^-1 . When Hyphomicrobium was grown in dialysis membrane within the bioreactor, MOR increased linearly up to 155·1 ± 1·0 mmol l^-1  day^-1 at 0·067, 0·1, 0·2 and 0·4 day^-1 , which is the highest observed value for a methanotrophic reactor.

CONCLUSIONS

Hyphomicrobium sp. NM3 is a promising helper micro-organism for methanotrophs. Hyphomicrobium-methanotroph consortia used concurrently with existing methods can produce an efficient and stable methane oxidation system.

SIGNIFICANCE AND IMPACT OF THE STUDY

This novel methanotrophic process is superior to those previously reported in the literature, and can provide efficient and stable methane oxidation.

Spatiotemporal dynamics and correlation networks of bacterial and fungal communities in a membrane bioreactor

To systematically study biofilm communities responsible for biofouling in membrane bioreactors (MBRs), we characterized the spatiotemporal dynamics of bacterial and fungal biofilm communities, and their networks, in a pilot-scale flat-sheet MBR treating actual municipal wastewater. Activated sludge (AS) and membrane samples were collected on days 4 and 8. The membranes were cut into 18 tiles, and bacterial and fungal communities were analyzed using next generation sequencing. Nonmetric multidimensional scaling (NMDS) plots revealed significant temporal variations in bacterial and fungal biofilm communities due to changes in the abundances of a few dominant members. Although the experimental conditions and inoculum species pools remained constant, variogram plots of bacterial and fungal communities revealed decay in local community similarity with geographic distance at each sampling time. Variogram modeling (exponential rise to maximum, R² ≥ 0.79) revealed that decay patterns of both communities were different between days 4 and 8. In addition, networks of bacteria or fungi alone were distinct in network composition between days 4 and 8. The day-8 networks were more compact and clustered than those of the earlier time point. Bacteria-fungi networks show that the number of inter-domain associations decreased from 113 to 40 with time, confirming that membrane biofilm is a complex consortium of bacteria and fungi. Spatiotemporal succession in biofilm communities may be common on MBR membranes, resulting from different geographic distributions of initial microbial populations and their priority effects.

Comparison of microbial communities of activated sludge and membrane biofilm in 10 full-scale membrane bioreactors

Operation of membrane bioreactors (MBRs) for wastewater treatment is hampered by the membrane biofouling resulting from microbial activities. However, the knowledge of the microbial ecology of both biofilm and activated sludge in MBRs has not been sufficient. In this study, we scrutinized microbial communities of biofilm and activated sludge from 10 full-scale MBR plants. Overall, Flavobacterium, Dechloromonas and Nitrospira were abundant in order of abundance in biofilm, whereas Dechloromonas, Flavobacterium and Haliscomenobacter in activated sludge. Community structure was analyzed in either biofilm or activated sludge. Among MBRs, as expected, not only diversity of microbial community but also its composition was different from one another (p < 0.05). Between the biofilm and activated sludge, community composition made significant difference, but its diversity measures (i.e., alpha diversity, e.g., richness, diversity and evenness) did not (p > 0.05). Effects of ten environmental factors on community change were investigated using Spearman correlation. MLSS, HRT, F/M ratio and SADm explained the variation of microbial composition in the biofilm, whereas only MLSS did in the activated sludge. Microbial networks were constructed with the 10 environmental factors. The network results revealed that there were different topological characteristics between the biofilm and activated sludge networks, in which each of the 4 factors had different associations with microbial nodes. These results indicated that the different microbial associations were responsible for the variation of community composition between the biofilm and activated sludge.

Isolation and characterization of a novel electricity-producing yeast, Candida sp. IR11

A novel iron-reducing yeast, Candida sp. IR11, was isolated from an anodic biofilm in a MFC reactor fed glucose as a feedstock. 200-250 mV of voltage was produced in the air-cathode MFC inoculated with a pure culture of the strain IR11 where glucose was supplied as a feedstock. When the strain IR11 was inoculated into a conventional MFC treating rejected wastewater from an upflow anaerobic sludge blanket, maximum power density and coulombic efficiency were enhanced from 15.2 ± 0.36 to 20.6 ± 1.52 mW m(-2) and from 14.4 ± 0.45% to 21.9 ± 0.71%, respectively. In addition, the inoculation with IR11 improved COD removal from 79.1 ± 1.53% to 91.3 ± 5.29%. The quantitative PCR results showed that the strain IR11 successfully attached the anodic biofilm of the MFC reactors. These results indicate that Candida sp. IR11 is a promising biocatalyst for the enhancement of MFC performance.

Suppression of methanogenesis in hydrogen fermentation by intermittent feeding

This study investigated whether intermittent feeding by using a concentrated carbon source is an appropriate method for selective enrichment of hydrogenesis by means of methanogen suppression. In a conventional reactor fed continuously for 10 d, methanogens increased from 2.8 × 10(7) to 1.1 × 10(9) gene copy number (GCN)/mg-cell dry weight, and methane concentration in the resulting biogas was 5.8%. However, when a carbon source was intermittently supplied for 10 d to the reactor, the number of methanogens was reduced 98.9% from 2.77 × 10(7) to 1.2 × 10(3) GCN/mg-cell dry weight, and methane was not detected during this period of intermittent feeding. Intermittent feeding shifted the dominants in the reactor from Clostridiaceae (70.5%) and Lactobacillaceae (11.0%) to Acetobacteraceae (62.0%) and Clostridiaceae (38.0%). In the reactor operated in continuous feeding mode after intermittent feeding, methane concentration was below 0.3% and the portion of methanogens in the bacterial community was maintained below 0.2%. These results suggest that the intermittent feeding of a carbon source during hydrogen production processes is a suitable method to suppress the activity of methanogens.

Effects of proton exchange membrane on the performance and microbial community composition of air-cathode microbial fuel cells

This study investigated the effects of proton exchange membranes (PEMs) on performance and microbial community of air-cathode microbial fuel cells (MFCs). Air-cathode MFCs with reactor volume of 1L were constructed in duplicate with or without PEM (designated as ACM-MFC and AC-MFC, respectively) and fed with a mixture of glucose and acetate (1:1, w:w). The maximum power density and coulombic efficiency did not differ between MFCs in the absence or presence of a PEM. However, PEM use adversely affected maximum voltage production and the rate of organic compound removal (p<0.05). Quantitative droplet digital PCR indicated that AC-MFCs had a greater bacterial population than ACM-MFCs (p<0.05). Likewise, ribosomal tag pyrosequencing revealed that the diversity index of bacterial communities was greater for AC-MFCs (p<0.05). Network analysis revealed that the most abundant genus was Enterococcus, which comprised ≥62% of the community and was positively associated with PEM and negatively associated with the rate of chemical oxygen demand (COD) removal (Pearson correlation>0.9 and p<0.05). Geobacter, which is known as an exoelectrogen, was positively associated with maximum power density and negatively associated with PEM. Thus, these results suggest that the absence of PEM favored the growth of Geobacter, a key player for electricity generation in MFC systems. Taken together, these findings demonstrate that MFC systems without PEM are more efficient with respect to power production and COD removal as well as exoelectrogen growth.

Long-term survival of methanogens of an anaerobic digestion sludge under starvation and temperature variation

To investigate starvation effect on methanogen community, two identical membrane reactors were continuously operated for 84 consecutive days, with a temperature change from 50 degrees C to 20 degrees C. Continuous feeding washed out 97% biomass from reactors during the experimental period. Quantitative PCR, using mcrA genes, indicated that the methanogen abundance decreased from 7.0 x 10(7) to 1.2 x 10(7) mcrA copies ml(-1) (volume basis) at 50 degrees C, and then increased to 4.4 x 10(7) mcrA copies ml(7) at 20 degrees C (p<0.05). Correspondence analysis indicated that methanogen communities were distinctly grouped by each temperature. Canonical correspondence analysis indicated that temperature showed a significant correlation with the methanogen community composition. These results suggest that methanogens can survive for a long time (at least more than 84 days) under starvation conditions, and that temperature could be a primary factor determining the density and community of methanogens.

Effects of granular activated carbon on methane removal performance and methanotrophic community of a lab-scale bioreactor

Two identical lab-scale bioreactor systems were operated to examine the effects of granular activated carbon (GAC) on methane removal performance and methanotrophic community. Both bioreactor systems removed methane completely at a CH4 loading rate of 71.2 g-CH4·d(-1) for 17 days. However, the methane removal efficiency declined to 88% in the bioreactor without GAC, while the bioreactor amended with GAC showed greater methane removal efficiency of 97% at a CH4 loading rate of 107.5 g-CH4·d(-1). Although quantitative real-time PCR showed that methanotrophic populations were similar levels of 5-10 × 10(8) pmoA gene copy number·VSS(-1) in both systems, GAC addition changed the methanotrophic community composition of the bioreactor systems. Microarray assay revealed that GAC enhanced the type I methanotrophic genera including Methylobacter, Methylomicrobium, and Methylomonas of the system, which suggests that GAC probably provided a favorable environment for type I methanotrophs. These results indicated that GAC is a promising support material in bioreactor systems for CH4 mitigation.

Fate and behavior of extended-spectrum β-lactamase-producing genes in municipal sewage treatment plants

Extended-spectrum β-lactamases (ESBLs) have the capability of hydrolyzing a variety of the newer β-lactam antibiotics, including the third-generation cephalosporins and monobactams known as a rapidly evolving group of ESBLs. The purpose of this study was to investigate the occurrence and fate of β-lactamase producing genes (CTX-M type 1, type2, CTX-M probe for all groups except CTX-M-1, and TEM, SHV, OXA) through wastewater treatment utilities. β-lactamase producing genes in influent, digested sludge, activated sludge, and disinfected effluent were monitored. The results showed that influent contained high level of all target genes, and all CTX-M types, SHV, and OXA gene decreased significantly in biological treatment process such as activated sludge process and anaerobic digestion, however, TEM type was not effectively eliminated. Possibly, host microbes of TEM could be most resistant in target genes or to some extent gene transfer occurred in wastewater treatment processes. All target genes were significantly reduced during disinfection. Consequently, wastewater treatment process apparently reduced host microbes carrying β-lactamase producing genes effectively, although they are selectively removed in biological processes. In addition, the significant reduction during disinfection was shown, although slightly differences of removal efficiency were observed in resistance.

Development of inorganic and organic hybrid nanocoating based on carbon nanotubes for corrosion resistance

In this study, we report the synthesis and characterization of novel hybrid nanocoating based on carbon nanotubes (CNTs) on anodized aluminum surfaces (AAO). The hybrid nanocoating was deposited by number of methods which include spray coating, spin coating and dip coating. The bonding of nanocoating with metal surface is an important parameter for successful modification of the metal surfaces. The improved adhesion of nanocoating on metal surfaces could be attributed to chemical bonding of sol-gel nanocoating with anodized surfaces. The nanocoated anodized aluminum surfaces showed superior adhesion and excellent anticorrosive properties. The nanocoated panels showed enhanced galvanic protection comparable to 80% of titanium metal as determined by galvanic corrosion measurements. It also showed higher thermal conductivities than stainless steel and bare anodized surfaces.

Density-dependent enhancement of methane oxidation activity and growth of Methylocystis sp. by a non-methanotrophic bacterium Sphingopyxis sp

Methanotrophs are a biological resource as they degrade the greenhouse gas methane and various organic contaminants. Several non-methanotrophic bacteria have shown potential to stimulate growth of methanotrophs when co-cultured, and however, the ecology is largely unknown. Effects of Sphingopyxis sp. NM1 on methanotrophic activity and growth of Methylocystis sp. M6 were investigated in this study. M6 and NM1 were mixed at mixing ratios of 9:1, 1:1, and 1:9 (v/v), using cell suspensions of 7.5 × 10¹¹ cells L^-1. Methane oxidation of M6 was monitored, and M6 population was estimated using fluorescence in situ hybridization (FISH). Real-time PCR was applied to quantify rRNA and expression of transcripts for three enzymes involved in the methane oxidation pathway. NM1 had a positive effect on M6 growth at a 1:9 ratio (p < 0.05), while no significant effects were observed at 9:1 and 1:1 ratios. NM1 enhanced the methane oxidation 1.34-fold at the 1:9 ratio. NM1 increased the population density and relative rRNA level of M6 by 2.4-fold and 5.4-fold at the 1:9 ratio, indicating that NM1 stimulated the population growth of M6. NM1 increased the relative transcriptional expression of all mRNA targets only at the 1:9 ratio. These results demonstrated that NM1 enhanced the methanotrophic activity and growth of M6, which was dependent on the proportion of NM1 present in the culture. This stimulation can be used as management and enhancement strategies for methanotrophic biotechnological processes.

The presence of significant methylotrophic population in biological activated carbon of a full-scale drinking water plant

Methylotrophs within biological activated carbon (BAC) systems have not received attention although they are a valuable biological resource for degradation of organic pollutants. In this study, methylotrophic populations were monitored for four consecutive seasons in BAC of an actual drinking water plant, using ribosomal tag pyrosequencing. Methylotrophs constituted up to 5.6% of the bacterial community, and the methanotrophs Methylosoma and Methylobacter were most abundant. Community comparison showed that the temperature was an important factor affecting community composition, since it had an impact on the growth of particular methylotrophic genera. These results demonstrated that BAC possesses a substantial methylotrophic activity and harbors the relevant microbes.

The adequacy of the distal resection margin after preoperative chemoradiotherapy for rectal cancer

AIM

The study aimed to determine the adequacy of the distal margin in patients having preoperative chemoradiotherapy (CRT) followed by restorative surgery for rectal cancer.

METHOD

A total of 368 patients with locally advanced rectal cancer treated for cure at our institution between July 1999 and March 2009 were included in the study. All underwent preoperative CRT and sphincter-sparing surgery. The distal margin and other factors were examined for their effect on recurrence and survival. The median duration of follow-up was 48 months.

RESULTS

The length of distal margin ranged from 0 to 9.0 cm (median 1.5 cm). The pelvic control and disease-free survival rates at 5 years for patients with a margin of ≤ 3 mm were no different from those in whom it was > 3 mm (P = 0.6 and 0.8). The 5-year pelvic control rates between the ≤ 3 mm and > 3 mm groups were 66.7 and 86.2% in patients with a ypT3-4 tumour (P = 0.049) and 70.0 and 89.1% in patients who showed no response to CRT (P = 0.039).

CONCLUSION

The results suggest that a distal margin of < 3 mm in the surgical specimen after preoperative CRT is associated with a lower rate of pelvic tumour control at 5 years in patients with Stage ypT3-4 tumours or in those who do not respond to CRT.

Comparison of droplet digital PCR and quantitative real-time PCR in mcrA-based methanogen community analysis

Two different quantitative PCR platforms, droplet digital PCR (dd-PCR) and quantitative real-time PCR (qPCR), were compared in a mcrA-based methanogen community assay that quantifies ten methanogen sub-groups. Both technologies exhibited similar PCR efficiencies over at least four orders of magnitude and the same lower limits of detection (8 copies μL-DNA extract⁻¹). The mcrA-based methanogen communities in three full-scale anaerobic digesters were examined using the two technologies. dd-PCR detected seven groups from the digesters, while qPCR did five groups, indicating that dd-PCR is more sensitive for DNA quantification. Linear regression showed quantitative agreements between both of the technologies (R² = 0.59–0.98) in the five groups that were concurrently detected. Principal component analysis from the two datasets consistently indicated a substantial difference in the community composition among the digesters and revealed similar levels of differentiation among the communities. The combined results suggest that dd-PCR is more promising for examining methanogenic archaeal communities in biotechnological processes.

Estimation of size of cord blood inventory based on high-resolution typing of HLAs

Methods for estimating the cord blood (CB) inventory size required vary according to the ethnic diversity of the HLA, degree of HLA matching and HLA-typing resolution. We estimated the CB inventory size required using 7190 stored CB units (CBU) and 2450 patients who were awaiting or underwent allogeneic hematopoietic stem cell transplantation. With high-resolution typing of HLA-A, B and DRB1, 94.6% of Korean patients could find CBUs in 100 000 CBUs with a 5/6 match, and 95.7% could find CBUs in 5000 CBUs with a 4/6 match. With low-resolution typing of HLA-A and B and high-resolution typing of leukocyte antigen-DRB1, 95% of patients could find CBUs in 50 000 CBUs with a 5/6 match, and 96.7% could find CBUs in 3000 CBUs  with a 4/6 match. With additional high-resolution typing for HLA-A and B, which could improve transplantation outcome, the size of the CB inventory would need to increase twofold for Koreans.

Effects of ultrasonic pretreatment on quantity and composition of bacterial DNA recovered from granular activated carbon used for drinking water treatment

Effects of ultrasonic pretreatment on bacterial DNA recovery from granular activated carbon (GAC) were investigated. GAC (Calgon F400), biologically activated, was sampled from an actual drinking water plant. Different ultrasonic energy densities (0-400 J·cm(-3)) were applied with agitation (250 rpm for 30 min), and recovered bacterial DNA was quantified using quantitative PCR. Energy density was linearly correlated with the concentration of carbon fines produced from GAC during ultrasonication. Ultrasonication alone had no effect on DNA recovery at ≤60 J·cm(-3), but a strongly adverse effect at >67 J·cm(-3) due to the produced carbon fines. Agitation along with ultrasonication strongly enhanced the bacterial DNA recovery when ≤40 J·cm(-3) was applied, although it did not affect the production of carbon fines. Ribosomal tag pyrosequencing was used to compare recovered bacterial communities (0, 20 and 30 J·cm(-3) with or without agitation). Ultrasonication allowed for obtaining a more diverse and richer bacterial community from GAC, compared with the control. Agitation did not show a positive effect on community organization (richness and diversity). Consistently, canonical correspondence analysis indicated that the energy density was associated with the relative abundances of particular bacterial members (P < 0.05), while agitation did not. Correspondence analysis revealed that the recovered bacterial communities were grouped according to the applied energy densities. In conclusion, ultrasonication and agitation influence the recovered DNA in quality and quantity, respectively, and carbon fines as a by-product by ultrasonication interfere with the DNA recovery.

Association of KIR genes and HLA-C alleles with HPV-related uterine cervical disease in Korean women

This study investigated whether killer-cell immunoglobulin-like receptor (KIR) genes and human leukocyte antigen (HLA)-C alleles, receptors and ligands of natural killer cells are associated with the development of human papillomavirus (HPV)-related cervical disease in Korean women. Blood samples from 132 women with HPV-related cervical disease and 159 women without HPV infection were collected for genotyping of KIR genes and HLA-C alleles. Although no relationship was found between KIR genes and HPV-related cervical disease, a significant relationship was found between HLA-C alleles as ligands of KIR and HPV-related cervical disease. Women with HPV-related cervical disease were found to be significantly more likely to carry HLA-C*0303, particularly those with HPV 16 or 18 infection, and less likely to carry HLA-C*01 compared to women without HPV infection. HLA-C*0303 was found to confer susceptibility to HPV-related cervical disease, whereas HLA-C*01 was found to confer a protective effect against HPV-related cervical disease.

A comparison of inflammatory mediator expression between palmoplantar pustulosis and pompholyx

BACKGROUND

Both palmoplantar pustulosis (PPP) and pompholyx are clinically characterized by acute eruptions of vesicles or pustules on the palms or soles.

OBJECTIVES

This study aims to compare the expression of certain inflammatory mediator genes and proteins between patients with PPP and pompholyx using skin tissue samples.

METHODS

Skin biopsies obtained from lesional skin from patients with PPP (n = 7) and pompholyx (n = 5) were analysed by quantitative RT-PCR to measure the mRNA levels of nine genes, including IL-4, IL-8, IL-9, IL-17, IL-22, IFN-γ, CCL-20, granzyme and perforin. For immunohistochemical analysis, 34 paraffin-embedded skin specimens (PPP, n = 22; pompholyx, n = 12) were stained with anti-IL-8, IL-17A, IL-22 and granzyme B antibodies.

RESULTS

Of genes analysed, IL-8 and IL-17A mRNA expression levels were significantly higher in the PPP group than the pompholyx group (P = 0.012 in both), whereas the mRNA expression of granzyme B was significantly higher in pompholyx when compared with PPP (P = 0.004). Regarding the IL-17A immunohistochemical staining, tissue from the PPP lesions contained significantly more IL-17A(+) cells in both the epidermis and papillary dermis when compared with pompholyx (P < 0.001 and P = 0.019 respectively). Moreover, the intensity of the IL-8 immunoreactivity was also greater in the PPP skin lesions than the pompholyx tissue (P < 0.001).

CONCLUSIONS

IL-8 and IL-17A, both are increased in PPP tissue, may represent important immunologic mediators that help to differentiate this clinical entity from pompholyx. This study may provide useful clues in distinguishing PPP from pompholyx, as well as helping to understand the pathogeneses of these two diseases.

Biodegradation capacity utilization as a new index for evaluating biodegradation rate of methane

Density of catalytic organisms can determine the biodegradation capacity and specific biodegradation rate (SBR). A new index, biodegradation capacity utilization (BCU, %), was developed for estimating the extent of actual biodegradation of a gas compound over the full capacity. Three methanotrophic cultures were serially diluted (1-1/25), and methane SBR and BCU were measured. Consistently, biomass reduction increased the SBR and decreased the BCU. Linearity (p < 0.05, r > 0.97) between the BCU and cell density indicated the reflection of biodegradation capacity by BCU. Therefore, BCU is indicative of whether the density of catalytic organisms is pertinent for SBR evaluation of low-soluble gaseous compounds.

Use of artificial DNA with multiple probe sites as reference DNA templates for quantitative real-time PCR to examine methanogen communities

Isolation of reference DNA templates for quantitative real-time PCR assays is an expensive, labor-intensive and time-consuming process if they are not readily available. Two artificial DNA templates with multiple probe sites were designed for quantifying methanogens and their 10 subgroups, based on the methyl coenzyme M reductase gene (mcrA). Their standards were comparable to each other. PCR amplification efficiencies (cycle vs. cumulative fluorescence) of the artificial DNAs were also comparable to those of the observed methanogen groups from anaerobic digesters. The artificial templates can be alternatives to the actual references.

Isolation and characterization of a facultative methanotroph degrading malodor-causing volatile sulfur compounds

Simultaneous removal of methane and malodor-causing volatile sulfur compounds (MVSCs), both emitted from landfills, is a desirable characteristic for methane-mitigation approaches. A methanotrophic bacterium was isolated from a microbial consortium, enriched with methane and dimethyl sulfide (DMS). It grew in the complex nutrient medium R2A without methane, and stably exhibited methanotrophic activity after facultative growth. It was identified as Sphingopyxis sp. MD2 by comparison of the 16S rRNA gene. It belongs to Sphingomonadales, whose members have not shown methanotrophic activity, phylogenetically distinct from orders of known methanotrophs. The MD2 biomass increased at a growth rate of 1.18d(-1) when methane was used as the sole growth substrate. An inhibition test with allylthiourea and PCR/sequencing confirmed the presence of particulate methane monooxygenase in MD2. DMS decreased the methane oxidation rate (2634±146 μmole g DCW(-1) h(-1)) by 12%, while H(2)S had no effect on the methane oxidation rate. Interestingly, methanethiol (MT) enhanced the methane oxidation rate by more than 50%. MD2 degraded H(2)S and MT, regardless of the presence of methane. MD2 also degraded DMS in the presence of methane, indicating co-metabolism. These combined results indicate that MD2 may be a promising biological resource for simultaneous removal of methane and MVSCs.

Characterization of a methane-oxidizing biofilm using microarray, and confocal microscopy with image and geostatic analyses

A mixed methane-oxidizing biofilm was characterized, concurrently using a number of advanced techniques. Community analysis results by microarray exhibited that type II members dominated the methanotrophic community, in which Methylocystis was most abundant, followed by Methylosinus. Observation results by fluorescent in situ hybridization and confocal microscopy showed multiple biofilm colonies that were irregular, bell-shaped, with mean thickness of approximately 20 μm. Image analysis results indicated that the relative abundance of methanotrophs peaked at a depth of about 5 μm. Although the biofilm colonies differed in size, methanotrophs accounted for 4-9%. Gaussian and linear regression results between the biofilm volumes and types I (r (2) = 0.86) and II volumes (r (2) = 0.92), respectively, revealed that type I members played a role in the growth of the biofilm but only below a threshold volume, whereas type II members supported the overall growth. Geostatistical analyses results revealed concentration of types I and II methanotrophic individuals with decreasing depth, and randomness between the spatial locations and population levels. Collectively, the methane-oxidizing biofilm was a highly organized system with methanotrophs and their cohabitants.