In vitro Inoculation of Fresh or Frozen Rumen Fluid Distinguishes Contrasting Microbial Communities and Fermentation Induced by Increasing Forage to Concentrate Ratio

In vitro rumen batch culture is a technology to simulate rumen fermentation by inoculating microorganisms from rumen fluids. Although inocula (INO) are commonly derived from fresh rumen fluids, frozen rumen fluids are also employed for the advantages of storing, transporting, and preserving rumen microorganisms. The effects of frozen INO on microbial fermentation and community may be interfered with by substrate type, which has not been reported. This study was designed to test whether rumen fluid treatments (i.e., fresh and frozen) could interact with incubated substrates. A complete block design with fractional arrangement treatment was used to investigate the effects of INO (fresh or frozen rumen fluids) and concentrate-to-forage ratios (C/F, 1:4 or 1:1) on rumen fermentation and microbial community. The effects of increasing C/F were typical, including increased dry matter (DM) degradation and total volatile fatty acids (VFA) concentration (P < 0.001), and decreased acetate to propionate ratio (P = 0.01) and bacterial diversity of richness and evenness (P ≤ 0.005) with especially higher fermentative bacteria such as genus Rikenellaceae_RC, F082, Prevotella, Bacteroidales_BS11, Muribaculaceaege, and Christensenellaceae_R-7 (P ≤ 0.04). Although frozen INO decreased (P < 0.001) DM degradation and altered rumen fermentation with lower (P ≤ 0.01) acetate to propionate ratio and molar proportion of butyrate than fresh INO, typical effects of C/F were independent of INO, as indicated by insignificant INO × C/F interaction on substrate degradation, VFA profile and bacterial community (P ≥ 0.20). In summary, the effect of C/F on fermentation and bacterial diversity is not interfered with by INO type, and frozen INO can be used to distinguish the effect of starch content.

Nghiên cứu mức độ kháng kháng sinh của các vi khuẩn gram âm không lên men gây viêm phổi ở bệnh nhân thở máy

TÓM TẮT Đặt vấn đề: Viêm phổi liên quan thở máy là bệnh lý nhiễm khuẩn bệnh viện rất thường gặp trong đơn vị hồi sức tích cực. Có nhiều vi khuẩn gây viêm phổi liên quan thở máy, trong đó các vi khuẩn Gram âm không lên men như Acinetobacterbaumannii, Pseudomonasaeruginosa,.. là những vi khuẩn gây bệnh hàng đầu và có mức độ kháng kháng sinh cao. Phương pháp: Một nghiên cứu mô tả cắt ngang được thực hiện ở các chủng vi khuẩn Gram âm không lên men phân lập được từ các mẫu đờm của bệnh nhân thở máy trên 48 giờ điều trị tại các khoa Hồi sức tích cực - Ngoại khoa Bệnh viện Hữu nghị Đa khoa Nghệ An năm từ 1/2020 đến 6/2021. Kết quả: Phân lập được 120 chủng Vi khuẩn Gram âm không lên men, trong đó, Acinetobacter baumannii 85 chủng, Pseudomonas aeruginosa 31 chủng. Acinetobacter baumannii có mức độ đề kháng trên 70% với tất cả các kháng sinh thử nghiệm, trong đó kháng cao nhất với Ceftriaxone 96,9%. Pseudomonas aeriginosa kháng với tất cả các kháng sinh thử nghiệm, kháng cao nhất với Gentamycin 80,0%, kháng thấp nhất với Piperacillin/Tazobactam 32,3%. Kết luận: Vi khuẩn không lên men là những tác nhân chính gây viêm phổi liên quan thở máy, phổ biến nhất là Acinetobacter baumannii và Pseudomonas aeruginosa. Những vi khuẩn này kháng cao với các kháng sinh thử nghiệm, trong đó, A. baumannii kháng trên 70% các kháng sinh thử nghiệm, P. aeruginosa kháng tất cả kháng sinh thử nghiệm với mức độ khác nhau tử 32,3 - 80,0%. ABSTRACT ANTIBIOTIC RESISTANCE OF NON - FERMENTABLE GRAM - NEGATIVE BACTERIA CAUSING PNEUMONIA IN PATIENTS WITH MECHANICALLY VENTILATION Background: Ventilator - associated pneumonia is a very common nosocomial infection in the intensive care unit. Many bacteria cause ventilator - associated pneumonia, in which non - fermentative Gram - negative bacteria such as Acinetobacter baumannii, Pseudomonas aeruginosa, etc., are the leading pathogens and have high antibiotic resistance. Methods: A cross sectional descriptive study was conducted on non - fermentative bacteria strains causing ventilator - associated pneumonia which were isolated at the Surgical Intensive Care Unit Department of Nghe An General Friendship Hospital from January 2020 to June 2021. Results: A total of 120 strains of non - fermenting Gram - negative bacteria were isolated. Of these, 85 strains were Acinetobacter baumannii, 31 strains was Pseudomonas aeruginosa. Acinetobacter baumannii has a resistance rate of more than 70% with all tested antibiotics, of which the highest resistance is to Ceftriaxone 96.9%. Pseudomonas aeriginosa was resistant to all tested antibiotics, with the highest resistance to Gentamycin80.0%, the lowest resistance to Piperacillin/Tazobactam 32.3%. Conclusion: Non - fermentative bacteria are the main pathogens of ventilator - associated pneumonia. The most common pathogens were Acinetobacter baumannii and Pseudomonas aeruginosa. These bacteria were highly resistant to the tested antibiotics. In which, A. baumannii resisted over 70% of the tested antibiotics, and P. aeruginosa resisted all tested antibiotics with varying degrees from 32.3 to 80.0%. Keywords: Ventilation associated pneumonia, VAP, P. aeruginosa, A. baumannii.

Microbial Community Successional Changes in a Full-Scale Mesophilic Anaerobic Digester from the Start-Up to the Steady-State Conditions

Anaerobic digestion is a widely used technology for sewage sludge stabilization and biogas production. Although the structure and composition of the microbial communities responsible for the process in full-scale anaerobic digesters have been investigated, little is known about the microbial successional dynamics during the start-up phase and the response to variations occurring in such systems under real operating conditions. In this study, bacterial and archaeal population dynamics of a full-scale mesophilic digester treating activated sludge were investigated for the first time from the start-up, performed without adding external inoculum, to steady-state operation. High-throughput 16S rRNA gene sequencing was used to describe the microbiome evolution. The large majority of the reads were affiliated to fermentative bacteria. Bacteroidetes increased over time, reaching 22% of the total sequences. Furthermore, Methanosaeta represented the most abundant methanogenic component. The specific quantitative data generated by real-time PCR indicated an enrichment of bacteria and methanogens once the steady state was reached. The analysis allowed evaluation of the microbial components more susceptible to the shift from aerobic to anaerobic conditions and estimation of the microbial components growing or declining in the system. Additionally, activated sludge was investigated to evaluate the microbial core selected by the WWTP operative conditions.

Stress-Responses of Performance and Microbial Community in Anaerobic Digestion System Under Long-Term Enrichment of Phenanthrene

The expanded granular sludge blanket reactor (EGSB) was operated for 198 days to study the long-term effects of phenanthrene (PHE) enrichment on system performance and microbial community. The results showed that the PHE was significantly enriched in the reactor. The final PHE concentration in effluent and sludge reached to 1.764±0.05 mg/L and 12.52±0.42 mg/gTS, respectively. While the average daily methane production was decreased by 5.0%-9.8% under long-term PHE exposure. The 3D-EEM of effluent indicated that PHE stimulated the microbial metabolism with the higher intensity of soluble microbial byproduct-like materials (SMP) and proteins. Moreover, the removal efficiency of soluble chemical oxygen demand (SCOD) and NH4+-N gradually diminished with the enrichment of PHE. PHE shaped the microbial community, and the predominant fermentative bacteria (Mesotoga) was severely inhibited. Contrarily, the bacteria (Syntrophorhabdus, Acinetobacter, Desulfovibrio, Desulfomicrobium) involved in PHE-degradation was enriched at end of Phase V. In addition, the relative abundance (RA) of hydrotrophic methanogens (Methanofastidiosum, Methanolinea, Methanobacterium, Methanomassiliicoccus) increased by 0.96-fold with the long-term enrichment of PHE, while the RA of acetoclastic Methanosaeta obviously decreased.

Sulfidogenic Microbial Communities of the Uzen High-Temperature Oil Field in Kazakhstan

Application of seawater for secondary oil recovery stimulates the development of sulfidogenic bacteria in the oil field leading to microbially influenced corrosion of steel equipment, oil souring, and environmental issues. The aim of this work was to investigate potential sulfide producers in the high-temperature Uzen oil field (Republic of Kazakhstan) exploited with seawater flooding and the possibility of suppressing growth of sulfidogens in both planktonic and biofilm forms. Approaches used in the study included 16S rRNA and dsrAB gene sequencing, scanning electron microscopy, and culture-based techniques. Thermophilic hydrogenotrophic methanogens of the genus Methanothermococcus (phylum Euryarchaeota) predominated in water from the zone not affected by seawater flooding. Methanogens were accompanied by fermentative bacteria of the genera Thermovirga, Defliviitoga, Geotoga, and Thermosipho (phylum Thermotogae), which are potential thiosulfate- or/and sulfur-reducers. In the sulfate- and sulfide-rich formation water, the share of Desulfonauticus sulfate-reducing bacteria (SRB) increased. Thermodesulforhabdus, Thermodesulfobacterium, Desulfotomaculum, Desulfovibrio, and Desulfoglaeba were also detected. Mesophilic denitrifying bacteria of the genera Marinobacter, Halomonas, and Pelobacter inhabited the near-bottom zone of injection wells. Nitrate did not suppress sulfidogenesis in mesophilic enrichments because denitrifiers reduced nitrate to dinitrogen; however, thermophilic denitrifiers produced nitrite, an inhibitor of SRB. Enrichments and a pure culture Desulfovibrio alaskensis Kaz19 formed biofilms highly resistant to biocides. Our results suggest that seawater injection and temperature of the environment determine the composition and functional activity of prokaryotes in the Uzen oil field.

Microbial Shift in the Enteric Bacteriome of Coral Reef Fish Following Climate-Driven Regime Shifts

Replacement of coral by macroalgae in post-disturbance reefs, also called a “coral-macroalgal regime shift”, is increasing in response to climate-driven ocean warming. Such ecosystem change is known to impact planktonic and benthic reef microbial communities but few studies have examined the effect on animal microbiota. In order to understand the consequence of coral-macroalgal shifts on the coral reef fish enteric bacteriome, we used a metabarcoding approach to examine the gut bacteriomes of 99 individual fish representing 36 species collected on reefs of the Inner Seychelles islands that, following bleaching, had either recovered to coral domination, or shifted to macroalgae. While the coral-macroalgal shift did not influence the diversity, richness or variability of fish gut bacteriomes, we observed a significant effect on the composition (R2 = 0.02; p = 0.001), especially in herbivorous fishes (R2 = 0.07; p = 0.001). This change is accompanied by a significant increase in the proportion of fermentative bacteria (Rikenella, Akkermensia, Desulfovibrio, Brachyspira) and associated metabolisms (carbohydrates metabolism, DNA replication, and nitrogen metabolism) in relation to the strong turnover of Scarinae and Siganidae fishes. Predominance of fermentative metabolisms in fish found on macroalgal dominated reefs indicates that regime shifts not only affect the taxonomic composition of fish bacteriomes, but also have the potential to affect ecosystem functioning through microbial functions.

Enhancement of Biogas Production via Co-Digestion of Wastewater Treatment Sewage Sludge and Brewery Spent Grain: Physicochemical Characterization and Microbial Community

The present study intends to evaluate a synergy towards enhanced biogas production by co-digesting municipal sewage sludge (SS) with brewery spent grain (BSG). To execute this, physicochemical and metagenomics analysis was conducted on the sewage sludge substrate. The automatic methane potential test system II (AMPTS II) biochemical methane potential (BMP) batch setup was operated at 35 ± 5 °C, pH range of 6.5–7.5 for 30 days’ digestion time on AMPTS II and 150 days on semi-continuous setup, where the organic loading rate (OLR) was guided by pH and the volatile fatty acids to total alkalinity (VFA/TA) ratio. Metagenomics analysis revealed that Proteobacteria was the most abundant phyla, consisting of hydrolytic and fermentative bacteria. The archaea community of hydrogenotrophic methanogen genus was enriched by methanogens. The highest BMP was obtained with co-digestion of SS and BSG, and 9.65 g/kg of VS. This not only increased biogas production by 104% but also accelerated the biodegradation of organic matters. However, a significant reduction in the biogas yield, from 10.23 NL/day to 2.02 NL/day, was observed in a semi-continuous process. As such, it can be concluded that different species in different types of sludge can synergistically enhance the production of biogas. However, the operating conditions should be optimized and monitored at all times. The anaerobic co-digestion of SS and BSG might be considered as a cost-effective solution that could contribute to the energy self-efficiency of wastewater treatment works (WWTWs) and sustainable waste management. It is recommended to upscale co-digestion of the feed for the pilot biogas plant. This will also go a long way in curtailing and minimizing the impacts of sludge disposal in the environment.

Disentangling the syntrophic electron transfer mechanisms of Candidatus geobacter eutrophica through electrochemical stimulation and machine learning

Interspecies hydrogen transfer (IHT) and direct interspecies electron transfer (DIET) are two syntrophy models for methanogenesis. Their relative importance in methanogenic environments is still unclear. Our recent discovery of a novel species Candidatus Geobacter eutrophica with the genetic potential of IHT and DIET may serve as a model species to address this knowledge gap. To experimentally demonstrate its DIET ability, we performed electrochemical enrichment of Ca. G. eutrophica-dominating communities under 0 and 0.4 V vs. Ag/AgCl based on the presumption that DIET and extracellular electron transfer (EET) share similar metabolic pathways. After three batches of enrichment, Geobacter OTU650, which was phylogenetically close to Ca. G. eutrophica, was outcompeted in the control but remained abundant and active under electrochemical stimulation, indicating Ca. G. eutrophica’s EET ability. The high-quality draft genome further showed high phylogenomic similarity with Ca. G. eutrophica, and the genes encoding outer membrane cytochromes and enzymes for hydrogen metabolism were actively expressed. A Bayesian network was trained with the genes encoding enzymes for alcohol metabolism, hydrogen metabolism, EET, and methanogenesis from dominant fermentative bacteria, Geobacter, and Methanobacterium. Methane production could not be accurately predicted when the genes for IHT were in silico knocked out, inferring its more important role in methanogenesis. The genomics-enabled machine learning modeling approach can provide predictive insights into the importance of IHT and DIET.

Microbial Communities of Hydrothermal Guaymas Basin Surficial Sediment Profiled at 2 Millimeter-Scale Resolution

The surficial hydrothermal sediments of Guaymas Basin harbor complex microbial communities where oxidative and reductive nitrogen, sulfur, and carbon-cycling populations and processes overlap and coexist. Here, we resolve microbial community profiles in hydrothermal sediment cores of Guaymas Basin on a scale of 2 millimeters, using Denaturing Gradient Gel Electrophoresis (DGGE) to visualize the rapid downcore changes among dominant bacteria and archaea. DGGE analysis of bacterial 16S rRNA gene amplicons identified free-living and syntrophic deltaproteobacterial sulfate-reducing bacteria, fermentative Cytophagales, members of the Chloroflexi (Thermoflexia), Aminicenantes, and uncultured sediment clades. The DGGE pattern indicates a gradually changing downcore community structure where small changes on a 2-millimeter scale accumulate to significantly changing populations within the top 4 cm sediment layer. Functional gene DGGE analyses identified anaerobic methane-oxidizing archaea (ANME) based on methyl-coenzyme M reductase genes, and members of the Betaproteobacteria and Thaumarchaeota based on bacterial and archaeal ammonia monooxygenase genes, respectively. The co-existence and overlapping habitat range of aerobic, nitrifying, sulfate-reducing and fermentative bacteria and archaea, including thermophiles, in the surficial sediments is consistent with dynamic redox and thermal gradients that sustain highly complex microbial communities in the hydrothermal sediments of Guaymas Basin.

Review on landfill gas formation from leachate biodegradation

Landfill waste management is a very crucial procedure in handling Municipal Solid Waste (MSW) because it may create significant environmental issues if it is not managed properly. Landfill leachate and landfill gas (LFG) is part of the landfill waste management which triggered lot of researchers especially in terms of the environmental implications associated with the movement of the gasses during the waste constituents’ processes. Hence, this paper review is aiming to understand the behaviour of leachate itself as a decomposition agent in producing landfill gas (biogas). Biogas is naturally produced by anaerobic bacteria through anaerobic digestion which is affected by operating parameters and substrate characteristic. The results indicate that temperature, pH, and C/N ratio of leachate are the important factors that could increase the production of biogas with high content of methane. Furthermore, in terms of microbial activity during anaerobic digestion process, hydrogenotrophic and acetoclastic methanogen are the dominant substrate that contribute in producing methane gas as the final product. Firmicutes and Bacteroidetes are the common fermentative bacteria that had been found during fermentation process in hydrolysis and acidogenic phases. While, methanobacterial, methanococcal, methanomicrobial, methanosarcinal, and methanopyral are being classified as orders among 65 types of methanogenic archaea during methanogenesis stage. Overall, the relationships between operating parameters and microbial structure are important aspects that need to be considered in order to optimize the production of methane gas.