Plastics biodegradation and recycling - the introduction of China-Europe cooperation project "Synthetic microorganism communities for plastic degradation and transformation" / 生物工程学报

The China-European environmental biotechnology cooperation research project on the biodegradation of waste plastics is jointly funded by the National Natural Science Foundation of China (NSFC) and the European Commission (EC), and aims to encourage Chinese and European scientists to carry out substantive research in the field of "Microorganism communities for plastics biodegradation". The goal of the project is to use the metabolic capacity of microbial communities to degrade petrochemical plastics that are easy to cause environmental pollution into monomers and small molecules, thereby realizing the biosynthesis of high-value biochemicals by microorganisms. This can not only solve the problem of plastic pollution, but also "turn waste into treasure" and create higher economic benefits. The China-European cooperative research project will promote in-depth cooperation between scientists from both sides in the field of synthetic biology, and help the two sides establish long-term and stable international exchanges and cooperation. Both China and the EU will work to solve the global plastic pollution problem, form a strategic force of science and technology, and jointly open a new chapter in the field of resource utilization of non-degradable plastics.

Reactores Bioquímicos Pasivos: Una alternativa biotecnológica para la remediación de drenajes ácidos de mina / Biochemical passive reactors: a biotechnological alternative to remediation of acid mine drainage

RESUMEN El Drenaje ácido de mina (DAM) es actualmente el principal contaminante de las regiones mineras. Los reactores bioquímicos pasivos son una tecnología sostenible fácil de instalar que utiliza desechos agroindustriales de la región y puede operar en áreas remotas con poco mantenimiento. Además, son una tecnología limpia que involucra bioprocesos, reacciones químicas y precipitación de metales, minimizando el impacto de los vertimientos ácidos sobre suelos y cuerpos de aguas. Los reactores bioquímicos pasivos son columnas empacadas con una "mezcla reactiva" conformada por materiales orgánicos, inorgánicos y un inóculo microbiano. En esta mezcla se remedia el DAM por medio de procesos fisicoquímicos como la adsorción, precipitación, coprecipitación de los metales y de la reducción del sulfato a sulfuro, mientras se incrementa el pH y la alcalinidad. Con el fin de brindar información reciente, así como las necesidades de investigación en el tema, este documento presenta una revisión de literatura sobre la generación química y biológica de los DAM, así como su remedición utilizando reactores bioquímicos pasivos. El conocimiento de los conceptos básicos de estos procesos es extremadamente útil para evaluar las posibles aplicaciones, beneficios y limitaciones de estos sistemas de tratamiento utilizados por la biotecnología durante la biorremediación de efluentes mineros.

ABSTRACT Acid Mine Drainage (AMD) is currently the main pollutant in mining areas. Passive biochemical reactors are a sustainable technology easy to install using agro-industry waste from the mining region and operating in remote locations. Besides, bioreactors are clean technology that involves bioprocesses, chemical reactions, and metal precipitation, minimizing the impact of AMD on soils and fresh water sources. The passive biochemical reactors are columns packed with a "reactive mixture" consisting of organic, inorganic materials and a microbial inoculum. In this reactive mixture, AMD is remediated through physicochemical processes such as metals adsorption, precipitation, and co-precipitation, as well as, the reduction of sulfate to sulfur, while pH and alkalinity are in-creased. To provide recent information and research needs in the subject, this document presents a review of the literature about the chemical and biological generation of AMD and its remediation using passive biochemical reactors. The knowledge of the basic concepts of these processes is extremely useful to evaluate the possible applications, benefits and limitations of these treatment systems used by biotechnology during the bioremediation of mining effluents.

Antagonistic activity of Microbial Association of Kefir Grains and the areas of its usage

One of the newest areas of using the potential of a microbial association of kefir grains is obtaining a biodegradable film. The research was aimed at creating a packaging material with new properties of suppressing the development of concomitant microflora in dried berries and fruits.

Tuber borchii Shapes the Ectomycorrhizosphere Microbial Communities of Corylus avellana

In this study, eight-month-old ectomycorrhizae of Tuber borchii with Corylus avellana were synthesized to explore the influence of T. borchii colonization on the soil properties and the microbial communities associated with C. avellana during the early symbiotic stage. The results showed that the bacterial richness and diversity in the ectomycorrhizae were significantly higher than those in the control roots, whereas the fungal diversity was not changed in response to T. borchii colonization. Tuber was the dominant taxon (82.97%) in ectomycorrhizae. Some pathogenic fungi, including Ilyonectria and Podospora, and other competitive mycorrhizal fungi, such as Hymenochaete, had significantly lower abundance in the T. borchii inoculation treatment. It was found that the ectomycorrhizae of C. avellana contained some more abundant bacterial genera (e.g., Rhizobium, Pedomicrobium, Ilumatobacter, Streptomyces, and Geobacillus) and fungal genera (e.g., Trechispora and Humicola) than the control roots. The properties of rhizosphere soils were also changed by T. borchii colonization, like available nitrogen, available phosphorus and exchangeable magnesium, which indicated a feedback effect of mycorrhizal synthesis on soil properties. Overall, this work highlighted the interactions between the symbionts and the microbes present in the host, which shed light on our understanding of the ecological functions of T. borchii and facilitate its commercial cultivation.

Agricultural Risk Factors Influence Microbial Ecology in Honghu Lake / 基因组蛋白质组与生物信息学报·英文版

Agricultural activities, including stock-farming, planting industry, and fish aquaculture, can affect the physicochemical and biological characters of freshwater lakes. However, the effects of pollution producing by agricultural activities on microbial ecosystem of lakes remain unclear. Hence, in this work, we selected Honghu Lake as a typical lake that is influenced by agriculture activities. We collected water and sediment samples from 18 sites, which span a wide range of areas from impacted and less-impacted areas. We performed a geospatial analysis on the composition of microbial communities associated with physicochemical properties and antibiotic pollution of samples. The co-occurrence networks of water and sediment were also built and analyzed. Our results showed that the microbial communities of impacted and less-impacted samples of water were largely driven by the concentrations of TN, TP, NO-N, and NO-N, while those of sediment were affected by the concentrations of Sed-OM and Sed-TN. Antibiotics have also played important roles in shaping these microbial communities: the concentrations of oxytetracycline and tetracycline clearly reflected the variance in taxonomic diversity and predicted functional diversity between impacted and less-impacted sites in water and sediment samples, respectively. Furthermore, for samples from both water and sediment, large differences of network topology structures between impacted and less-impacted were also observed. Our results provide compelling evidence that the microbial community can be used as a sentinel of eutrophication and antibiotics pollution risk associated with agricultural activity; and that proper monitoring of this environment is vital to maintain a sustainable environment in Honghu Lake.

Cultivated bacterial diversity associated with the carnivorous plant Utricularia breviscapa (Lentibulariaceae) from floodplains in Brazil

ABSTRACT Carnivorous plant species, such as Utricularia spp., capture and digest prey. This digestion can occur through the secretion of plant digestive enzymes and/or by bacterial digestive enzymes. To comprehend the physiological mechanisms of carnivorous plants, it is essential to understand the microbial diversity related to these plants. Therefore, in the present study, we isolated and classified bacteria from different organs of Utricularia breviscapa (stolons and utricles) and from different geographic locations (São Paulo and Mato Grosso). We were able to build the first bacterium collection for U. breviscapa and study the diversity of cultivable bacteria. The results show that U. breviscapa bacterial diversity varied according to the geographic isolation site (São Paulo and Mato Grosso) but not the analyzed organs (utricle and stolon). We reported that six genera were common to both sample sites (São Paulo and Mato Grosso). These genera have previously been reported to be beneficial to plants, as well as related to the bioremediation process, showing that these isolates present great biotechnological and agricultural potential. This is the first report of an Acidobacteria isolated from U. breviscapa. The role of these bacteria inside the plant must be further investigated in order to understand their population dynamics within the host.

Rhizospheric microbial communities are driven by at different growth stages and biocontrol bacteria alleviates replanting mortality

The cultivation of plants is hindered by replanting problems, which may be caused by plant-driven changes in the soil microbial community. Inoculation with microbial antagonists may efficiently alleviate replanting issues. Through high-throughput sequencing, this study revealed that bacterial diversity decreased, whereas fungal diversity increased, in the rhizosphere soils of adult ginseng plants at the root growth stage under different ages. Few microbial community, such as , Cytophagaceae, , , Sphingomonadaceae, and Zygomycota, were observed; the relative abundance of microorganisms, namely, , Enterobacteriaceae, , Cantharellales, , , and Chytridiomycota, increased in the soils of adult ginseng plants compared with those in the soils of 2-year-old seedlings. 50-1, a microbial antagonist against the pathogenic , was isolated through a dual culture technique. These bacteria acted with a biocontrol efficacy of 67.8%. The ginseng death rate and abundance decreased by 63.3% and 46.1%, respectively, after inoculation with 50-1. Data revealed that microecological degradation could result from ginseng-driven changes in rhizospheric microbial communities; these changes are associated with the different ages and developmental stages of ginseng plants. Biocontrol using microbial antagonists alleviated the replanting problem.

Research advances in ham microorganisms / 生物工程学报

Microbial communities of fermented foods have provided a tool for humans to preserve and develop flavor for long history. And they can also provide opportunities to study microbial community formation because of their reproducible and easy-to-manipulate feature. Dry-cured ham is one of the traditional fermented products. Some of the compounds produced during the hydrolysis and oxidation of proteins and fats in ham processing form a distinctive flavor of ham. Many microbes are involved in this process and biochemical reactions. In this review, we describe the ham microbial communities in different regions and their role in the formation of ham quality, and prospect the future research of ham microbiology.

Shotgun metagenomic analysis of microbial communities in the surface waters of the Eastern South China Sea

Aims: The South China Sea (SCS) harbours a rich biodiversity. However, few studies have been published on its diverse communities, particularly its microbial counterparts. As key players behind many of the vital processes carried out in the ocean, microbes are the focus of this study, placing particular emphasis on community composition, structure, and function. Methodology and results: By employing next generation shotgun sequencing technologies (Illumina HiSeq2000), we assessed the taxonomic structure and functional diversity of the prokaryotic communities in surface waters collected from 3 representative sites in the Eastern SCS: Sarawak (Kuching), Sabah (Kota Kinabalu), and Philippines (Manila). Comparisons were undertaken to similar studies from coastal and open ocean environments. All 3 locations were dominated by members of the Proteobacteria (Alpha- and Gamma-) and Cyanobacteria (Synechococcus sp. and Prochlorococcus sp.). The highest proportion of Gammaproteobacteria was found in Sarawak, representing an approximate 20% of total sequences. Archaeal assemblages were made up largely of Euryarchaeota and unclassified sequences, while Crenarchaeota and Thaumarchaeota were present in much smaller proportions, except in the Philippines where Thaumarchaeota made up almost 40% of the entire taxa. Conclusion, significance and impact of study: The majority of the microbial communities adhered to a core set of functional genes across the different locations. However, differences existed particularly in Sarawak waters which are hypothesized to be due to local environmental parameters such as riverine influence. The results obtained from this study provide the first comparison of prokaryotic communities in the surface waters of the eastern SCS and will serve as a good platform for prospective studies in the field of environmental science.

Degradation of polynuclear aromatic hydrocarbons by two strains of Pseudomonas

ABSTRACT The goal of this investigation was to isolate competent polynuclear aromatic hydrocarbons degraders that can utilize polynuclear aromatic hydrocarbons of former industrial sites at McDoel Switchyard in Bloomington, Indiana. Using conventional enrichment method based on soil slurry, we isolated, screened and purified two bacterial species strains PB1 and PB2. Applying the ribotyping technique using the 16S rRNA gene analysis, the strains were assigned to the genus Pseudomonas (Pseudomonas plecoglossicida strain PB1 and Pseudomonas sp. PB2). Both isolates showed promising metabolic capacity on pyrene sprayed MS agar plates during the preliminary investigations. Using time course studies in the liquid cultures at calculated concentrations 123, 64, 97 and 94 ppm for naphthalene, chrysene, fluroanthene and pyrene, P. plecoglossicida strain PB1 and Pseudomonas sp. PB2 showed partial utilization of the polynuclear aromatic hydrocarbons. Naphthalene was degraded between 26% and 40%, chrysene 14% and 16%, fluroanthene 5% and 7%; pyrene 8% and 13% by P. plecoglossicida strain PB1 and Pseudomonas sp. PB2 respectively. Based on their growth profile, we developed a model R2 = 1 to predict the degradation rate of slow polynuclear aromatic hydrocarbon-degraders where all the necessary parameters are constant. From this investigation, we confirm that the former industrial site soil microbial communities may be explored for the biorestoration of the industrial site.

Biofilm production by Escherichia coli in poultry water drinkers

This study evaluated the microbiological quality of the water of 33 poultry sheds seeking to identify the presence of biofilm-producing Escherichia coli. The swab samples of the surface of the drinkers were analyzed by the inhibition test to detect the most effective disinfectant for removing these bacterial communities. The multiple-tube and mesophilic counts techniques were used to analyze the water samples. The swabs were plated on EMB agar followed by Rugai medium to identify E. coli. The biofilm was detected by the optical density readings and the Congo red agar method. Overall, 15 strains of Escherichia coli were detected in the swabs of the drinkers, of which 8 were biofilm producers. Regarding the water quality, 15 (45.45%) of the 33 evaluated water samples had bacterial growth while only two (13.33%) produced gas. The test with disinfectants showed that chlorine and chlorhexidine were not effective to control the E. coli biofilm production. Therefore, a strict control is essential to ensure the safety of the water supplied to the animals in broiler sheds and to eliminate the biofilm-forming E. coli that have shown to be potentially resistant to the sanitizers commonly used in the cleaning processes.

Objetivou-se avaliar a qualidade microbiológica da água de 33 galpões avícolas, identificar a presença de Escherichia coli produtoras de biofilmes em amostras de suabes de superfície dos bebedouros e analisar por teste de inibição o desinfetante mais eficiente para remoção dessas comunidades bacterianas. Foi utilizada a técnica dos tubos múltiplos e contagem de mesófilas para as amostras de água. Os suabes foram semeados em Ágar EMB, e posteriormente em meio Rugai para identificação de E. coli. Para análise de produção de biofilme foi feita a leitura da Densidade Óptica e o método do Ágar Vermelho Congo. Foram identificadas 15 cepas de E. coli nos suabes de bebedouros, sendo que 8 foram produtoras de biofilme. Quanto ao padrão de qualidade da água, observou-se que das 33 amostras de água avaliadas, 15 (45,45%) tiveram crescimento bacteriano, sendo que somente duas (13,33%) produziram gás. Para o teste com desinfetantes, o cloro e o clorexidine não se mostraram eficientes no controle da produção de biofilmes de E. coli. Dessa forma, torna-se essencial o controle rigoroso nos galpões de frangos de corte para garantir a inocuidade da água fornecida aos animais e a eliminação de E. coli potencialmente formadoras de biofilmes resistentes aos sanitizantes mais comumente usados nos processos de limpeza.

Comparing how land use change impacts soil microbial catabolic respiration in Southwestern Amazon

Abstract Land use changes strongly impact soil functions, particularly microbial biomass diversity and activity. We hypothesized that the catabolic respiration response of the microbial biomass would differ depending on land use and that these differences would be consistent at the landscape scale. In the present study, we analyzed the catabolic response profile of the soil microbial biomass through substrate-induced respiration in different land uses over a wide geographical range in Mato Grosso and Rondônia state (Southwest Amazon region). We analyzed the differences among native areas, pastures and crop areas and within each land use and examined only native areas (Forest, Dense Cerrado and Cerrado), pastures (Nominal, Degraded and Improved) and crop areas (Perennial, No-Tillage, Conventional Tillage). The metabolic profile of the microbial biomass was accessed using substrate-induced respiration. Pasture soils showed significant responses to amino acids and carboxylic acids, whereas native areas showed higher responses to malonic acid, malic acid and succinic acid. Within each land use category, the catabolic responses showed similar patterns in both large general comparisons (native area, pasture and crop areas) and more specific comparisons (biomes, pastures and crop types). The results showed that the catabolic responses of the microbial biomass are highly correlated with land use, independent of soil type or climate. The substrate induced respiration approach is useful to discriminate microbial communities, even on a large scale.

Comparison of DNA extraction protocols for microbial communities from soil treated with biochar

Many studies have evaluated the effects of biochar application on soil structure and plant growth. However, there are very few studies describing the effect of biochar on native soil microbial communities. Microbial analysis of environmental samples requires accurate and reproducible methods for the extraction of DNA from samples. Because of the variety among microbial species and the strong adsorption of the phosphate backbone of the DNA molecule to biochar, extracting and purifying high quality microbial DNA from biochar-amended soil is not a trivial process and can be considerably more difficult than the extraction of DNA from other environmental samples. The aim of this study was to compare the relative efficacies of three commercial DNA extraction kits, the FastDNA® SPIN Kit for Soil (FD kit), the PowerSoil® DNA Isolation Kit (PS kit) and the ZR Soil Microbe DNA Kit MiniprepTM (ZR kit), for extracting microbial genomic DNA from sand treated with different types of biochar. The methods were evaluated by comparing the DNA yields and purity and by analysing the bacterial and fungal community profiles generated by PCR-DGGE. Our results showed that the PCR-DGGE profiles for bacterial and fungal communities were highly affected by the purity and yield of the different DNA extracts. Among the tested kits, the PS kit was the most efficient with respect to the amount and purity of recovered DNA and considering the complexity of the generated DGGE microbial fingerprint from the sand-biochar samples.

Formation of aerobic granular sludge under adverse conditions: Low DO and high ammonia.

In this study, two adverse environments: low dissolved oxygen (DO) and high ammonia concentration, were employed to investigate the morphology, interspecies quorum sensing, extracellular polymers (EPS) characterization and microbial communities in the formation of aerobic granular sludge. Results showed that low DO could promote filamentous bacterial outgrowth. Under high ammonia concentration aerobic granular sludge (AGS) could still be cultivated, although it was looser and lighter than the control group. During the early stage of the AGS cultivation process, AI-2 activity reached a peak value in all three reactors, and ultrasonic pre-treatment was not beneficial to the release of AI-2. During AGS formation, the production of polysaccharide exhibited increases from 12.2 % to 40.3 %, 49.6 %, and 29.3 %. And PS in R2 was the highest as the result of sludge bulking. PS/PN was 1.5~8 in the three reactors. Three-dimensional EEM fuorescence spectroscopy variation indicated the change of protein in EPS, and the highest intensity of Peak T1 was obtained. The location shift of Peak T1 was not obvious, and Peaks A, C, and T2 shifted toward longer wavelengths (red shift) of 5~60 nm, or shorter wavelengths (blue shift) of 10~25 nm on the emission scale and / or excitation scale in all three reactors. This provided spectral information on the chemical structure changes. Bacteria in R3 had the highest species diversity, and all bacteria in b-Proteobacteria were identified as genus Thauera, which suggested that simultaneous nitrification and denitrification occurred in R3. The filamentous bacteria in seed sludge and R2 were species-richer. There was a low abundance of filamentous bacteria in R1 and R3, which contributed to the granule structure stability.

Structure and composition of bacterial and fungal community in soil under soybean monoculture in the Brazilian cerrado

Soybean is the most important oilseed cultivated in the world and Brazil is the second major producer. Expansion of soybean cultivation has direct and indirect impacts on natural habitats of high conservation value, such as the Brazilian savannas (Cerrado). In addition to deforestation, land conversion includes the use of fertilizers and pesticides and can lead to changes in the soil microbial communities. This study evaluated the soil bacterial and fungal communities and the microbial biomass C in a native Cerrado and in a similar no-tillage soybean monoculture area using PCR-DGGE and sequencing of bands. Compared to the native area, microbial biomass C was lower in the soybean area and cluster analysis indicated that the structure of soil microbial communities differed. 16S and 18S rDNA dendrograms analysis did not show differences between row and inter-row samples, but microbial biomass C values were higher in inter-rows during soybean fructification and harvest. The study pointed to different responses and alterations in bacterial and fungal communities due to soil cover changes (fallow x growth period) and crop development. These changes might be related to differences in the pattern of root exudates affecting the soil microbial community. Among the bands chosen for sequencing there was a predominance of actinobacteria, y-proteobacteria and ascomycetous divisions. Even under no-tillage management methods, the soil microbial community was affected due to changes in the soil cover and crop development, hence warning of the impacts caused by changes in land use.