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Clarholm M 《Antonie van Leeuwenhoek》2002,81(1-4):309-318
The paper explores interactions between the two first organism groups to appear on earth, the bacteria and protozoa, and their
interplay with the rest of the ecosystem focusing upon northern boreal forests. The microbial loop is suggested as a mechanism
for local inputs of new N to the ecosystem. The possibility to couple short-term microbial processes with their long-term
effects, — as registered in plants, soil and the atmosphere, via the abiotic variables — is explored. The latter are investigated
in relation to the environments they create for the micro-organisms, and how this results in varying soil fertility. A chain
of events is presented that relate high Ca concentration in the mineral soil and high water availability to increased nitrogen
availability for plants via the micro-organisms. An example is given of the influence of these parameters directly upon protozoa
along an extreme fertility gradient, and also indirect evidence from a Finnish field study of 30 sites with four fertility
levels. Finally, there is a discussion about ways to convert knowledge gained in detailed studies of microbial interactions
into forms useful when evaluating the present status of and effects of ameliorative management on ecosystems strongly affected
by humans.
This revised version was published online in August 2006 with corrections to the Cover Date. 相似文献
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Olga Savichtcheva Didier Debroas Marie Elodie Perga Fabien Arnaud Clément Villar Emilie Lyautey Amy Kirkham Cécile Chardon Benjamin Alric Isabelle Domaizon 《Freshwater Biology》2015,60(1):31-49
- Decennial changes in Planktothrix rubescens diversity and dynamics were reconstructed by applying molecular tools to analyse DNA and RNA extracted from lake sediments. The sediments studied were sampled from a deep peri‐alpine lake that has experienced both dramatic shifts in trophic conditions and large‐scale climatic changes. Palaeolimnological proxies were combined with statistical modelling to investigate the relative influence of phosphorus concentrations and temperature changes on the extent of Planktothrix blooms over the last century.
- Phylogenetic analysis revealed that the overall composition of the cyanobacterial community changed over the transition from oligotrophic to eutrophic conditions. When the relative abundance of Planktothrix decreased in the 1970s, concomitant with eutrophication, total cyanobacterial abundance remained high and more Anabaena and Microcystis sequences were detected. In spite of such drastic environmental changes, the lake provided a constant niche for one particular Planktothrix species, which was consistently present from the 1920s to the present day.
- Phosphorus concentration was found to be the dominant driver of the relative abundance of P. rubescens, with the highest abundances observed during mesotrophic conditions. The relative role of climate was nutrient‐dependent, with warmer springs having a positive effect on P. rubescens abundance only during mesotrophic periods.
- Overall, this study confirms that analysis of genetic signatures preserved in sediment archives allows assessment of key palaeoenvironmental indicator species that have no diagnostic microscopic cellular features in the sediment record. In the case of cyanobacteria, palaeogenetics offer unique opportunities to anticipate how future climate change might affect the response of P. rubescens to phosphorus concentration.
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Yubo Hou Nanjing Ji Huan Zhang Xinguo Shi Hansen Han Senjie Lin 《Journal of phycology》2019,55(1):37-46
Proliferating cell nuclear antigen (PCNA) plays critical roles in eukaryotic DNA replication and replication‐associated processes. It is typically encoded by one or two gene copies (pcna) in eukaryotic genomes. Recently reported higher copy numbers of pcna in some dinoflagellates raised a question of how this gene has uniquely evolved in this phylum. Through real‐time PCR quantification, we found a wide range of pcna copy number (2–287 copies) in 11 dinoflagellate species (n = 38), and a strong positive correlation between pcna copy number and genome size (log10–log10 transformed). Intraspecific pcna diverged up to 21% and are dominated by nonsynonymous substitutions, indicating strong purifying selection pressure on and hence functional necessity of this gene. By surveying pcna copy numbers in eukaryotes, we observed a genome size threshold at 4 pg DNA, above which more than two pcna copies are found. To examine whether retrotransposition is a mechanism of pcna duplication, we measured the copy number of retroposed pcna, taking advantage of the 22‐nt dinoflagellate‐specific spliced leader (DinoSL) capping the 5′ end of dinoflagellate nuclear‐encoded mRNAs, which would exist in the upstream region of a retroposed gene copy. We found that retroposed pcna copy number increased with total pcna copy number and genome size. These results indicate co‐evolution of dinoflagellate pcna copy number with genome size, and retroposition as a major mechanism of pcna duplication in dinoflagellates. Furthermore, we posit that the demand of faithful replication and maintenance of the large dinoflagellate genomes might have favored the preservation of the retroposed pcna as functional genes. 相似文献
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Eliana Bignotti Stefano Calza Renata A. Tassi Laura Zanotti Elisabetta Bandiera Enrico Sartori Franco E. Odicino Antonella Ravaggi Chiara Romani 《Journal of cellular and molecular medicine》2016,20(12):2341-2348
MicroRNAs (miRNAs) belong to a family of small non‐coding RNAs (sncRNAs) playing important roles in human carcinogenesis. Multiple investigations reported miRNAs aberrantly expressed in several cancers, including high‐grade serous ovarian carcinoma (HGS‐OvCa). Quantitative PCR is widely used in studies investigating miRNA expression and the identification of reliable endogenous controls is crucial for proper data normalization. In this study, we aimed to experimentally identify the most stable reference sncRNAs for normalization of miRNA qPCR expression data in HGS‐OvCa. Eleven putative reference sncRNAs for normalization (U6, SNORD48, miR‐92a‐3p, let‐7a‐5p, SNORD61, SNORD72, SNORD68, miR‐103a‐3p, miR‐423‐3p, miR‐191‐5p, miR‐16‐5p) were analysed on a total of 75 HGS‐OvCa and 30 normal tissues, using a highly specific qPCR. Both the normal tissues considered to initiate HGS‐OvCa malignant transformation, namely ovary and fallopian tube epithelia, were included in our study. Stability of candidate endogenous controls was evaluated using an equivalence test and validated by geNorm and NormFinder algorithms. Combining results from the three different statistical approaches, SNORD48 emerged as stably and equivalently expressed between malignant and normal tissues. Among malignant samples, considering groups based on residual tumour, miR‐191‐5p was identified as the most equivalent sncRNA. On the basis of our results, we support the use of SNORD48 as best reference sncRNA for relative quantification in miRNA expression studies between HGS‐OvCa and normal controls, including the first time both the normal tissues supposed to be HGS‐OvCa progenitors. In addition, we recommend miR‐191‐5p as best reference sncRNA in miRNA expression studies with prognostic intent on HGS‐OvCa tissues. 相似文献
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Anna Barbanti Hector Torrado Enrique Macpherson Luca Bargelloni Rafaella Franch Carlos Carreras Marta Pascual 《Molecular ecology resources》2020,20(3):795-806
High‐throughput sequencing has revolutionized population and conservation genetics. RAD sequencing methods, such as 2b‐RAD, can be used on species lacking a reference genome. However, transferring protocols across taxa can potentially lead to poor results. We tested two different IIB enzymes (AlfI and CspCI) on two species with different genome sizes (the loggerhead turtle Caretta caretta and the sharpsnout seabream Diplodus puntazzo) to build a set of guidelines to improve 2b‐RAD protocols on non‐model organisms while optimising costs. Good results were obtained even with degraded samples, showing the value of 2b‐RAD in studies with poor DNA quality. However, library quality was found to be a critical parameter on the number of reads and loci obtained for genotyping. Resampling analyses with different number of reads per individual showed a trade‐off between number of loci and number of reads per sample. The resulting accumulation curves can be used as a tool to calculate the number of sequences per individual needed to reach a mean depth ≥20 reads to acquire good genotyping results. Finally, we demonstrated that selective‐base ligation does not affect genomic differentiation between individuals, indicating that this technique can be used in species with large genome sizes to adjust the number of loci to the study scope, to reduce sequencing costs and to maintain suitable sequencing depth for a reliable genotyping without compromising the results. Here, we provide a set of guidelines to improve 2b‐RAD protocols on non‐model organisms with different genome sizes, helping decision‐making for a reliable and cost‐effective genotyping. 相似文献
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Twenty popular rice hybrids were used to screen for rice tungro virus (RTV) disease reaction. Virulent green leafhoppers (GLH) were used as vector to introduce RTV to the rice hybrids. Virus symptoms scores were recorded at 14, 21, 34, 41 and 59 days postinoculation (DPI), which suggested that virus symptoms are greatly influenced by growth stage of plants. To confirm the presence of virus, polymerase chain reaction (PCR)‐based detection of Rice tungro bacilliform virus (RTBV) was carried out at 7, 14, 21 and 59 DPI using virus genome‐specific primers. Virus presence was observed in all the rice hybrids and check varieties, particularly at later stages of infection. This study shows that phenotyping for tungro virus resistance in rice hybrids at 21 DPI gives most reliable results based on both virus symptoms and presence of virus. Further, to assess the relative difference in population of RTBV, quantitative PCR was performed in all the genotypes at 21 DPI. Yield data were also recorded from control and virus‐infected plants to estimate yield loss percentage due to tungro disease. This study is important to understand the response of rice hybrids to tungro virus disease. Results obtained in this study emphasize that molecular detection of virus is very important to screen the rice plants accurately for tungro disease reaction. 相似文献
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R. Boss A. Baumgartner S. Kroos M. Blattner R. Fretz D. Moor 《Journal of applied microbiology》2018,125(4):1216-1225
Aims
A molecular method for a rapid detection of viable Legionella pneumophila of all serogroups in tap water samples was developed as an alternative to the reference method (ISO). Legionellae are responsible for Legionnaires’ disease, a severe pneumonia in humans with high lethality.Methods and Results
The developed method is based on a nutritional stimulation and detection of an increase in precursor 16S rRNA as an indicator for viability. For quantification, DNA was detected by qPCR. This method was compared to the ISO method using water samples obtained from public sports facilities in Switzerland. The sensitivity and specificity were 91 and 97%, respectively, when testing samples for compliance with a microbiological criterion of 1000 cell equivalents per l.Conclusion
The new method is sensitive and specific for Leg. pneumophila and allows results to be obtained within 8 h upon arrival, compared to one week or more by the ISO method.Significance and Impact of the Study
The method represents a useful tool for a rapid detection of viable Leg. pneumophila of all serogroups in water by molecular biology. It can be used as an alternative to the ISO method for official water analysis for legionellae and particularly when a short test time is required. 相似文献10.
Stephen F. Jane Taylor M. Wilcox Kevin S. McKelvey Michael K. Young Michael K. Schwartz Winsor H. Lowe Benjamin H. Letcher Andrew R. Whiteley 《Molecular ecology resources》2015,15(1):216-227
Environmental DNA (eDNA) detection has emerged as a powerful tool for monitoring aquatic organisms, but much remains unknown about the dynamics of aquatic eDNA over a range of environmental conditions. DNA concentrations in streams and rivers will depend not only on the equilibrium between DNA entering the water and DNA leaving the system through degradation, but also on downstream transport. To improve understanding of the dynamics of eDNA concentration in lotic systems, we introduced caged trout into two fishless headwater streams and took eDNA samples at evenly spaced downstream intervals. This was repeated 18 times from mid‐summer through autumn, over flows ranging from approximately 1–96 L/s. We used quantitative PCR to relate DNA copy number to distance from source. We found that regardless of flow, there were detectable levels of DNA at 239.5 m. The main effect of flow on eDNA counts was in opposite directions in the two streams. At the lowest flows, eDNA counts were highest close to the source and quickly trailed off over distance. At the highest flows, DNA counts were relatively low both near and far from the source. Biomass was positively related to eDNA copy number in both streams. A combination of cell settling, turbulence and dilution effects is probably responsible for our observations. Additionally, during high leaf deposition periods, the presence of inhibitors resulted in no amplification for high copy number samples in the absence of an inhibition‐releasing strategy, demonstrating the necessity to carefully consider inhibition in eDNA analysis. 相似文献
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Duccio Migliorini Luisa Ghelardini Elena Tondini Nicola Luchi Alberto Santini 《Diversity & distributions》2015,21(10):1218-1229
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Lisa Siegmund Michael Schweikert Martin S. Fischer Johannes Wöstemeyer 《The Journal of eukaryotic microbiology》2018,65(5):600-611
Endosymbiotic interactions are frequently found in nature, especially in the group of protists. Even though many endosymbioses have been studied in detail, little is known about the mechanistic origins and physiological prerequisites of endosymbiont establishment. A logical step towards the development of endocytobiotic associations is evading digestion and escaping from the host's food vacuoles. Surface properties of bacteria are probably involved in these processes. Therefore, we chemically modified the surface of a transformant strain of Escherichia coli prior to feeding to Tetrahymena pyriformis. N‐(3‐dimethylaminopropyl)‐N’‐ethylcarbodiimide allows any substance carrying amino‐ or carboxyl groups to be bound covalently to the bacterial surface by forming a peptide bond, thus, altering its properties biochemically and biophysically in a predictable manner. The effect of different traits on digestion of T. pyriformis was examined by fluorescence and transmission electron microscopy. The efficiency of digestion differs considerably depending on the coupled substances. Alkaline substances inhibit digestion partially, resulting in incomplete digestion and slightly enhanced escape rates. Increasing hydrophobicity leads to much higher escape frequencies. Both results point to possible mechanisms employed by pathogenic bacteria or potential endosymbionts in evading digestion and transmission to the host's cytoplasm. 相似文献
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Insect pathogenic fungi (IPF) need to overcome the host immune system in order to sporulate and ensure transmission to new hosts. Some IPF produce immunosuppressive toxins, whereas others rely on rapid fungal proliferation to kill the host by sheer fungal mass, resulting in a trade‐off between allocating resources to toxin production and fungal proliferation. The obligate entomopathogenic fungus, Entomophthora muscae sensu stricto, is host specific to the common house fly, Musca domestica. E. muscae grows as protoplast cells without cell walls and is not known to produce toxins. Here, we assessed the growth of E. muscae, in vivo, using real‐time PCR to measure the amount of a single‐copy actin gene. We find that E. muscae exhibits S‐shaped logistic growth between time post‐exposure and the number of fungal nuclei. The results show that E. muscae initially grows exponentially inside the host until depletion of available nutrient sources signifies the ‘limiting capacity’ where after the host is killed. This growth pattern differs markedly from toxin‐producing IPF species of Metarhizium and Beauveria in which maximal (plateau) growth and sporulation do not occur until well after the death of the host. 相似文献
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Nonactivated titanium‐dioxide nanoparticles promote the growth of Chlamydia trachomatis and decrease the antimicrobial activity of silver nanoparticles 
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下载免费PDF全文 A. Bogdanov L. Janovák I. Lantos V. Endrész D. Sebők T. Szabó I. Dékány J. Deák Z. Rázga K. Burián D.P. Virok 《Journal of applied microbiology》2017,123(5):1335-1345
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Cédric Berney Andreea Ciuprina Sara Bender Juliet Brodie Virginia Edgcomb Eunsoo Kim Jeena Rajan Laura Wegener Parfrey Sina Adl Stéphane Audic David Bass David A. Caron Guy Cochrane Lucas Czech Micah Dunthorn Stefan Geisen Frank Oliver Glöckner Frédéric Mahé Christian Quast Jonathan Z. Kaye Alastair G. B. Simpson Alexandros Stamatakis Javier del Campo Pelin Yilmaz Colomban de Vargas 《The Journal of eukaryotic microbiology》2017,64(3):407-411
Universal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, mycology, and bacteriology as well as their large research communities. Animals, plants, and fungi have relatively solid, stable morpho‐taxonomies built over the last three centuries, while bacteria have been classified for the last three decades under a coherent molecular taxonomic framework. By contrast, no such common language exists for microbial eukaryotes, even though environmental ‘‐omics’ surveys suggest that protists make up most of the organismal and genetic complexity of our planet's ecosystems! With the current deluge of eukaryotic meta‐omics data, we urgently need to build up a universal eukaryotic taxonomy bridging the protist ‐omics age to the fragile, centuries‐old body of classical knowledge that has effectively linked protist taxa to morphological, physiological, and ecological information. UniEuk is an open, inclusive, community‐based and expert‐driven international initiative to build a flexible, adaptive universal taxonomic framework for eukaryotes. It unites three complementary modules, EukRef, EukBank, and EukMap, which use phylogenetic markers, environmental metabarcoding surveys, and expert knowledge to inform the taxonomic framework. The UniEuk taxonomy is directly implemented in the European Nucleotide Archive at EMBL‐EBI, ensuring its broad use and long‐term preservation as a reference taxonomy for eukaryotes. 相似文献