Microbial population dynamics and temperature changes during fermentation of kimjang kimchi

A distinct subset of lactic acid bacteria that are greatly influenced by temperature play an important role during kimchi fermentation. However, microbial population dynamics and temperature control during kimjang kimchi fermentation, which is traditionally fermented underground, are not known. Here we show that Lactobacillus sakei predominates in kimjang kimchi, perhaps due to suitable fermentation (5∼9°C) and storage (−2°C) temperatures. The temperature of this kimchi gradually decreased to 3.2°C during the first 20 days of fermentation (−0.3°C/day) and then was stably maintained around 1.6°C, indicating that this simple approach is very efficient both for fermentation and storage. These findings provide important information towards the development of temperature controlling systems for kimchi fermentation.     

Microbial growth dynamics on the basis of individual budgets

The popular theories for microbial dynamics by Monod, Pirt and Droop are shown to be special cases of a model for individual budgets, in which growth and maintenance are on the expense of reserve materials. The dynamics of reserve materials is a first order process with a relaxation time proportional to cell length; maintenance is proportional to cell volume, and uptake, which depends hyperbolically on substrate density, is proportional to cell volume as well. Because of the latter, population dynamics depends on the behaviour of the individuals in a simple way, such that the cell volume distribution has no quantitative effect.When uptake is proportional to the surface area of the cell, which is realistic from a physical point of view, the relation between the individual level and the population one becomes more complicated and the cell size and shape distribution affects population dynamics. It is shown how the changing shape of rods modifies uptake and, consequently, growth.The concept of energy conductance, defined as the ratio, of the maximum surface area specific uptake and the volume specific energy reserve has been introduced in the analysis of microbial dynamics. The first tentative results indicate that the value for E. coli is close to the mean value for a wide variety of animals.Properties of the model for cell suspension at constant substrate densities are analyzed and tested against a variety of experimental data from the literature on both the individual and the population level.     

水稻秸秆低温复合菌系多样性及发酵动态

【目的】为解决中国寒冷地区水稻秸秆大面积废弃问题,加快低温地区水稻秸秆饲料转化,本文筛选了可以低温下加速秸秆发酵过程的微生物复合菌系,研究其微生物组成并跟踪其发酵动态。【方法】通过5℃下连续定向富集筛选,获得低温复合菌系。采用克隆文库方法分析复合菌系的组成。将复合菌系和商业接种剂(由Lactobacillus plantarum,Enterococcus faecium,L.salivarilus,Pediococcus acidilactici组成)分别接入稻秸进行10℃发酵。气质联机(GC-MS)测定发酵产物的同时,通过变性梯度凝胶电泳检测微生物在发酵体系的定殖情况。采用定量PCR方法追踪复合菌系组成菌在发酵过程中的动态。【结果】16S rDNA克隆文库分析结果表明复合系主要由两种微生物组成,一种属乳酸杆菌(Lactobacillus),一种属乳酸球菌(Leuconostoc)。10℃稻秸发酵结果表明,在发酵第6天接种复合菌系处理的pH已经下降到4.3,乳酸菌菌落形成单位为2.9×109CFU/g鲜样,而接种商业接种剂的处理pH为5.3,乳酸菌菌落形成单位为3.6×108 CFU/g鲜样;在发酵30 d时,接种复合菌系处理的乳酸含量为8.1 g/kg鲜样,接种商业接种剂处理的乳酸含量为2.0 g/kg鲜样。变性梯度凝胶电泳结果表明,在接种复合菌系的稻秸中,从发酵的第6天开始,检测到的微生物主要为L.sakei和Leuconostoc inhae,在整个发酵过程中,两菌一直存在;在商业接种剂处理中,发酵第6天检测到的微生物除其四种组成菌外,还包括Uncultured bacterium;而在发酵第16天和第30天,只检测到组成菌中的L.plantarum和E.faecium。定量PCR结果显示,接种复合菌系处理中,L.sakeiDNA在发酵第6天达到41.0%,在发酵第16天已达到65%,Le inhae在发酵的第6天达到整个发酵过程中的最大值(5.5%)。【结论】接种复合菌系,可以有效促进水稻秸秆的低温发酵进程。复合菌系组成菌可以定殖在发酵体系中,并占据优势。复合菌系的关键菌为L.sakei。     

Microbial community dynamics in the forefield of glaciers

Retreating ice fronts (as a result of a warming climate) expose large expanses of deglaciated forefield, which become colonized by microbes and plants. There has been increasing interest in characterizing the biogeochemical development of these ecosystems using a chronosequence approach. Prior to the establishment of plants, microbes use autochthonously produced and allochthonously delivered nutrients for growth. The microbial community composition is largely made up of heterotrophic microbes (both bacteria and fungi), autotrophic microbes and nitrogen-fixing diazotrophs. Microbial activity is thought to be responsible for the initial build-up of labile nutrient pools, facilitating the growth of higher order plant life in developed soils. However, it is unclear to what extent these ecosystems rely on external sources of nutrients such as ancient carbon pools and periodic nitrogen deposition. Furthermore, the seasonal variation of chronosequence dynamics and the effect of winter are largely unexplored. Modelling this ecosystem will provide a quantitative evaluation of the key processes and could guide the focus of future research. Year-round datasets combined with novel metagenomic techniques will help answer some of the pressing questions in this relatively new but rapidly expanding field, which is of growing interest in the context of future large-scale ice retreat.     

Mineralization by mesenchymal stromal cells is variously modulated depending on commercial platelet lysate preparations

Background aims

Numerous cellular models have been developed to investigate calcification for regenerative medicine applications and for the identification of therapeutic targets in various complications associated with age-related diseases. However, results have often been contradictory due to specific culture conditions, cell type ontogeny and aging status. Human platelet lysate (hPL) has been recently investigated as valuable alternative to fetal bovine serum (FBS) in cell culture and bone regeneration. A parallel comparison of how all these multiple factors may converge to influence mineralization has yet to be reported.

Growth of Kluyveromyces marxianus and formation of ethyl acetate depending on temperature

Conversion of lactose into ethyl acetate by Kluyveromyces marxianus allows economic reuse of whey-borne sugar. The high volatility of ethyl acetate enables its process-integrated recovery by stripping. This stripping is governed by both the aeration rate and the partition coefficient, K _EA,L/G. Cultivation at elevated temperatures should decrease the K _EA,L/G value and thus favor stripping. K. marxianus DSM 5422 as a potent producer of ethyl acetate was cultivated aerobically in whey-borne media for studying temperature-dependent growth and ester formation. Shake flask cultivation proved thermal tolerance of this yeast growing from 7 to 47 °C with a maximum rate of 0.75 h^?1 at 40 °C. The biomass yield was 0.41 g/g at moderate temperatures while low and high temperatures caused distinct drops. The observed μ-T and Y _X/S-T dependencies were described by mathematical models. Further cultivations were done in an 1-L stirred reactor for exploring the effect of temperature on ester synthesis. Cultivation at 32 °C caused significant ester formation (Y _EA/S?=?0.197 g/g) while cultivation at 42 °C suppressed ester synthesis (Y _EA/S?=?0.002 g/g). The high temperature affected metal dissolution from the bioreactor delivering iron for yeast growth and preventing ester synthesis. Cultivation at 32 °C with a switch to 42 °C at the onset of ester synthesis allowed quick and efficient ester production (Y _EA/S?=?0.289 g/g). The high temperature lowered the K _EA,L/G value from 78 to 44 L/L which heightened the gas-phase ester concentration (favoring ester recovery) without increasing the liquid-phase concentration (avoiding product inhibition).     

Phage spread dynamics in clonal bacterial populations is depending on features of the founder cell

Plate-cultured bacterial colonies are intriguing models to study host-parasite interactions in senescent populations. During the growth of bacteriophage-infected colonies there is a synchronous prophage induction episode among lysogenic cells that allows a dramatic but time-restricted amplification of viral particles. We report here that the dynamics of phage spread depends on the history of the lysogenic cell that establishes the clonal population, the duration of the pre-burst period being shorter when the founder, infected cell derives from older colonies. These results offer a physiologic explanation for the self-contained progression of the viral spread in closed environments, that ensures both viral dissemination but also survival of most of the host cells.     

Determinism of bacterial metacommunity dynamics in the southern East China Sea varies depending on hydrography

Spatial variation of communities composition (metacommunities) results from multiple assembly mechanisms, including environmental filtering and dispersal; however, whether and why the relative importance of the assembly mechanisms in shaping bacterial metacommunity changes through time in marine pelagic systems remains poorly studied. Here, we applied the elements of metacommunity structure framework and the variation partitioning framework to examine whether temporal variation of hydrographic conditions influences bacterioplankton metacommunity dynamics in the southern East China Sea (ECS). The spatiotemporal variation of bacterial communities composition was revealed using 454 pyrosequencing of 16S rDNA. In addition to the whole bacterial community, we analyzed four dominant taxonomic groups (Cyanobacteria, Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria) separately. Our analyses indicate that, considering the whole community level, the determinism of metacommunity structure varied among seasons. When the degree of connectivity was low (December), the metacommunity exhibited random distribution and was explained mainly by the environmental component. However, Clementsian metacommunity was found at intermediate connectivity (May), during which the environmental and spatial predictors were both significant. When connectivity was high (August), a random distribution pattern was found and no significant effect of environmental filtering or dispersal limitation was detected. Nevertheless, when considering different taxonomic groups, the differences in metacommunity dynamics among groups were found. Our results suggest that the driving forces of metacommunity dynamics varied depending on hydrography, as the degrees of environmental heterogeneity and connectivity among habitat patches were determined by circulation pattern. Moreover, mechanisms varied among different taxonomic groups, suggesting that differential dispersal capacity among taxonomic groups should be integrated into community assembly studies.     

Microbial content of commercial South African high-moisture dried fruits

AIM: The aim was to evaluate commercially available South African high-moisture dried fruits (HMDF) for the microbial, moisture and SO2 contents, as well as aw and pH. METHODS AND RESULTS: The microbial content of commercially available HMDF was evaluated using nine different growth media. The moisture content, aw) SO2 and pH of each product were determined using standard analytical methods. It was found that the highest total aerobic counts were generated from high-moisture dried (HMD) prunes and raisins. The most frequent spoilers were members of the genus Bacillus. Fungal counts were also very high in the apricot products, exceeding the limit of 1000 CFU g(-1) as set by HMDF producers. Members of the genus Staphylococcus were found in the HMD raisins and Salmonella and thermoduric organisms were isolated from the HMD prunes. CONCLUSIONS: The microbial levels of South African HMDF were within the limits set, with the exception of apricots. SIGNIFICANCE AND IMPACT OF STUDY: The study shows the presence of Salmonella, Staphylococcus and Clostridium in South African HMDF. The presence of thermoduric organisms indicated that the current pasteurization process is not adequate and that the addition of preservatives would be an additional method to ensure safety and quality.     

Microbial production of surfactants and their commercial potential.

Many microorganisms, especially bacteria, produce biosurfactants when grown on water-immiscible substrates. Biosurfactants are more effective, selective, environmentally friendly, and stable than many synthetic surfactants. Most common biosurfactants are glycolipids in which carbohydrates are attached to a long-chain aliphatic acid, while others, like lipopeptides, lipoproteins, and heteropolysaccharides, are more complex. Rapid and reliable methods for screening and selection of biosurfactant-producing microorganisms and evaluation of their activity have been developed. Genes involved in rhamnolipid synthesis (rhlAB) and regulation (rhlI and rhlR) in Pseudomonas aeruginosa are characterized, and expression of rhlAB in heterologous hosts is discussed. Genes for surfactin production (sfp, srfA, and comA) in Bacillus spp. are also characterized. Fermentative production of biosurfactants depends primarily on the microbial strain, source of carbon and nitrogen, pH, temperature, and concentration of oxygen and metal ions. Addition of water-immiscible substrates to media and nitrogen and iron limitations in the media result in an overproduction of some biosurfactants. Other important advances are the use of water-soluble substrates and agroindustrial wastes for production, development of continuous recovery processes, and production through biotransformation. Commercialization of biosurfactants in the cosmetic, food, health care, pulp- and paper-processing, coal, ceramic, and metal industries has been proposed. However, the most promising applications are cleaning of oil-contaminated tankers, oil spill management, transportation of heavy crude oil, enhanced oil recovery, recovery of crude oil from sludge, and bioremediation of sites contaminated with hydrocarbons, heavy metals, and other pollutants. Perspectives for future research and applications are also discussed.     

Energy storage and the evolution of population dynamics

We explore the mutual dependence of life history evolution and population dynamics by modeling a structured rotifer population that preys on a dynamic food supply. We focus on the ecological role of energy storage. A physiologically based submodel describes how individual predators allocate assimilated energy among growth, reproduction, and storage. We use invasibility analyses to predict evolutionary stable strategies for energy allocation. Various proxy measures of fitness based on measurable biological quantities, such as average population size or average per-capita fecundity, fail to predict evolutionary stable strategies. The predicted strategies indicate that selection strongly favors storage allocation for juveniles, but only for adults when prey densities are high. With the evolution of energy storage, population dynamics can shift from aperiodic to stable cycles without any need to invoke group selection.     

传统醋曲储存过程中的微生物多样性

【背景】醋曲是我国传统谷物醋酿造中的重要微生物来源,通常一次制备分批使用。【目的】解析传统醋曲储存过程中微生物群落结构变化规律。【方法】从山西晋南一家百年老醋坊分别采集大曲原料、新制醋曲、储存7个月和12个月的醋曲,利用高通量测序技术分析微生物多样性。【结果】从4组样品中共找到610个真菌可操作分类单元(operational taxonomic unit, OTU)和747个细菌OTU。子囊菌门(Ascomycota,占比95%)和厚壁菌门(Firmicutes,占比81%)分别为优势的真菌和细菌类群。醋曲成品中约1/3的真菌OTU和约95%的细菌OTU可在醋曲原料中找到,说明原料是醋曲的重要微生物来源。相较于新制醋曲,储存7个月和12个月醋曲中的真菌和细菌多样性均显著降低。醋曲贮存过程中微生物群落结构发生明显改变,并且相较于真菌群落结构,细菌群落结构更易波动。相较于醋曲原料,醋曲成品中显著富集扣囊复膜孢酵母(Saccharomycopsis fibuligera)、东方伊萨酵母(Issatchenkiaorientalis)等真菌,以及克罗彭斯特菌属(Kroppenstedtia)...     

Temporal dynamics and impact of manure storage on antibiotic resistance patterns and population structure of Escherichia coli isolates from a commercial swine farm

Many confined-livestock farms store their wastes for several months prior to use as a fertilizer. Storing manure for extended periods could significantly bias the composition of enteric bacterial populations subsequently released into the environment. Here, we compared populations of Escherichia coli isolated from fresh feces and from the manure-holding tank (stored manure) of a commercial swine farm, each sampled monthly for 6 months. The 4,668 confirmed E. coli isolates were evaluated for resistance to amikacin, ampicillin, cephalothin, chloramphenicol, kanamycin, nalidixic acid, streptomycin, sulfamethoxazole, tetracycline, trimethoprim, and trimethoprim plus sulfamethoxazole. A subset of 1,687 isolates was fingerprinted by repetitive extragenic palindromic PCR (rep-PCR) with the BOXA1R primer to evaluate the diversity and the population structure of the collection. The population in the stored manure was generally more diverse than that in the fresh feces. Half of the genotypes detected in the stored manure were never detected in the fresh fecal material, and only 16% were detected only in the fresh feces. But the majority of the isolates (84%) were assigned to the 34% of genotypes shared between the two environments. The structure of the E. coli population showed important monthly variations both in the extent and distribution of the diversity of the observed genotypes. The frequency of detection of resistance to specific antibiotics was not significantly different between the two collections and varied importantly between monthly samples. Resistance to multiple antibiotics was much more temporally dynamic in the fresh feces than in the stored manure. There was no relationship between the distribution of rep-PCR fingerprints and the distribution of antibiotic resistance profiles, suggesting that specific antibiotic resistance determinants were dynamically distributed within the population.