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121.
We introduce a novel computational approach to predict effective genome size (EGS; a measure that includes multiple plasmid copies, inserted sequences, and associated phages and viruses) from short sequencing reads of environmental genomics (or metagenomics) projects. We observe considerable EGS differences between environments and link this with ecologic complexity as well as species composition (for instance, the presence of eukaryotes). For example, we estimate EGS in a complex, organism-dense farm soil sample at about 6.3 megabases (Mb) whereas that of the bacteria therein is only 4.7 Mb; for bacteria in a nutrient-poor, organism-sparse ocean surface water sample, EGS is as low as 1.6 Mb. The method also permits evaluation of completion status and assembly bias in single-genome sequencing projects. 相似文献
122.
Inventory and monitoring of wine microbial consortia 总被引:2,自引:0,他引:2
The evolution of the wine microbial ecosystem is generally restricted to Saccharomyces cerevisiae and Oenococcus oeni, which are the two main agents in the transformation of grape must into wine by acting during alcoholic and malolactic fermentation,
respectively. But others species like the yeast Brettanomyces bruxellensis and certain ropy strains of Pediococcus parvulus can spoil the wine. The aim of this study was to address the composition of the system more precisely, identifying other
components. The advantages of the polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) approach to
wine microbial ecology studies are illustrated by bacteria and yeast species identification and their monitoring at each stage
of wine production. After direct DNA extraction, PCR-DGGE was used to make the most exhaustive possible inventory of bacteria
and yeast species found in a wine environment. Phylogenetic neighbor-joining trees were built to illustrate microbial diversity.
PCR-DGGE was also combined with population enumeration in selective media to monitor microbial changes at all stages of production.
Moreover, enrichment media helped to detect the appearance of spoilage species. The genetic diversity of the wine microbial
community and its dynamics during winemaking were also described. Most importantly, our study provides a better understanding
of the complexity and diversity of the wine microbial consortium at all stages of the winemaking process: on grape berries,
in must during fermentation, and in wine during aging. On grapes, 52 different yeast species and 40 bacteria could be identified.
The diversity was dramatically reduced during winemaking then during aging. Yeast and lactic acid bacteria were also isolated
from very old vintages. B. bruxellensis and O. oeni were the most frequent. 相似文献
123.
Don A. Driscoll Annabel L. Smith Samantha Blight John Maindonald 《Biodiversity and Conservation》2012,21(6):1607-1625
Altered fire regimes are a driver of biodiversity decline. To plan effective management, we need to know how species are influenced
by fire and to develop theory describing fire responses. Animal responses to fire are usually measured using methods that
rely on animal activity, but animal activity may vary with time since fire, potentially biasing results. Using a novel approach
for detecting bias in the pit-fall trap method, we found that leaf-litter dependent reptiles were more active up to 6 weeks
after fire, giving a misleading impression of abundance. This effect was not discovered when modelling detectability with
zero-inflated binomial models. Two species without detection bias showed early-successional responses to time since fire,
consistent with a habitat-accommodation succession model. However, a habitat specialist did not have the predicted low abundance
after fire due to increased post-fire movement and non-linear recovery of a key habitat component. Interactions between fire
and other processes therefore must be better understood to predict reptile responses to changing fire-regimes. We conclude
that there is substantial bias when trapping reptiles after fire, with species that are otherwise hard to detect appearing
to be abundant. Studies that use a survey method based on animal activity such as bird calls or animal movements, likely face
a similar risk of bias when comparing recently-disturbed with control sites. 相似文献
124.
Little information exists on mixed-species groups between primates and other mammals in Neotropical forests. In this paper, we describe three such associations observed during an extensive large-vertebrate survey in central Amazonia, Brazil. Mixed-species groups between a primate species and another mammal were observed on seven occasions between squirrel monkeys (Saimiri cf. ustus) and either South American coatis (Nasua nasua) or tayras (Eira barbara) and between brown capuchins (Cebus apella) and coatis. All associations were restricted to floodplain forest during its dry stage. We suggest that the associations involving the coatis are connected to foraging and vigilance but may be induced by a common alternative food resource at a time of food shortage. 相似文献
125.
Lentiviral vectors have been used for gene transfer into the liver but their ability to efficiently transduce quiescent hepatocytes
remains controversial. Lentivirus-mediated gene transfer is more efficient in cycling cells. We determine the effect of H-IL6
in the lentiviral transduction. The lentiviral vector was used to transduce HepG2 cells and mice liver cells, previously treated
with H-IL6. The highest transduction level was observed in HepG2 cells treated with 30 ng/mL H-IL6 and in the mice that received
4 μg H-IL6. Our results suggest that H-IL6 is an inducer of lentiviral gene transfer into the liver cells without any toxicity. 相似文献
126.
Thomas Proft 《Biotechnology letters》2010,32(1):1-10
Sortases are transpeptidases produced by Gram-positive bacteria to anchor cell surface proteins covalently to the cell wall.
The Staphylococcus aureus sortase A (SrtA) cleaves a short C-terminal recognition motif (LPXTG) on the target protein followed by the formation of an amide bond with the pentaglycine
cross-bridge in the cell wall. Over recent years, several researchers have exploited this specific reaction for a range of
biotechnology applications, including the incorporation of non-native peptides and non-peptidic molecules into proteins, the
generation of nucleic acid–peptide conjugates and neoglycoconjugates, protein circularisation, and labelling of cell surface
proteins on living cells. 相似文献
127.
‘Green tides’ are overwhelming the coastline of our blue planet: taking the world’s largest example 总被引:8,自引:0,他引:8
Nai-hao Ye Xiao-wen Zhang Yu-ze Mao Cheng-wei Liang Dong Xu Jian Zou Zhi-meng Zhuang Qing-yin Wang 《Ecological Research》2011,26(3):477-485
A broad spectrum of events that come under the category of green tide are recognized world-wide as a response to elevated
levels of seawater nutrients in coastal areas. Green tides involve a wide diversity of sites, macroalgal species, consequences,
and possible causes. Here we review the effect of natural and man-induced environmental fluctuations on the frequency and
apparent spread of green tides. This article highlights the need for interdisciplinary research aimed at shedding light on
the basic mechanisms governing the occurrence and succession of green algae in coastal seas. This will result in more effective
management and mitigation of the effects of green tides, thus safeguarding the intrinsic and commercial value of coastal marine
ecosystems. 相似文献
128.
Seedlings of two barley genotypes (‘Maresi’ and wild form of Hordeum spontaneum) were treated with jasmonic acid (JA 5 μM and 15 μM) for 24 h, and then subjected to water stress (PEG 6000 solution of −
1.5 MPa). JA caused an increase in the content of ABA but not in that of proline and spermidine in the two studied genotypes.
The effect of the treatment did not depend on the applied JA concentration. The pre-stress treatment with JA changed plant
response to water deficit with regard to membrane injury. Treatment with a lower JA concentration (5 μM) caused a substantial
reduction of the stress-induced membrane damage in the both genotypes. A higher JA concentration (15 μM) caused the reduction
of membrane injury only in H. spontaneum and was ineffective in ‘Maresi’. JA had no influence on the leaf water status in water-stressed plants. A possible role of
JA in leaf ABA accumulation and alleviation of cell membrane injury under water deficit is discussed.
The work was partly supported by the Polish Committee For Scientific Research, grant No 5 PO6A 036 18 相似文献
129.
Aims
The present study was planned to investigate the diversity of 1-aminocyclopropane-1-carboxylate (ACC) deaminase producing bacteria from the rhizosphere of wheat plants and subsequent evaluation of selected PGPR on growth enhancement of wheat seedlings under drought and saline conditions.Methods
ACC deaminase producing plant growth promoting rhizobacteria (PGPR) were isolated from the rhizosphere of wheat and identified using 16S rRNA gene sequence analysis. Isolates were evaluated for various direct and indirect plant growth promoting (PGP) traits. Plant inoculation experiment was conducted using isolates IG 19 and IG 22 in wheat to assess their plant growth promotion potential under salinity and drought stress.Results
Thirty-eight ACC deaminase producing PGPR were isolated which belonged to 12 distinct genera and falling into four phyla γ-proteobacteria, β-proteobacteria, Flavobacteria and Firmicutes. Klebsiella sp. was the most abundant genera and followed by Enterobacter sp. The isolates exhibited ACC deaminase activities ranging from 0.106–0.980 μM α- ketobutyrate μg protein?1 h?1. The isolates showed multiple PGP traits such as IAA production, phosphate, zinc, potassium solubilization and siderophore production. Enterobacter cloacae (IG 19) and Citrobacter sp. (IG 22) inoculated wheat seedlings showed notable increases in fresh and dry biomass under non-stress as well as under stressed condition.Conclusion
To the best of our knowledge this is the first report of presence of ACC deaminase activity and other PGP traits from the genus Citrobacter and Empedobacter. Our finding revealed that the γ-proteobacteria group dominated the wheat rhizosphere. Plant inoculation with PGPR could be a sustainable approach to alleviate abiotic stresses in wheat plants. These native PGPR isolates could be used as potential biofertilizers for sustainable agriculture.130.
Hiroyuki Inoue Chiaki Kitao Shinichi Yano Shigeki Sawayama 《World journal of microbiology & biotechnology》2016,32(11):186
On-site cellulase and hemicellulase production is a promising way to reduce enzyme cost in the commercialization of the lignocellulose-to-ethanol process. A hemicellulase-producing fungal strain suitable for on-site enzyme production was selected from cultures prepared using wet disc-milling rice straw (WDM-RS) and identified as Trichoderma asperellum KIF125. KIF125 hemicellulase showed uniquely high abundance of β-xylosidase in the xylanolytic enzyme system compared to other fungal hemicellulase preparations. Supplementation of Talaromyces cellulolyticus cellulase with KIF125 hemicellulase was more effective than that with the hemicellulases from other fungal sources in reducing the total enzyme loading for the improvement of xylose yield in the hydrolysis of ball-milling RS, due to its high β-xylosidase dominance. β-Xylosidase in KIF125 hemicellulase was purified and classified as a glycosyl hydrolase family 3 enzyme with relatively high specificity for xylobiose. The production of KIF125 β-xylosidase in the fermentor was estimated as 118 U/g-WDM-RS (2350 U/L culture) at 48 h. These results demonstrate that KIF125 is promising as a practical hemicellulase source to combine with on-site cellulase production using T. cellulolyticus. 相似文献