Fermentation of pentose sugars to ethanol and other neutral products by microorganisms

The current and projected shortage of petroleum and natural gas has led to renewed interest in processes for the microbial conversion of renewable biomass resources to liquid and gaseous fuels. Pentose sugars represent a significant fraction of the total fermentable carbohydrate content of biomass. A number of biochemical pathways are known for the conversion of pentose to ethanol and other neutral products. Beside ethanol, potential neutral fermentation products include 2,3-butanediol, acetone, isopropanol, butanol and hydrogen. Other products include carbon dioxide and organic acids. Specific ethanol-producing fermentations are reviewed, and future directions for research and development are suggested.     

Inoculation of potatoes with microorganisms under field conditions

The effect of inoculation of potatoes with isolates ofPseudomonas putida andTrichoderma sp. suspension and in preparations with kaolin and peat carriers on growth of potatoes, yields and physiological proporties of tubers was investigated on seven locations of the potato-rye and sugar-beet regions. In 57.5% of experiments increased yields could be detected. More favorable results were obtained in the sugar-beet region and on commercially utilized fields when using suspensions of the isolates. Variability of the results can be partially explained by soil-climatic factors affecting colonization of the rhizosphere by the microorganisms and their effect on the environment. Physiological properties and the quality of the harvested tubers were comparable with those of the control. The results are discussed from the point of view of a possible inoculation of potatoes with rhizobacteria and, in the presence ofTrichoderma sp., improvement of their growth and yields.     

共生条件下三种荒漠灌木的根系分布特征及其对降水的响应

以全根系挖掘法,对共生于原始盐生荒漠生境中的多枝柽柳[Tamarix ramosissima (Ledeb.)]、梭梭[Haloxylon ammodendron(C. A. Mey.)Bunge]、琵琶柴[Reaumuria soongorica (Pall.) Maxim.]的根系分布特征进行了研究;对降水引发的湿润-干旱周期中植物同化枝水势、蒸腾速率的变化过程进行了跟踪观测,并据此计算3种植物的水分胁迫效应指数和土壤-植物系统导水度,以最终确定3种植物用水策略和其对降水的响应特征.研究结果表明,多枝柽柳的吸收根系分布范围从地下50cm到310cm,单株平均总吸收根表面积为30249.2cm2;梭梭的根系分布范围0～250cm,单株平均总吸收根表面积12847.3 cm2;琵琶柴的根系分布范围0～80cm,单株平均总吸收根表面积361.8 cm2.多枝柽柳为深根植物,主要利用地下水和深层土壤水,在降水引发的湿润-干旱周期中,其植物水分生理参数对降水无响应.琵琶柴为浅根植物,对降水响应极为显著.梭梭的根系分布特征介于多枝柽柳和琵琶柴之间,对地下水和降水都有利用,对降水响应显著.3种荒漠灌木对降水的响应差异显然与其根系分布、水分利用策略密切相关,在未来降水发生变化的情景下,根系分布特征的差异将决定着植物在水分资源竞争中的地位.具有较强根系形态可塑性的物种,如梭梭,将具有明显的竞争优势.     

Biotic interactions limit species richness in an alpine plant community,especially under experimental warming

The determinants of local species richness in plant communities have been the subject of much debate. Is species richness the result of stochastic events such as dispersal processes, or do local environmental filters sort species into communities according to their ecological niches? Recent studies suggest that these two processes simultaneously limit species richness, although their relative importance may vary in space and time. Understanding the limiting factors for species richness is especially important in light of the ongoing global warming, as new species establish in resident plant communities as a result of climate‐driven migration. We examined the relative importance of dispersal and environmental filtering during seedling recruitment and plant establishment in an alpine plant community subjected to seed addition and long‐term experimental warming. Seed addition increased species richness during the seedling recruitment stage, but this initial increase was cancelled out by a corresponding decrease in species richness during plant establishment, suggesting that environmental filters limit local species richness in the long term. While initial recruitment success of the sown species was related to both abiotic and biotic factors, long‐term establishment was controlled mainly by biotic factors, indicating an increase in the relative importance of biotic interactions once plants have germinated in a microhabitat with favourable abiotic conditions. The relative importance of biotic interactions also seemed to increase with experimental warming, suggesting that increased competition within the resident vegetation may decrease community invasibility as the climate warms.     

Isolation and characterization of microorganisms able to produce 1,3-propanediol under aerobic conditions

Microbial fermentation under strictly anaerobic conditions has been conventionally used for the production of 1,3-propanediol, a key raw material required for the synthesis of polytrimethylene terephthalate (PTT) and other polyester fibers. In the current study, we have identified eight strains of microorganism which are able to produce 1,3-propanediol under aerobic condition. Those strains were isolated from garden soil, which were enriched by culturing in LB medium with glycerol added under aerobic condition. The identities of those strains were established based on their 16S rRNA sequences and physiological characteristics. Results indicated 6 strains are Citrobacter freundii and 2 strains are Klebsiella pneumoniae subsp Penumoniae. One of Klebsiella pneumoniae subsp Penumoniae strains, designated as TUAC01, demonstrated comparable levels of 1,3-propanediol oxidoreductase, glycerol dehydratase and glycerol dehydrogenase activity to the anaerobic microorganisms described in the literature. Accordingly, in larger scales (5 l) fed-batch culture the TUAC01 strain showed a remarkable 1,3-propanediol producing potency under aerobic conditions. 60.1 g/l of 1,3-propanediol was yield after 42 h incubation in an agitating bioreactor; and in air-lift bioreactor 66.3 g/l of 1,3-propanediol was yield after 58.5 h incubation. The aerobic ferment process, reduced the product cost and made the biological method of 1,3-propanediol production more attractive.     

Antagonistic interactions between stress factors during the growth of microorganisms under conditions simulating the parameters of their natural ecotopes

Two stress factors, hypoxia (microaerobic conditions) and a high salt concentration, if applied simultaneously to aerobic microorganisms, display an antagonistic mode of interaction. As a result, the NaCl level that is usually optimal for moderate halophiles (5-6%) becomes optimal for the growth of weak halophiles (Rhodococcus erythropolis and Shewanella sp. CN32); the halotolerant yeast Yarrowia lypolytica acquires halophilic properties (with a growth optimum at a NaCl concentration of 10%), and the growth rate of the extremely halophilic Halobacterium salinarum increases at supraoptimal salt concentrations (25-34%). This phenomenon is apparently due to multiple changes in metabolic reactions. In particular, high salt concentrations suppress respiration and the formation of enzymes (superoxide dismutase and catalase) that protect the cell from toxic oxygen species. Therefore, establishment of microaerobic conditions compensates for the loss of these protective mechanisms and enables cell growth at higher salt concentrations than under aerobic conditions. Of some importance can also be the increase in the intracellular concentrations of osmoprotectants caused by the suppression of their intracellular oxidation. The implications of this phenomenon for the ecophysiology of microorganisms (including oiloxidizing species) and for the classification of weak and moderate halophiles are discussed.     

Behavior of sulfate reducing bacteria under oligotrophic conditions and oxygen stress in particle-free systems related to drinking water

The response of sulfate reducing bacteria (SRB) to oxygen stress under oligotrophic conditions in particle-free systems was studied in (i) sterile Berlin drinking water; (ii) mineral medium; and (iii) in coculture experiments with aerobic bacteria. Using a polyphasic approach including anaerobic cultivation, fluorescent in situ hybridization (FISH) and digital image analysis, the behavior of the strains zt3l and zt10e, isolated from Berlin groundwater and affiliated to the family Desulfovibrionaceae, was compared to the type strains Desulfomicrobium baculatum and Desulfovibrio desulfuricans. Anaerobic deep agar dilution series were performed for the determination of cell culturability. FISH and subsequent digital image analysis of probe-conferred fluorescence intensities were used for the assessment of metabolic activity. For the in situ identification of both isolates in coculture tests, two strain-specific oligonucleotides were developed and evaluated. The total cell counts of stressed SRB in drinking water decreased during the course of the assay dependent on the strain. Both environmental isolates could be cultured for a longer period than cells of D. baculatum and D. desulfuricans, respectively. The FISH intensities showed a strain-specific behavior. When exposed to simultaneous oxygen stress and carbon limitation in mineral medium, total cell counts of all four strains remained constant throughout a period of 72 days. The rate of culturability differed between the investigated strains. The decrease of metabolic activity as assessed by FISH was a strain-specific property. Exposure of SRB to oxygen stress and carbon starvation in coculture experiments with Aquabacterium commune resulted in strain dependent prolonged culturability and a delayed decrease of the metabolic activity compared to pure culture tests for all strains tested. Total cell counts of SRB were constant throughout the whole experiment.     

Contribution of quinone-reducing microorganisms to the anaerobic biodegradation of organic compounds under different redox conditions

The capacity of two anaerobic consortia to oxidize different organic compounds, including acetate, propionate, lactate, phenol and p-cresol, in the presence of nitrate, sulfate and the humic model compound, anthraquinone-2,6-disulfonate (AQDS) as terminal electron acceptors, was evaluated. Denitrification showed the highest respiratory rates in both consortia studied and occurred exclusively during the first hours of incubation for most organic substrates degraded. Reduction of AQDS and sulfate generally started after complete denitrification, or even occurred at the same time during the biodegradation of p-cresol, in anaerobic sludge incubations; whereas methanogenesis did not significantly occur during the reduction of nitrate, sulfate, and AQDS. AQDS reduction was the preferred respiratory pathway over sulfate reduction and methanogenesis during the anaerobic oxidation of most organic substrates by the anaerobic sludge studied. In contrast, sulfate reduction out-competed AQDS reduction during incubations performed with anaerobic wetland sediment, which did not achieve any methanogenic activity. Propionate was a poor electron donor to achieve AQDS reduction; however, denitrifying and sulfate-reducing activities carried out by both consortia promoted the reduction of AQDS via acetate accumulated from propionate oxidation. Our results suggest that microbial reduction of humic substances (HS) may play an important role during the anaerobic oxidation of organic pollutants in anaerobic environments despite the presence of alternative electron acceptors, such as sulfate and nitrate. Methane inhibition, imposed by the inclusion of AQDS as terminal electron acceptor, suggests that microbial reduction of HS may also have important implications on the global climate preservation, considering the green-house effects of methane.     

Functional evaluation of cultured cells under hypotonic conditions by intravital staining with neutral red

A high stability of pig embryo kidney-cells to hypotony was shown with neutral red vital staining. In the medium, diluted 1 : 1, the cells kept their ability to make granules during 6 days. In the medium diluted by water 1 : 3, both granular and diffuse staining of cells was shown within 6-12 hours. Later (18-48 hours) the cell ability to make granules was kept, but the neutral red was deposed as large vacuoles. In the normal medium the cell ability to make granules was kept too. In the medium, diluted by water 1 : 7, the cells lost their ability to make granules. The ability was recovered when cells were returned to the normal medium. Thus, after 6-18 hours of incubation in such a hypotonic medium, the cells produced small granules of neutral red, and 24-48 hours later they made large granules.     

不同土地利用方式下土壤呼吸及其温度敏感性

采用静态箱-气相色谱法对四川盆地中部紫色土丘陵区3种土地利用方式（林地、草地和轮作旱地）土壤呼吸进行测定,结果表明,林地、草地和旱地土壤呼吸速率变化范围分别为78．63～577．97、39．28～584．18和34．48～484．65mgCO2·m^-2·h^-1,年平均土壤呼吸速率分别为264．68、242．91、182．21mgCO2·m^-2h^-1。3种土地利用方式的土壤呼吸速率季节变化趋势均呈单峰曲线,林地和草地土壤呼吸速率最大值均出现在夏末（7月底与8月初之间）,旱地土壤呼吸速率最大值出现的时间比林地和草地要早,在6月底与7月初之间;最小值均出现在12月底与翌年1月初之间。土壤温度和土壤湿度是影响本地区土壤呼吸的主要因子,双因素关系模型（R=αe^bTw^c）较好地拟合了土壤温度和土壤湿度对土壤呼吸的影响,二者共同解释了土壤呼吸变化的64％～90％。土壤呼吸的温度敏感性指数Q10值受土壤（5cm处）温度和土壤（0～10cm）湿度的影响。分析表明3种土地利用土壤的Q10值与土壤温度呈显著负相关关系,而与土壤湿度呈显著正相关关系。     

The bacterial genus Collimonas: mycophagy,weathering and other adaptive solutions to life in oligotrophic soil environments

This minireview provides a synopsis of past and present research on the biology and ecology of members of the bacterial genus Collimonas. From the distribution, abundance and functional behaviours of these so‐called collimonads emerges a general picture of bacterial adaptation to low‐nutrient soil environments. Among these adaptations is the ability to extract nutrients from living fungi (mycophagy) and from rocks and minerals (weathering). This unique combination of properties will be discussed in the context of other interactions that collimonads have with their biotic and abiotic surroundings, such as the ability to inhibit fungal growth (fungistasis), protect plant roots from fungal disease (biocontrol), and degrade natural polymers and synthetic pollutants (biodegradation). Future research on Collimonas is expected to take advantage of the genomic tools and resources that are becoming available to uncover and describe the genes and gene functions that distinguish this group of bacteria and are the basis for its phenotypes. Potential applications of collimonads include the control of unwanted fungi, for example in agriculture, their use as biological indicators of soil quality and fertility, and as a source of bioactive compounds.     

Phytoplankton production in relation to physico-chemical conditions in a small, oligotrophic subarctic lake in South Greenland

Phytoplankton production and physico-chemical parameters were measured during the summers of 1976 and 1977 in Lake 95 at 60°52'N, 46°01'W (area 8 ha, z 6.9 m). The duration of lake stratification during summer was weather dependent. Concentrations of total-CO₂ ranged from 2.04 mg l⁻¹ (surface) to 4.02 mg l⁻¹ (bottom during stratification). Nutrient concentrations were generally low, and systematic seasonal variation could not be detected with certainty. Vertical distribution of primary production typically showed a distinct maximum followed by a decline with depth. The low production, both per unit area (max. 60 mg C m⁻² d⁻¹) and per unit volume (max, 14.3 mg C m⁻³ d⁻¹), and the annual production of 4.7 g C m⁻² classified the lake as extremely oligotrophic.     

Soil and plant factors driving the community of soil-borne microorganisms across chronosequences of secondary succession of chalk grasslands with a neutral pH

Although soil pH has been shown to be an important factor driving microbial communities, relatively little is known about the other potentially important factors that shape soil-borne microbial community structure. This study examined plant and microbial communities across a series of neutral pH fields (pH=7.0-7.5) representing a chronosequence of secondary succession after former arable fields were taken out of production. These fields ranged from 17 to >66 years since the time of abandonment, and an adjacent arable field was included as a reference. Hierarchical clustering analysis, nonmetric multidimensional scaling and analysis of similarity of 52 different plant species showed that the plant community composition was significantly different in the different chronosequences, and that plant species richness and diversity increased with time since abandonment. The microbial community structure, as analyzed by phylogenetic microarrays (PhyloChips), was significantly different in arable field and the early succession stage, but no distinct microbial communities were observed for the intermediate and the late succession stages. The most determinant factors in shaping the soil-borne microbial communities were phosphorous and NH(4)(+). Plant community composition and diversity did not have a significant effect on the belowground microbial community structure or diversity.