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Situ Activity (situ + activity)
Selected AbstractsCombined bromodeoxyuridine immunocapture and terminal-restriction fragment length polymorphism analysis highlights differences in the active soil bacterial metagenome due to Glomus mosseae inoculation or plant speciesENVIRONMENTAL MICROBIOLOGY, Issue 12 2005Veronica Artursson Summary High numbers of bacteria are associated with arbuscular mycorrhizal (AM) fungi, but their functions and in situ activities are largely unknown and most have never been characterized. The aim of the present study was to study the impact of Glomus mosseae inoculation and plant type on the active bacterial communities in soil by using a molecular approach, bromodeoxyuridine (BrdU) immunocapture in combination with terminal-restriction fragment length polymorphism (T-RFLP). This approach combined with sequence information from clone libraries, enabled the identification of actively growing populations, within the total bacterial community. Distinct differences in active bacterial community compositions were found according to G. mosseae inoculation, treatment with an antifungal compound (Benomyl) and plant type. The putative identities of the dominant bacterial species that were activated as a result of G. mosseae inoculation were found to be mostly uncultured bacteria and Paenibacillus species. These populations may represent novel bacterial groups that are able to influence the AM relationship and its subsequent effect on plant growth. [source] In situ measurement of methane fluxes and analysis of transcribed particulate methane monooxygenase in desert soilsENVIRONMENTAL MICROBIOLOGY, Issue 10 2009Roey Angel Summary Aerated soils are a biological sink for atmospheric methane. However, the activity of desert soils and the presence of methanotrophs in these soils have hardly been studied. We studied on-site atmospheric methane consumption rates as well as the diversity and expression of the pmoA gene, coding for a subunit of the particulate methane monooxygenase, in arid and hyperarid soils in the Negev Desert, Israel. Methane uptake was only detected in undisturbed soils in the arid region (,90 mm year,1) and vertical methane profiles in soil showed the active layer to be at 0,20 cm depth. No methane uptake was detected in the hyperarid soils (,20 mm year,1) as well as in disturbed soils in the arid region (i.e. agricultural field and a mini-catchment). Molecular analysis of the methanotrophic community using terminal restriction fragment length polymorphism (T-RFLP) and cloning/sequencing of the pmoA gene detected methanotrophs in the active soils, whereas the inactive ones were dominated by sequences of the homologous gene amoA, coding for a subunit of the ammonia monooxygenase. Even in the active soils, methanotrophs (as well as in situ activity) could not be detected in the soil crust, which is the biologically most important layer in desert soils. All pmoA sequences belonged to yet uncultured strains. Transcript analysis showed dominance of sequences clustering within the JR3, formerly identified in Californian grassland soils. Our results show that although active methanotrophs are prevalent in arid soils they seem to be absent or inactive in hyperarid and disturbed arid soils. Furthermore, we postulate that methanotrophs of the yet uncultured JR3 cluster are the dominant atmospheric methane oxidizers in this ecosystem. [source] Prokaryotic diversity and metabolically active microbial populations in sediments from an active mud volcano in the Gulf of MexicoENVIRONMENTAL MICROBIOLOGY, Issue 10 2006Robert J. Martinez Summary In this study, ribosomes and genomic DNA were extracted from three sediment depths (0,2, 6,8 and 10,12 cm) to determine the vertical changes in the microbial community composition and identify metabolically active microbial populations in sediments obtained from an active seafloor mud volcano site in the northern Gulf of Mexico. Domain-specific Bacteria and Archaea 16S polymerase chain reaction primers were used to amplify 16S rDNA gene sequences from extracted DNA. Complementary 16S ribosomal DNA (crDNA) was obtained from rRNA extracted from each sediment depth that had been subjected to reverse transcription polymerase chain reaction amplification. Twelve different 16S clone libraries, representing the three sediment depths, were constructed and a total of 154 rDNA (DNA-derived) and 142 crDNA (RNA-derived) Bacteria clones and 134 rDNA and 146 crDNA Archaea clones obtained. Analyses of the 576 clones revealed distinct differences in the composition and patterns of metabolically active microbial phylotypes relative to sediment depth. For example, ,- Proteobacteria rDNA clones dominated the 0,2 cm clone library whereas ,-Proteobacteria dominated the 0,2 cm crDNA library suggesting , to be among the most active in situ populations detected at 0,2 cm. Some microbial lineages, although detected at a frequency as high as 9% or greater in the total DNA library (i.e. Actinobacteria, ,- Proteobacteria), were markedly absent from the RNA-derived libraries suggesting a lack of in situ activity at any depth in the mud volcano sediments. This study is one of the first to report the composition of the microbial assemblages and physiologically active members of archaeal and bacterial populations extant in a Gulf of Mexico submarine mud volcano. [source] In situ analysis of enzymes involved in sucrose to hexose-phosphate conversion during stolon-to-tuber transition of potatoPHYSIOLOGIA PLANTARUM, Issue 2 2002Niek J.G. Appeldoorn An in situ study of enzymes involved in sucrose to hexose-phosphate conversion during in vitro stolon-to-tuber transition of potato (Solanum tuberosum L. cv. Bintje) was employed to follow developmental changes in spatial patterns. In situ activity of the respective enzymes was visualized by specific activity-staining techniques and they revealed distinct spatially and developmentally regulated patterns. Two of the enzymes studied were also subject to in situ investigations at the transcriptional level. During the stages of stolon formation high hexokinase (EC 2.7.1.1) and acid (cell wall-bound) invertase (EC 3.2.1.26) activities were restricted to the mitotically active (sub)apical region, suggesting a possible importance of these enzymes for cell division. At the onset of tuberization sucrose synthase (EC 2.4.1.13) and fructokinase (EC 2.7.1.4) were strongly induced (visualized at transcriptional and translational level) and the acid invertase activities disappeared from the swelling subapical region as expected. The high degree of similarity in the spatial pattern and the temporal induction of sucrose synthase and fructokinase suggests a tightly co-ordinated coarse (up)regulation, which may be subject to a sugar-modulated mechanism(s) by which genes involved in the metabolic sucrose-starch converting potential are co-ordinately regulated during tuber growth. The overall activity of uridine-5-diphosphoglucose pyrophosphorylase (EC 2.7.7.9) was present in all tissues during stolon and tuber development, implying that its coarse control is not subject to (in)direct developmental regulation. [source] | ||||||||||