Search results for "Sediment"
showing 10 items of 1648 documents
Impact of biocide treatments on the bacterial communities of the Lascaux Cave.
2009
The Lascaux Cave contains a remarkable set of paintings from the Upper Palaeolithic. Shortly after discovery in 1940, the cave was modified for public viewing and, in 2001, was invaded by a Fusarium solani species complex. Benzalkonium chloride was used from 2001 to 2004 to eliminate the fungal outbreak. In this study, we carried out a sampling in most of the cave halls and galleries. Sequence analysis and isolation methods detected that the most abundant genera of bacteria were Ralstonia and Pseudomonas. We suggest that, as a result of years of benzalkonium chloride treatments, the indigenous microbial community has been replaced by microbial populations selected by biocide application.
Manganese/polymetallic nodules: Micro-structural characterization of exolithobiontic- and endolithobiontic microbial biofilms by scanning electron mi…
2009
Polymetallic/ferromanganese nodules (Mn-nodules) provide a rich source for manganese. It is not yet known if the nodules have a biogenic or an abiogenic origin. Here we applied the technique of high-resolution scanning electron microscopy, in combination with energy dispersive X-ray spectroscopical (EDX) analysis, to trace the existence of microbial biofilms. Two spatially separated assemblies exist, the exolithobiontic- and endolithobiontic colonizations. The exolithobiontic colonization is seen in the micro-canals, which traverse the outer surface layer of the nodules and are formed by elongated filamentous organisms, which show no signs of mineralization. In the center of the nodules thr…
Psychrotolerant Sulfate-reducing Bacteria from an Oxic Freshwater Sediment Description of Desulfovibrio cuneatus sp. nov. and Desulfovibrio litoralis…
1998
The most abundant culturable sulfate-reducing bacteria were isolated from the littoral sediment of the oligotrophic Lake Stechlin. The strains STL1 and STL4 were obtained from the oxic uppermost layer, while strain STL6 was isolated from the anoxic zone in 20 to 30 mm depth. The isolates showed a striking morphological feature in tapering off at one end of the cell. Physiological characteristics related them to the genus Desulfovibrio. They contained desulfoviridin. H2, formate, pyruvate, lactate, and fumarate were utilized with sulfate, sulfite, thiosulfate, or elemental sulfur as electron acceptors. All isolates were able to reduce oxygen and survived 120 h of aeration. However, aerobic g…
Sphingobium aromaticiconvertens sp. nov., a xenobiotic-compound-degrading bacterium from polluted river sediment.
2007
A bacterial strain capable of degrading some monochlorinated dibenzofurans, designated RW16T, was isolated from aerobic River Elbe sediments. The strain was characterized based on 16S rRNA gene sequence analysis, DNA G+C content, physiological characteristics, polyamines, ubiquinone and polar lipid pattern and fatty acid composition. This analysis revealed that strain RW16T represents a novel species of the genus Sphingobium. The DNA G+C content of strain RW16T, 60.7 mol%, is the lowest yet reported for the genus. 16S rRNA gene sequence analysis placed strain RW16T as an outlier in the genus Sphingobium. The name Sphingobium aromaticiconvertens sp. nov. is proposed for this dibenzofuran-min…
Quantification of a novel group of nitrate-reducing bacteria in the environment by real-time PCR
2004
Abstract Nitrate reduction is performed by phylogenetically diverse bacteria. Analysis of narG (alpha subunit of the membrane bound nitrate reductase) trees constructed using environmental sequences revealed a new cluster that is not related to narG gene from known nitrate-reducing bacteria. In this study, primers targeting this as yet uncultivated nitrate-reducing group were designed and used to develop a real-time SYBR® Green PCR assay. The assay was tested with clones from distinct nitrate-reducing groups and applied to various environmental samples. narG copy number was high ranging between 5.08×108 and 1.12×1011 copies per gram of dry weight of environmental sample. Environmental real-…
Comparison of different primer sets for use in Automated Ribosomal Intergenic Spacer Analysis of complex bacterial communities.
2004
ABSTRACT ITSF and ITSReub, constituting a new primer set designed for the amplification of the 16S-23S rRNA intergenic transcribed spacers, have been compared with primer sets consisting of 1406F and 23Sr (M. M. Fisher and E. W. Triplett, Appl. Environ. Microbiol. 65:4630-4636, 1999) and S-D-Bact-1522-b-S-20 and L-D-Bact-132-a-A-18 (L. Ranjard et al., Appl. Environ. Microbiol. 67:4479-4487, 2001), previously proposed for automated ribosomal intergenic spacer analysis (ARISA) of complex bacterial communities. An agricultural soil and a polluted soil, maize silage, goat milk, a small marble sample from the façade of the Certosa of Pavia (Pavia, Italy), and brine from a deep hypersaline anoxi…
Functional and genomic diversity of methylotrophic Rhodocyclaceae: description of Methyloversatilis discipulorum sp. nov.
2015
Three strains of methylotrophic Rhodocyclaceae (FAM1T, RZ18-153 and RZ94) isolated from Lake Washington sediment samples were characterized. Based on phylogenetic analysis of 16S rRNA gene sequences the strains should be assigned to the genus Methyloversatilis. Similarly to other members of the family, the strains show broad metabolic capabilities and are able to utilize a number of organic acids, alcohols and aromatic compounds in addition to methanol and methylamine. The main fatty acids were 16:1ω7c (49–59 %) and 16:0 (32–29 %). Genomes of all isolates were sequenced, assembled and annotated in collaboration with the DOE Joint Genome Institute (JGI). Genome comparison revealed that the s…
Sediment diffusion method improves wastewater nitrogen removal in the receiving lake sediments
2018
Sediment microbes have a great potential to transform reactive N to harmless N2, thus decreasing wastewater nitrogen load into aquatic ecosystems. Here, we examined if spatial allocation of the wastewater discharge by a specially constructed sediment diffuser pipe system enhanced the microbial nitrate reduction processes. Full-scale experiments were set on two Finnish lake sites, Keuruu and Petäjävesi, and effects on the nitrate removal processes were studied using the stable isotope pairing technique. All nitrate reduction rates followed nitrate concentrations, being highest at the wastewater-influenced sampling points. Complete denitrification with N2 as an end-product was the main nitrat…
CH4 oxidation in a boreal lake during the development of hypolimnetic hypoxia
2020
AbstractFreshwater ecosystems represent a significant natural source of methane (CH4). CH4 produced through anaerobic decomposition of organic matter (OM) in lake sediment and water column can be either oxidized to carbon dioxide (CO2) by methanotrophic microbes or emitted to the atmosphere. While the role of CH4 oxidation as a CH4 sink is widely accepted, neither the magnitude nor the drivers behind CH4 oxidation are well constrained. In this study, we aimed to gain more specific insight into CH4 oxidation in the water column of a seasonally stratified, typical boreal lake, particularly under hypoxic conditions. We used 13CH4 incubations to determine the active CH4 oxidation sites and the …
Vulnerability of the North Water ecosystem to climate change
2021
High Arctic ecosystems and Indigenous livelihoods are tightly linked and exposed to climate change, yet assessing their sensitivity requires a long-term perspective. Here, we assess the vulnerability of the North Water polynya, a unique seaice ecosystem that sustains the world’s northernmost Inuit communities and several keystone Arctic species. We reconstruct mid-to-late Holocene changes in sea ice, marine primary production, and little auk colony dynamics through multi-proxy analysis of marine and lake sediment cores. Our results suggest a productive ecosystem by 4400–4200 cal yrs b2k coincident with the arrival of the first humans in Greenland. Climate forcing during the late Holocene, l…