Copper dynamics and impact on microbial communities in soils of variable organic status

The effect of soil organic status on copper impact was investigated by means of a microcosm study carried out on a vineyard soil that had been amended with varying types of organic matter during a previous long-term field experiment. Soil microcosms were contaminated at 250 mg Cu kg(-1) and incubated for 35 days. Copper distribution and dynamics were assessed in the solid matrix by a sequential extraction procedure and in the soil solution by measuring total and free exchangeable copper concentrations. Copper bioavailability was also measured with a whole-cell biosensor. Modifications of microbial communities were assessed by means of biomass-C measurements and characterization of genetic structure using ARISA (automated-ribosomal-intergenic-spacer-analysis). The results showed that copper distribution, speciation, and bioavailability are strongly different between organically amended and nonamended soils. Surprisingly, in solution, bioavailable copper correlated with total copper but not with free copper. Similarly the observed differential copper impact on micro-organisms suggested that organic matter controlled copper toxicity. Bacterial-ARISA modifications also correlated with the estimated metal bioavailability and corresponded to the enrichment of the Actinobacteria. Contrarily, biomass-C and fungal-ARISA measurements did not relate trivially to copper speciation and bioavailability, suggesting that the specific composition of the indigenous-soil communities controls its sensitivity to this metal.     

四川泡菜微生态分布及其与盐度、酸度的关系

以眉山、成都两个地区的传统发酵泡菜水和两个泡菜生产企业的盐渍水为研究对象,对所有样品的pH、酸度、盐度及其微生态进行了测定与分析。结果显示:(1)样品的食盐含量对微生物影响很大,而微生物的数量又与样品pH、酸度密切相关。(2)传统发酵泡菜水样品中的乳杆菌、乳球菌、明串珠菌的含量均较高,有的甚至达到108CFU/mL;大部分传统发酵泡菜水中的酵母菌含量较高,在102～106CFU/mL之间;少量泡菜水中存在醋酸菌。企业盐渍菜样品中菌落总数在102～105CFU/mL之间,乳酸菌数和酵母菌数均在10～105CFU/mL之间。(3)另外,少数样品受到霉菌污染,大多数的传统发酵泡菜样品受到了假单胞菌或芽孢杆菌的污染。     

好氧微生物与厌氧微生物处理制浆造纸废水

制浆造纸废水是工业废水中的重要污染源。本文介绍近些年来制浆造纸行业在好氧微生物法和厌氧微生物法处理制浆造纸废水方面所采取的工艺和所进行的研究以及最近的发展。     

浓香型大曲真核微生物群落的PCR-SSCP解析

通过PCR-SSCP分析了浓香型大曲发酵过程中7个曲样中真核微生物群落的变化情况,结果表明:在大曲发酵过程中,微生物群落结构复杂,变化多样,不同微生物群落具有协同和制约的复杂生态学效应,并与外界因素相互作用,共同对大曲发酵过程产生影响.大曲发酵过程中温度的升高,对真核微生物多样性的影响较大.     

Pathways for the anaerobic microbial debromination of polybrominated diphenyl ethers

The debromination pathways of seven polybrominated diphenyl ethers (PBDEs) by three different cultures of anaerobic dehalogenating bacteria were investigated using comprehensive two-dimensional gas chromatography (GC x GC). The congeners analyzed were the five major components of the industrially used octa-BDE mixture (octa-BDEs 196, 203, and 197, hepta-BDE 183, and hexa-BDE 153) as well as the two most commonly detected PBDEs in the environment, penta-BDE 99 and tetra-BDE 47. Among the dehalogenating cultures evaluated in this study were a trichloroethene-enriched consortium containing multiple Dehalococcoides species, and two pure cultures, Dehalobacter restrictus PER-K23 and Desulfitobacterium hafniense PCP-1. PBDE samples were analyzed by GC x GC coupled to an electron capture detector to maximize separation and identification of the product congeners. All studied congeners were debrominated to some extent by the three cultures and all exhibited similar debromination pathways with preferential removal of para and meta bromines. Debromination of the highly brominated congeners was extremely slow, with usually less than 10% of nM concentrations of PBDEs transformed after three months. In contrast, debromination of the lesser brominated congeners, such as penta 99 and tetra 47, was faster, with some cultures completely debrominating nM levels of tetra 47 within weeks.     

Composition and physiological profiling of sprout-associated microbial communities

The native microfloras of various types of sprouts (alfalfa, clover, sunflower, mung bean, and broccoli sprouts) were examined to assess the relative effects of sprout type and inoculum factors (i.e., sprout-growing facility, seed lot, and inoculation with sprout-derived inocula) on the microbial community structure of sprouts. Sprouts were sonicated for 7 min or hand shaken with glass beads for 2 min to recover native microfloras from the surface, and the resulting suspensions were diluted and plated. The culturable fraction was characterized by the density (log CFU/g), richness (e.g., number of types of bacteria), and diversity (e.g., microbial richness and evenness) of colonies on tryptic soy agar plates incubated for 48 h at 30 degrees C. The relative similarity between sprout-associated microbial communities was assessed with the use of community-level physiological profiles (CLPPs) based on patterns of utilization of 95 separate carbon sources. Aerobic plate counts of 7.96 +/- 0.91 log CFU/g of sprout tissue (fresh weight) were observed, with no statistically significant differences in microbial cell density, richness, or diversity due to sprout type, sprout-growing facility, or seed lot. CLPP analyses revealed that the microbial communities associated with alfalfa and clover sprouts are more similar than those associated with the other sprout types tested. Variability among sprout types was more extensive than any differences between microbial communities associated with alfalfa and clover sprouts from different sprout-growing facilities and seed lots. These results indicate that the subsequent testing of biocontrol agents should focus on similar organisms for alfalfa and clover, but alternative types may be most suitable for the other sprout types tested. The inoculation of alfalfa sprouts with communities derived from various sprout types had a significant, source-independent effect on microbial community structure, indicating that the process of inoculation alters the dynamics of community development regardless of the types of organisms involved.     

碱处理对玉米秸秆固态厌氧消化过程中菌群结构的影响

从微生物菌群的动态变化来阐述厌氧消化过程已成为近年的研究热点之一.该文从微生物菌群变化的角度对碱预处理促进纤维质原料厌氧消化性能的原因进行了分析.通过对碱预处理组及对照组典型厌氧消化阶段进行取样、高通量测序后,比较二者在菌群结构方面的差异.结果表明,底物种类及碱处理均对厌氧消化菌群结构有显著影响.实验中共鉴定出10个门...     

Pollution-induced community tolerance of soil microbial communities caused by the antibiotic sulfachloropyridazine

Little is known about the environmental hazards linked to the treatment of farm animals with antibiotics and subsequent spreading of manure, especially regarding soil microbial communities. In this investigation, pollution-induced community tolerance (PICT) of bacteria from soils artificially spiked with the sulfonamide sulfachloropyridazine (SCP) was investigated. Tolerance of the bacterial communities after 3 weeks' exposure to SCP was determined by analyzing the sensitivity of 31 microbial metabolic processes in microtiter plates. Bacterial suspensions extracted from soils containing higher concentrations of SCP showed an increased tolerance of their metabolic activities to this antibiotic. An increase in tolerance by 10% was found at 7.3 mg/kg dw SCP. The PICT effect could be demonstrated by both a shift in the tolerance of the average of all metabolic activities and a shift of the physiological process sensitivity distributions made up from the single metabolic processes. The PICT effect was accompanied by smaller changes in the community-level physiological profile (CLPP). To conclude, PICT has been shown to be a versatile and illustrative method for the detection of the effects of antibacterial agents on soil microorganisms.     

Characterization of the microbial community in an anaerobic ammonium-oxidizing biofilm cultured on a nonwoven biomass carrier

The enrichment and characterization of anaerobic ammonium-oxidizing biofilm cultures are ongoing in our laboratories. Biomass, with a predominately red color, demonstrating simultaneous removal of ammonium and nitrite under autotrophic and anoxic conditions, which is characteristic of anaerobic ammonium-oxidizing planctomycetes, was enriched and maintained for an extended period on a polyester nonwoven carrier. To investigate the bacterial composition of the mature biofilm community, 16S rDNA sequences were amplified by PCR and comparative analyses using DNA databases were conducted. Only one sequence had a notable similarity (92.2%) to that of the first discovered anaerobic ammonium-oxidizing planctomycete and lesser, yet significant, similarities to the 16S rDNA sequences of other recently reported anaerobic ammonium-oxidizing strains. The newly discovered strain (designated KSU-1) reported here was dominant among detectable members of the biofilm community. By fluorescence imaging, KSU-1 was shown to form spherical clusters wrapped in a thin layer of Zoogloea sp. Possible interactions and interdependencies of these two species are discussed with regard to the putative unculturability of the anaerobic ammonium-oxidizing planctomycetes.     

Bacterial communities on electron-beam Pt-deposited electrodes in a mediator-less microbial fuel cell

The content of a bacterial consortium found on an electron beam (e-beam) Pt-deposited electrode in a mediator-less microbial fuel cell (MFC) using glucose and glutamate as fuel is reported in this paper. The e-beam Pt-deposited electrode and electrochemically active bacteria (EAB) consortium were developed to improve the mediator-less MFC performance. Denaturing gradient gel electrophoresis (DGGE), restriction fragment length polymorphism (RFLP), and 16S rRNA sequencing were used to identify the EAB consortia. Sequencing results showed that clone ASP-31 was predominant and was similar to Aeromonas hydrophila, an Fe(III)-reducing and EAB. The phylogenetic tree analysis disclosed the presence of gamma-proteobacteria groups such as Aeromonas genus, Enterobacter asburiae, and Klebsiella oxytoca. These results suggest that MFC performance of the e-beam Pt-deposited electrode with Aeromonas genus consortia dominated by A. hydrophila was higher than other MFCs within a short period. With the e-beam Pt-deposited electrode and Aeromonas genus consortia in the mediator-less MFC, it is possible to increase the efficiency of electron transfer between the bacteria and the electrode.     

Comparison of microbial communities in the fermentation starter used to brew Xiaoqu liquor

To reveal the brewing mechanism of Sichuan Xiaoqu liquor, microbial communities in Xiaoqu, a saccharification and fermentation agent, were characterized using microbial isolation and identification techniques, MiSeq high‐throughput sequencing and bioinformatics. From Xiaoqu commonly used in three different regions (Dazhu, Pengzhou and Hubei) in China, three yeast strains and seven moulds were isolated and identified. In addition, 17 bacteria and seven fungi were detected by high‐throughput sequencing. In Xiaoqu from Pengzhou (Huaxi Xiaoqu), the dominant species were Weissella cibaria (85.52%) and Rhizopus stolonifer (94.98%). On the other hand, W. cibaria (17.64%), Staphylococcus sp. (53.17%), Saccharomyces cerevisiae (43.33%), and Candida fennica (38.52%) were preponderant in Xiaoqu from Dazhu (Sichuan Dazhu Xiaoqu). Finally, Xiaoqu from Hubei consisted mostly of W. cibaria (29.64%), uncultured Empedobacter bacteria (32.60%), R. stolonifer (18.90%), Cunninghamella bertholletiae (67.41%) and S. cerevisiae (10.95%). Clearly, the bacterial community was relatively more complex than the fungal community. However, the fungal content in Xiaoqu of the three different regions was consistent. The results indicate that different flavours from different regions may result mainly from the bacterial and fungal diversity in their Xiaoqu. Copyright © 2017 The Institute of Brewing & Distilling     

榨菜发酵过程中原核微生物群落结构及其理化因子的动态演替

利用16S rRNA高通量测序技术探究榨菜发酵过程中原核微生物群落的演替,同时利用物理化学方法追踪发酵过程中理化因子的变化,并进行冗余分析。结果表明,随着榨菜发酵的不断进行,乳杆菌属的相对丰度从0. 92%增加至74. 77%,是发酵过程中的绝对优势属。明串珠菌属在发酵初始时的相对丰度可达3. 61%,在整个发酵过程中呈先增加后降低的变化趋势,可起到启动剂的作用。冗余分析表明:发酵初期的群落与p H及还原糖含量呈正相关;发酵中期的群落与亚硝酸盐、丙酮酸和琥珀酸含量呈正相关;而发酵后期的群落与总酸和其他有机酸含量呈正相关。该研究较系统地揭示了榨菜发酵过程中原核微生物群落的演替规律及其影响因素,可为进一步精确人工调控提供理论依据和筛选特性菌种提供数据参考。     

Effects of Leuconostoc mesenteroides starter cultures on microbial communities and metabolites during kimchi fermentation

Kimchi fermentation usually relies upon the growth of naturally-occurring various heterofermentative lactic acid bacteria (LAB). This sometimes makes it difficult to produce kimchi with uniform quality. The use of Leuconostoc mesenteroides as a starter has been considered to produce commercial fermented kimchi with uniform and good quality in Korea. In this study, a combination of a barcoded pyrosequencing strategy and a ¹H NMR technique was used to investigate the effects of Leu. mesenteroides strain B1 as a starter culture for kimchi fermentation. Baechu (Chinese cabbage) and Chonggak (radish) kimchi with and without Leu. mesenteroides inoculation were prepared, respectively and their characteristics that included pH, cell number, bacterial community, and metabolites were monitored periodically for 40 days. Barcoded pyrosequencing analysis showed that the numbers of bacterial operational taxonomic units (OTU) in starter kimchi decreased more quickly than that in non-starter kimchi. Members of the genera Leuconostoc, Lactobacillus, and Weissella were dominant LAB regardless of the kimchi type or starter inoculation. Among the three genera, Leuconostoc was the most abundant, followed by Lactobacillus and Weissella. The use of Leu. mesenteroides as a starter increased the Leuconostoc proportions and decreased the Lactobacillus proportions in both type of kimchi during kimchi fermentation. However, interestingly, the use of the kimchi starter more highly maintained the Weissella proportions of starter kimchi compared to that in the non-starter kimchi until fermentation was complete. Metabolite analysis using the ¹H NMR technique showed that both Baechu and Chonggak kimchi with the starter culture began to consume free sugars earlier and produced a little greater amounts of lactic and acetic acids and mannitol. Metabolite analysis demonstrated that kimchi fermentation using Leu. mesenteroides as a starter was completed earlier with more production of kimchi metabolites compared to that not using a starter, which coincided with the decreases in pH and the increases in bacterial cell number. The PCA strategy using all kimchi components including carbohydrates, amino acids, organic acids, and others also showed that starter kimchi fermented faster with more organic acid and mannitol production. In conclusion, the combination of the barcoded pyrosequencing strategy and the ¹H NMR technique was used to effectively monitor microbial succession and metabolite production and allowed for a greater understanding of the relationships between the microbial community and metabolite production in kimchi fermentation.     

Effects of inhibitors on anaerobic microbial consortium with enhanced dechlorination activity in polychlorinated biphenyl mixture

Characterization was carried out on the anaerobic microbial consortium with enhanced degradation activity toward polychlorinated biphenyls in Kanechlor-300 and Kanechlor-400 mixtures in a burnt soil (BS) culture. The addition of molybdate to the BS culture resulted in the accumulation of less-chlorinated biphenyls such as 4,4'-dichlorinated biphenyl and 2,3',4-trichlorinated biphenyl; however, no such accumulation occurred without molybdate supplementation. No significant effect was observed in individual congeners in the BS culture supplemented with 2-bromoethane sulfonic acid. Analyses involving both the polymerase chain reaction-denaturing gradient gel electrophoresis of partial 16S rRNA genes and respiratory quinones showed that the predominant microorganisms in the BS culture were anaerobic Firmicutes, while sulfate reducers of the phyla Deltaproteobacteria, Firmicutes and Chloroflexi were absent in the culture amended with the inhibitors. No positive correlation was observed between the dechlorination activity and a PCR-based detection of gene fragments of known dechlorinating bacteria. These results suggest that sulfate reducers played an important role in the enhanced anaerobic dechlorination of PCBs in the BS culture.