Quantitative and analytical tools to analyze the spatiotemporal population dynamics of microbial consortia

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Needles in a haystack. Genomic tools have become powerful tools for conservation biologists to monitor the spread of invasive species

Early detection and monitoring are key to controlling invasive species. Genomics and new sequencing technologies are now providing powerful new tools to track and combat relentless pestsIn the late 1960s, an Air France pilot and his family took a holiday in swampy Louisiana in the southeastern USA and were intrigued by the giant bullfrogs, Rana catesbeiana. The family introduced a dozen of the animals to a pond in the Bordeaux region of southwestern France, inadvertently starting a major invasion that affected thousands of lakes and creeks with devastating effects on the native fauna. “They eat everything and if you go to a pond where there are bullfrogs, there are no other amphibians [...] because bullfrogs prey on other animals or because they are spreading a disease—chytridiomycosis—that is absent from some European areas,” said conservation biologist Francesco Ficetola of the Department of Environmental Sciences at the University of Milano–Bicocca in Italy. “There was nothing like them in Europe,” he added.As part of his postdoctoral research, Ficetola studied the frog invasion in Europe at the Université de Savoie and the University of Grenoble in France. To monitor their distribution, he pioneered the use of environmental DNA (eDNA) to detect R. catesbeiana without observing the animals themselves. He and his colleagues took water samples, extracted eDNA and used primers monomorphic to nearly 400 bullfrog samples to demonstrate their presence in wetlands, even in low densities.“The significance was that we were able to detect the presence of the species without seeing or hearing the species,” Ficetola said. The eDNA technique has further potential: “As the environment can retain the molecular imprint of inhabiting species, our approach allows the reliable detection of secretive organisms in wetlands without direct observation. Combined with massive sequencing and the development of DNA barcodes that enable species identification, this approach opens new perspectives for the assessment of current biodiversity from environmental samples” (Ficetola et al, 2008)....molecular and genomic tools to identify, monitor and control invasive species have become increasingly sophisticated during the past five years...According to David Lodge, a biologist at the University of Notre Dame (South Bend, IN, USA), molecular and genomic tools to identify, monitor and control invasive species have become increasingly sophisticated during the past five years and are especially valuable in aquatic environments. “Hair traps and scat sampling have been used for mammals for a long time. You don''t have to catch the lynx, for example. You just put a piece of wire or tape on a trail and you get a little bit of hair and then you do genetic analysis to figure out which species it is. With enough sampling and genetic sequencing, you could even estimate the number of individuals in a population,” Lodge explained. Technological advances now make it possible to apply this technique to aquatic ecosystems to track everything from whales down to the smallest organisms.Most invasive species eventually find their ecological niche among the natives, but some can turn into pests, particularly if the new environment does not pose any threats for them such as predators or diseases. The American bullfrog in Europe, the cane toad, Bufo marinus, in Australia, or the zebra mussel, Dreissena polymorpha, in the Great Lakes have all wreaked havoc on the environment and have had an impact on commercial interests. In addition to standard control measures—such as killing animals or halting their further migration with barriers—scientists have also explored biological methods of tracking and controlling invasive species, but it is only in the past few years that these have become efficient enough to find the proverbial needle in a haystack.In the USA, these genomic tools are being applied to track Asian carp species in the Mississippi, its tributary Illinois River and the Great LakesIn the USA, these genomic tools are being applied to track Asian carp species in the Mississippi, its tributary Illinois river and the Great Lakes. The large, jumping carp have negative effects on the native fish and are even able to knock down boaters (http://www.youtube.com/watch?v=yS7zkTnQVaM). Christopher Dionigi, assistant director for National Policy and Programs of the US National Invasive Species Council (Washington, DC, USA), a cooperative of federal agencies created in 1999, said, “They''re large, they do jump out of the water, they can achieve very high densities in specific areas, and [have] impacted a lot of native fisheries, and also game fish.” The silver and bighead carp are harvesting phytoplankton and zooplankton, which are dietary mainstays for many other species. Lodge described the carp as “aquatic cows” that outgrow their predators and compete with other species for food....Lodge and his colleagues are using eDNA to tackle a raging political issue in the American Midwest: whether Asian carp are invading Lake Michigan around Chicago...Inspired by Ficetola''s eDNA work and his own research to develop detection tools for species in the ballast water of ships, Lodge and his colleagues are using eDNA to tackle a raging political issue in the American Midwest: whether Asian carp are invading Lake Michigan around Chicago—and potentially the rest of the Great Lakes—from the Mississippi River.Neighbouring states, led by Michigan, have taken the US Army Corps of Engineers and the Chicago Metropolitan Water Reclamation District to court to get Chicago to close locks on the Chicago Sanitary and Ship Canal, which was built to divert Chicago''s sewage away from Lake Michigan into the Mississippi instead. The main dispute is whether the canal allows the Asian carp to invade Lake Michigan.Since 2009, Lodge''s group has been conducting a risk assessment for the Army Corps to determine whether carp and other invasive species are able to move through the canal into the Great Lakes. The team collected more than 1,000 surface water samples, extracted DNA and used markers specific for Hypophthalmichthys nobilis and H. molitrix (Jerde et al, 2011). Subsequently, commercial fishermen caught an adult bighead carp within 13 km of Lake Michigan, only 4 km upstream from the nearest positive eDNA detection.“There has been a lot of hand-wringing about where the carp are. We wanted to see if we could detect the presence of Asian carp without even seeing them,” Lodge explained. “The most important thing we found (using eDNA) was DNA of both species in many places on the lake side of the electric barriers that the Army Corps of Engineers maintains in the canal [to keep the carp out of the lake]”....eDNA can help in early detection of invasive species, which is key to effective management on the basis of ''early detection, rapid response''He added that eDNA can help in early detection of invasive species, which is key to effective management on the basis of ''early detection, rapid response''. “Because eDNA evidence indicates that at least silver carp have entered Lake Michigan, surveillance is warranted within Great Lakes rivers that may be colonized and could support successful spawning,” Lodge said. “The eDNA method appears well-suited to rapid surveys across the large spatial scale that will be required in the Great Lakes.” He added that it might be possible to poison the carp when they aggregate to spawn.Nathan Bott, a molecular-diagnostic researcher at the South Australian Research and Development Institute (SARDI; Henley Beach, SA, Australia), is adapting a technique to extract DNA from soil to detect invasive species in the ballasts of ships. This approach involves identifying DNA from pests, some of which have the potential to destroy farmed or fished mussel, scallop and abalone. Bott has been working on assays for the Asian bag mussel, Musculista senhousia, northern Pacific sea star, Asterias amurensis, and European fan worm, Sabella spallanzanii.He said SARDI is in the process of purchasing a 454 sequencer to verify positive samples. “The idea is if we are getting positives in the ports, and particularly if the species in question is considered a significant threat, the authorities would want to conduct further surveys.” Bott explained that quantitative PCR can screen thousands of samples per day, and the 454 sequencer would be used to confirm the positives to deliver a rapid result. “If we can carry out a quick and relatively inexpensive experiment on the eDNA result with quantitative PCR using our 454, then we can save everyone a lot of time and money, and rather than concentrating on confirming the presence of the pest, a control strategy can be instigated.”Once an invasive species is identified, what can de done to remove it? The French took to shooting and trapping American bullfrogs, removing eggs and tadpoles and draining wetlands. The Americans built electrical fences to try to stop the Asian carp from entering the Great Lakes. The state of Illinois has even supported a fishing operation to catch Asian carp, shipping the fillets to China—a scheme that could potentially lead to perverse incentives to introduce more fish....biologists are refining an old concept for species control that disrupts the ratio of sexes in order to control or even kill off invasive speciesMeanwhile, biologists are refining an old concept for species control that disrupts the ratio of sexes in order to control or even kill off invasive species. The basic idea—creating sterile males, mainly by using irradiation, and releasing them by the millions—is not new. Sterile males compete with wild males for the females but do not produce offspring. Repeated introductions of these populations can control or even wipe out whole populations. Since its first application in the 1950s, there have been several success stories, including eradication of the screw-worm fly (Cochliomyia hominivorax) in North America and control of several species of fruit flies.In recent years, the concept has been improved by using molecular and genetic approaches. Ron Thresher, a marine ecologist who researches invasive species for the Australian Commonwealth Scientific and Industrial Research Organization in Hobart, Tasmania, Australia, said that common carp—bottom-feeders that foul water and dig up plants—were causing problems Down Under. However, he said that stakeholders, such as public and commercial fishing interests, resist biological controls—introducing predators, parasites or genetically modified viruses to make carp sterile—because these could have unintended consequences.As a result, his group has begun exploring another approach, while gently steering away from the transgenic controversies. “We''ve been careful to make it clear to people that we''re using genetic-modification technology but it''s not transgenic,” he said. “What we''re doing is taking a carp''s native genes and basically rearranging them a little bit. So it''s using wholly native fish genes at this point. This makes a large difference in terms of public acceptability.”Thresher said his group has been developing techniques that control gene activity with the goal of causing sterility in females or causing females to change sex. The approach has been proven in lab studies in zebra fish and is now being applied to carp. He estimates that it would take 50 years to eliminate the carp with this approach. “It''s generation and time dependent,” he said.Like Thresher, John Teem, a molecular biologist at the Florida Department of Agriculture and Consumer Services (Tallahassee, FL, USA), is tinkering with fish genetics and hormones to develop a Trojan fish with two Y chromosomes that would cause a population to collapse over time.Normally, a female has two X chromosomes and males have an X and a Y chromosome; it is the Y chromosome that determines ''maleness''. Teem said his strategy would create female fish with two Y chromosomes. This fish, when introduced into a target invasive population, will begin to mate with normal males (XY) producing only male progeny. Half of those males will be YY males that will themselves mate and produce only male progeny.“We''re trying to change the sex ratio of the population so that there are more males and fewer females at each generation. By flooding the system with Y chromosomes, more and more male fish are produced,” Teem explained. “Ultimately, the population collapses when there are no more females.” For a fish with a one-year mating cycle, he estimated that it would take 70 years to eradicate a population.Production of YY females involves selective breeding of fish that have been sex-reversed by hormone treatment as juveniles. The process uses techniques that are commonly employed in the aquaculture industry and does not rely on recombinant DNA technology. Teem said the approach could work on carp or other fish with an XY-chromosome sex determination, but he has been focusing on tilapia, which was introduced to control invasive aquatic plants in Florida but has now become a pest. “They''re very aggressive when they''re defending their nest,” he said. “They will attack other fish. If the native fish need that same territory to reproduce, tilapia can exclude them from that resource and negatively impact their reproduction.”...the idea of a tricorder has been around for decades and would be a useful tool to identify and monitor invasive species as well as any other plants and animalsUltimately, however, early detection and thorough monitoring is the best defence against invasions. Daniel Janzen, an evolutionary biologist from the University of Pennsylvania (Philadelphia, PA, USA), is working on a gadget that could enable the development of a dense surveillance system for invasive pests, using an army of volunteers. His tool resembles a species-level ''tricorder'', similar to that from the sci-fi franchise Star Trek, in which a character would use the portable device to detect life-forms and resources on an alien planet. Janzen said the idea of a tricorder has been around for decades and would be a useful tool to identify and monitor invasive species as well as any other plants and animals.Since 1978, Janzen has been studying moth and butterfly caterpillars in the northwestern corner of Costa Rica. By 2003, he had built a database of 3,000 species out of an estimated 12,500 in this region. That year, he connected with geneticist Paul Hebert, a researcher from the University of Guelph in Canada and inventor of the ''DNA-barcoding'' technique that uses short snippets of mitochondrial DNA to identify species. Their goal is to develop a hand-held personal reader the size and cost of a pocket comb. Janzen and Herbert envision that their ''barcorders'' would be used by farmers, game wardens, school children or anyone else.“I can''t think of any better way for anybody, everybody out there to be telling you whether invasive species are here, there and otherwise, than to have this device in their back pocket,” Janzen said. “How many farmers and other outdoors people are there in North America? If every one of them had a barcorder and every time he saw a weird weed growing in his wheat fields, he just pulled a little chip off a leaf and stuck it in his barcorder that would tell the USDA or some other central agency, ''Ah! This plant grows there.''”Bott, in South Australia, agreed that such devices would be a great help to monitor the spread of invasive species. “We can''t be everywhere at once sampling all these different areas. But having the ability to actually go down and test them on site would, in the future, really increase the throughput of our testing and make it a lot easier and possibly less expensive to test a wide range of species. It''s not a fantasy. It''s achievable.”     

Development of a large-scale biocalorimeter to monitor and control bioprocesses

Calorimetry has shown real potential at bench-scale for chemical and biochemical processes. The aim of this work was therefore to scale-up the system by adaptation of a standard commercially available 300-L pilot-scale bioreactor. To achieve this, all heat flows entering or leaving the bioreactor were identified and the necessary instrumentation implemented to enable on-line monitoring and dynamic heat balance estimation. Providing that the signals are sufficiently precise, such a heat balance would enable calculation of the heat released or taken up during an operational (bio)process. Two electrical Wattmeters were developed, the first for determination of the power consumption by the stirrer motor and the second for determination of the power released by an internal calibration heater. Experiments were designed to optimize the temperature controller of the bioreactor such that it was sufficiently rapid so as to enable the heat accumulation terms to be neglected. Further calibration experiments were designed to correlate the measured stirring power to frictional heat losses of the stirrer into the reaction mass. This allows the quantitative measurement of all background heat flows and the on-line quantitative calculation of the (bio)process power. Three test fermentations were then performed with B. sphaericus 1593M, a spore-forming bacterium pathogenic to mosquitoes. A first batch culture was performed on a complex medium, to enable optimization of the calorimeter system. A second batch culture, on defined medium containing three carbon sources, was used to show the fast, accurate response of the heat signal and the ability to perfectly monitor the different growth phases associated with growth on mixed substrates, in particular when carbon sources became depleted. A maximum heat output of 1100 W was measured at the end of the log-phase. A fed-batch culture on the same defined medium was then carried out with the feed rate controlled as a function of the calorimeter signal. A maximum heat output of 2250 W was measured at the end of the first log-phase. This work demonstrates that real-time quantitative calorimetry is not only possible at pilot-scale, but could be readily applied at even larger scales. The technique requires simple, readily available devices for determination of the few necessary heat flows, making it a robust, cost-effective technique for process development and routine monitoring and control of production processes.     

不同施肥模式下稻田土壤微生物生物量磷对土壤有机碳和磷素变化的响应

通过15年的红壤稻田长期定位试验,研究了不同施肥模式下土壤微生物生物量磷(MB-P)对土壤有机碳和磷素变化的响应.结果表明红壤稻田有机碳源的长期投入和土壤有机碳的逐年升高使土壤微生物生物量碳(MB-C)维持在较高水平(＞800 mg·kg-1),是稻田土壤MB-P(＞16.0 mg·kg-1)提高的主要原因.长期不施磷肥条件下,土壤全磷含量与试验前相比显著降低(P＜0.05),而土壤有机磷含量平均提高了29.3%;土壤亏损的磷形态主要是无机磷(Al-P、Fe-P、Ca-P和O-P),其中Al-P含量处于最低水平(平均0.5 mg·kg-1).另外,长期不施磷肥土壤的MB-P远高于Olsen法提取态磷(Olsen-P)(＜7.0 mg·kg-1),而稻田土壤MB-P与Al-P呈显著相关(P＜0.05),表明土壤微生物对稻田土壤Al-P、Fe-P、Ca-P和O-P的利用是促进其向有效磷方向转化的关键途径.磷肥配合有机养分循环利用不仅提高了土壤磷库的积累,而且通过土壤微生物的活化有效地提高了土壤磷的有效性.     

T cell tolerization in vitro: modulation of helper and suppressor cell activities

This paper analyzes the conditions for in vitro tolerization of purified whole T cell populations and the consequences on helper and suppressor T cell functions. Highly purified splenic T cells from adult DBA/2 mice were incubated in vitro for 24 hr with high doses of trinitrophenyl coupled to human gamma-globulins (TNP-HGG). A profound inhibition of the TNP-specific helper function of these T lymphocytes was observed in a cooperative culture with normal purified splenic B cells and TNP-SRBC as antigen. This state of specific unresponsiveness was maintained after trypsin treatment of the cells, at the end of the 24-hr incubation with the tolerogen. We checked that this procedure removed the vast majority of F23.1 T cell receptor determinants from the cells. This result indicates that T cell receptors for antigen were not merely blocked by the tolerogen. In addition, B cells preincubated with tolerized T cells for 24 hr remained as responsive to TNP as B cells mixed with normal T cells in similar conditions. This demonstrates that the decreased response is not the result of secondary B cell tolerization. In addition, anti-Ia monoclonal antibodies were shown to block the induction of tolerance. We also showed that tolerized T cells significantly decreased the anti-TNP response of normal T and B cells in vitro, whereas the anti-SRBC response in the same cultures was unaffected. When tolerized T cells were separated into Lyt-2- and Lyt-2+ cells, it was found that tolerized Lyt-2- cells had lost about 75% of their helper activity and that Lyt-2+ cells suppressed 70% of the response of a normal T and B cell culture. Thus, in vitro induction of T cell tolerance results in a specific T cell unresponsiveness which is due to both helper T cell inactivation and induction of specific suppressor T cells.     

Experimental tools to monitor the dynamics of endothelial barrier function: a survey of in vitro approaches

Endothelial cells line the inner surface of all blood vessels and constitute a selective barrier between blood and tissue. Permeation of solutes across the endothelial cell monolayer occurs either paracellularly through specialized endothelial cell-cell junctions or transcellularly via special transport mechanisms including transcytosis, via the formation of transcellular channels, or by cell membrane transport proteins. Several in vitro assays have been developed in the past few decades to analyze the molecular mechanisms of transendothelial permeability. Measurement of the electrical resistance of the cell monolayer has proven to be particularly suitable for analyzing paracellular barrier function with high-time resolution over long time periods. We review the various permeability assays and focus on the electrical impedance analysis of endothelial cell monolayers. We also address current progress in the development of techniques used to investigate endothelial permeability with high-lateral resolution and under mechanical loads.     

Changes in organic - C, N, P and K and enzyme activities in vermicompost of biodegradable organic wastes under liming and microbial inoculants

The aim of this work was to study the effect of different organic wastes, viz. cow dung, grass, aquatic weeds and municipal solid waste with lime and microbial inoculants on chemical and biochemical properties of vermicompost. Cow dung was the best substrate for vermicomposting. Application of lime (5 g/kg) and inoculation of microorganisms increased the nutrient content in vermicompost and also phosphatases and urease activities. Bacillus polymyxa, the free-living N-fixer, increased N-content of vermicompost significantly (p < or = 0.01) as compared to other inoculants.     

Expansion of murine T cells bearing a unique T cell receptor beta-chain in Friend virus-induced tumor in situ.

Heterogeneity of V alpha 1+ and V beta 10+ TCR alpha beta-chains, which are predominantly used in anti-FBL-3 CTL clones established in vitro, was investigated at a nucleotide level in FBL-3 tumor-infiltrating lymphocytes (TIL) in vivo. The majority (90%) of V beta 10+ beta-chains dominated in TIL used homogeneous V beta 10D beta 2.1 sequences identical to that used in the T cell clones with cytotoxic functions. The homogeneous TCR beta-chain expression was dominant and found to be about 10% of the total TCR beta-chains in the TIL population, which was a greater than 300-to 900-fold increase than in the regional lymph nodes. This is in good agreement with the in vitro data showing that about 11% CTL clones used the homogeneous V beta 10D beta 2.1+ beta-chain. However, the J beta segment does not seem to contribute greatly to the recognition and selection of this TCR because some of homogeneous VD+ beta-chains were associated with J beta segments other than J beta 2.7 of the CTL clones. The frequency of the V alpha 1J alpha 112-2+ alpha-chain expression of the CTL type was much less (3- to 80-fold increase compared to that of lymph node) and also varied in sample materials, indicating the lower contribution of the alpha-chain for the oligoclonality of the TCR. The results were also confirmed by quantitative PCR and RNase protection assays. This suggests that the dominant expression of the homogeneous TCR beta-chain is due to the expansion of the particular anti-FBL-3 CTL in the tumor in situ. Also, the TCR beta-chain, especially the V beta D beta region, rather than alpha-chain is more important for the recognition and selection of the anti-FBL-3 TIL with cytotoxic functions.     

Recent advances in the use of genetically encodable optical tools to elicit and monitor signaling events

Cells rely on a complex network of spatiotemporally regulated signaling activities to effectively transduce information from extracellular cues to intracellular machinery. To probe this activity architecture, researchers have developed an extensive molecular tool kit of fluorescent biosensors and optogenetic actuators capable of monitoring and manipulating various signaling activities with high spatiotemporal precision. The goal of this review is to provide readers with an overview of basic concepts and recent advances in the development and application of genetically encodable biosensors and optogenetic tools for understanding signaling activity.     

低磷石灰性土壤施磷和小麦秸秆后土壤微生物量磷的变化

通过室内培养试验,向低磷的石灰性土壤加入磷(0、25、50、100 mg P·kg^-1,KH₂PO₄)和小麦秸秆(5 g C·kg^-1),25 ℃下培养90 d,研究在施肥和秸秆还田条件下土壤微生物量磷及微生物含磷量的变化特点,及其与土壤有效磷之间的关系.结果表明：土壤微生物量磷、微生物含磷量随加入无机磷量的提高而增加,最高分别为71.37和105.34 mg·kg^-1;除非加入足够的无机磷(如100 mg·kg^-1),否则同时加入秸秆会降低土壤微生物量磷和微生物含磷量,这种效果在培养初期更加明显.土壤微生物量磷和微生物含磷量与土壤有效磷之间存在显著的正相关关系（相关系数R²分别为0.26和0.40,n=49）.加入的无机磷可迅速转化为微生物量磷,表观贡献率最高可达71%,秸秆的加入可使表观贡献率进一步提高.     

Development of a proteomic approach to monitor protein synthesis in mycotoxin producing moulds

In general, proteome studies compare different states of metabolism to investigate external or internal influences on protein expression. In the context of mycotoxin production the method could open another view on this complex and could be helpful to gain knowledge about proteins which are involved in metabolism (enzymes, transporters). In this short technical report, we describe a new protocol suitable for protein preparation for whole proteome analysis ofFusarium graminearum. Cell lysis was performed by grinding the mycelium with liquid nitrogen. Proteins were extracted with TCA/acetone and then cleaned; the isolated proteins were separated in a 2D-gel electrophoresis system (BioRad) using different pH gradients. The protocol established seems also generally applicable for other mycotoxin producing fungi. Presented at the 29th Mykotoxin-Workshop, Fellbach, Germany, May 14–16, 2007 Financial support: Cusanuswerk (doctoral scholarship)     

Development of a microtitre-based spectrophotometric method to monitor Babesia divergens growth in vitro

Babesia divergens multiplication cycle involves erythrocyte invasion, intracellular division, and erythrocyte lysis with the simultaneous liberation of hemoglobin. We have decided to set up a spectrophotometric protocol based on hemoglobin concentration in the culture supernatants to monitor B. divergens in vitro growth. After the selection of 405 nm as the most appropriate endpoint hemoglobin wavelength in our conditions (hemoglobin concentration in the supernatant), cultures were standardized [1 x 10(9) red blood cell (RBC)/ml, 1-2.5 x 10(5) infected red blood cell (iRBC)/ml] to allow their monitoring over 3 days. The protocol was then compared to the most commonly used growth measurement methods: parasitemia counting and [(3)H]hypoxanthine incorporation. An excellent correlation was demonstrated between A(405) of the culture supernatant and parasitemia of the iRBC, whatever the RBC concentration used in the medium. This correlation was also evidenced between A(405) and [(3)H]hypoxanthine incorporation for [(3)H]hypoxanthine concentrations lower than 4 microCi/ml. Our assays also highlighted the inhibitory effect of [(3)H]hypoxanthine on B. divergens growth even when used at low concentrations (0.8 microCi/ml) and for a short incorporation duration (24 h). This effect was confirmed by both A(405) and parasitemia counting. In conclusion, A(405) measurement of B. divergens culture supernatant represents a simple, rapid, safe, and reliable way to measure the in vitro growth of this parasite. Generation times of three different B. divergens strains were then determined by the protocol described here and varied between 8 h 36 min and 13 h 8 min.     

Effect of a temperature gradient on Sphagnum fallax and its associated living microbial communities: a study under controlled conditions

Microbial communities living in Sphagnum are known to constitute early indicators of ecosystem disturbances, but little is known about their response (including their trophic relationships) to climate change. A microcosm experiment was designed to test the effects of a temperature gradient (15, 20, and 25°C) on microbial communities including different trophic groups (primary producers, decomposers, and unicellular predators) in Sphagnum segments (0-3 cm and 3-6 cm of the capitulum). Relationships between microbial communities and abiotic factors (pH, conductivity, temperature, and polyphenols) were also studied. The density and the biomass of testate amoebae in Sphagnum upper segments increased and their community structure changed in heated treatments. The biomass of testate amoebae was linked to the biomass of bacteria and to the total biomass of other groups added and, thus, suggests that indirect effects on the food web structure occurred. Redundancy analysis revealed that microbial assemblages differed strongly in Sphagnum upper segments along a temperature gradient in relation to abiotic factors. The sensitivity of these assemblages made them interesting indicators of climate change. Phenolic compounds represented an important explicative factor in microbial assemblages and outlined the potential direct and (or) indirect effects of phenolics on microbial communities.     

Characterization of a factor produced by human T cell clones exhibiting eosinophil-activating and burst-promoting activities

It has long been suggested that eosinophil response observed in certain immunological reactions depends on the release of soluble products from sensitized lymphocytes when exposed to the challenging antigen. We were able to show that alloreactive T cell clones (ATLC) obtained from human rejected kidney produced, when stimulated with specific antigen (kidney donor-B lymphoblastoid cell line) and interleukin 2, a factor triggering the proliferation of a subline (DA-2) of the interleukin 3 sensitive DA-1 murine cell line. The biochemical features of this factor called HILDA (human interleukin DA) and the DA-2 nonresponsiveness to several human T cell lymphokines and cytokines lead us to the conclusion that this 41,000 m.w. glycoprotein could not be likened to already known T cell lymphokines. Highly purified HILDA turned out to be a potent chemoattractant and activator of, respectively, mouse and human eosinophils. It also displayed burst-promoting activity on human marrow.     

轮作与休闲对日光温室黄瓜连作土壤微生物和酶活性的影响

采用盆栽试验,研究了不同作物轮作和休闲方式对日光温室黄瓜连作土壤微生物数量、酶活性及后茬黄瓜生长和产量的影响.结果表明： 与连作相比,轮作有利于改善土壤微生物结构,增加细菌和放线菌数量,减少真菌数量;轮作与休闲有利于提高土壤转化酶、脲酶、过氧化氢酶和多酚氧化酶活性.在不同作物轮作和休闲方式下,后茬黄瓜结果期的细菌、放线菌数量和土壤转化酶活性均呈先升后降趋势,在盛瓜期达到最大值;真菌数量随生育期延长而增加;脲酶、过氧化氢酶和多酚氧化酶活性则随生育期延长而降低,在初瓜期最高.不同栽培模式下,以大葱-黄瓜轮作和糯玉米-黄瓜轮作的效果更佳,明显改善了后茬黄瓜的生长,提高了产量.     

Soil N/P and C/P ratio regulate the responses of soil microbial community composition and enzyme activities in a long-term nitrogen loaded Chinese fir forest

Plant and Soil - Phosphorus (P) is an essential mineral element required in large quantities by plants. Globally, the availability of P in many soils is poor. Breeding crops that can acquire and...     

Structure and activities of ectomycorrhizal and microbial communities in the rhizosphere of Fagus sylvatica under ozone and pathogen stress in a lysimeter study

The aim was to study the influence of abiotic (elevated ozone) or biotic stress (Phytophthora citricola) or their combination on soil biological components and processes in the rhizosphere of young beech trees. Ectomycorrhizal and overall microbial community composition was studied at two soil depths in a lysimeter experiment with 7 year old trees of Fagus sylvatica. As a functional parameter, potential enzyme activities were measured in mycorrhizosphere soil and on excised mycorrhizal tips. The degree of mycorrhization, structure and potential enzymatic activities of mycorrhizal communities were only slightly influenced by treatments. Soil enzyme activities were depressed under elevated ozone and stimulated by P. citricola under ambient but not under elevated ozone. Overall microbial community composition (PLFA) and ectomycorrhizal diversity changed with depth. PLFA analyses not only suggested a reaction of the microbial community to elevated ozone but also indicated an increase in plant stress related components. No influence of the biotic stress on ectomycorrhizal or overall microbial community structure was detected. Changes in the mycorrhizosphere community structure and function due to ozone may be explained by the quality of plant derived carbon.     

Electricity generation coupled to oxidation of propionate in a microbial fuel cell

Propionate was used as fuel to enrich an electrochemically-active microbial consortium in a microbial fuel cell, and the bacterial consortium was analyzed by culture-independent methods including denaturing gradient gel electrophoresis (DGGE) of the 16S rDNA, and by fluorescent in situ hybridization (FISH). MFCs fed with propionate produced a current of 4.88 ± 0.1 mA stably on 100 mg propionate/l as COD within 3 weeks of the enrichment. When the MFCs were fed with H₂-saturated fuel containing propionate, the current dropped to 3.82 ± 0.07 mA. The maximum current generated was up to 8.8 mA when MFCs were fed with 200 mg propionate/l as COD. The DGGE of 16S rDNA showed that propionate-enriched MFCs have a different bacterial population from that enriched with acetate and from the inoculum used for enrichment. The major member (42%) of the consortium was an unidentified bacterium followed by γ, β, and δ-proteobacteria.