[Show abstract][Hide abstract] ABSTRACT: Methylobacter tundripaludum SV96T (ATCC BAA-1195) is a psychrotolerant aerobic methane-oxidizing gammaproteobacterium (Methylococcales, Methylococcaceae) living in High Arctic wetland soil. The strain was isolated from soil harvested in July 1996 close to the settlement Ny-Ålesund,
Svalbard, Norway (78°56′N, 11°53′E), and described as a novel species in 2006. The genome includes pmo and pxm operons encoding copper membrane monooxygenases (Cu-MMOs), genes required for nitrogen fixation, and the nirS gene implicated in dissimilatory nitrite reduction to NO but no identifiable inventory for further processing of nitrogen
oxides. These genome data provide the basis to investigate M. tundripaludum SV96, identified as a major player in the biogeochemistry of Arctic environments.
Full-text · Article · Jul 2011 · Journal of Bacteriology
[Show abstract][Hide abstract] ABSTRACT: The diazotrophic communities in a rice paddy field were characterized by a molecular polyphasic approach including DNA/RNA-DGGE
fingerprinting, real time RT-PCR analysis of nifH gene and the measurement of nitrogen fixation activities. The investigation was performed on a diurnal cycle and comparisons
were made between bulk and rhizosphere / root soil as well as between fertilized / unfertilized soils. Real time RT-PCR showed
no significant difference in the total quantity of nifH expression under the conditions investigated. The functional diversity and dynamics of the nifH gene expressing diazotroph community investigated using RT-PCR-DGGE revealed high diurnal variations, as well as variation
between different soil types. Most of the sequence types recovered from the DGGE gels and clone libraries clustered within
nifH Cluster I and III (65 different nifH sequences in total). Sequence types most similar to Azoarcus spp., Metylococcus spp., Rhizobium spp., Methylocystis spp., Desulfovibrio spp., Geobacter spp., Chlorobium spp., were abundant and indicate that these species may be responsible for the observed diurnal variation in the diazotrophic
community structure in these rice field samples. Previously described diazotrophic cyanobacterial genera in rice fields, such
as Nostoc and Cyanothece, were present in the samples but not detectable in RT-PCR assays.
[Show abstract][Hide abstract] ABSTRACT: Biological nitrogen fixation (BNF) is an important source of nitrogen input in many natural ecosystems. The rice production today depends on large amounts of chemical nitrogen fertilizer, which is an environmental hazard in rice producing areas. Better exploitation of BNF is one way to reduce the use of chemical nitrogen fertilizer in the future. In this study the active diazotrophic community was investigated in nitrogen fertilized and un-fertilized rice field soils in Fujian Province, southeast China by PCR-DGGE of nifH mRNA, and the potential community by PCR-DGGE of the nifH gene. A total of 45 sequences representing 33 different sequence types were recovered from the DGGE gels. The retrieved cDNA sequences representing the active population of diazotrophs both in fertilized and un-fertilized soils dispersed throughout the nifH clades (alpha-, beta- and gamma Proteobacteria, Firmicutes and Archaea). Thirteen of the sequence types were most closely related to Azoarcus endophytes indicating widespread associations between heterotrophic nitrogen fixing bacteria and rice (Oryza sativa). The majority of the 13 sequence types were identified from the cDNA samples, showing that the Azoarcus might be an important active nitrogen fixing diazotroph in the paddy field. None of the sequence types were closely related to cyanobacteria, nevertheless previous studies from the same area had documented the presence of cyanobacteira in rice fields. The lack of identified cyanobacteria might be due to template discrimination in the PCR reactions, or low abundance of cyanobacteria compared to heterotrophic nitrogen fixing bacteria.
Full-text · Article · May 2008 · Applied Soil Ecology
[Show abstract][Hide abstract] ABSTRACT: The aim of this study was to analyze a total euryarchaeal community at DNA and RNA levels in a Swedish barley field with relation to soil depth (0-10 and 20-30 cm layers), soil fraction (bulk soil and rhizosphere) and time (August and November sample collection). Amplification of 16S rRNA gene using the archaeal universal A2F and Euryarchaea specific EK510R/(EURY498) primer pair, combined with denaturing gradient gel electrophoresis (DGGE), revealed distinct differences between rDNA and rRNA DGGE profiles. The soil depth, time, or rhizosphere effects did not significantly influence Archaeal community structure. Surprisingly, sequence analysis of DGGE-derived amplicons revealed the presence of Euryarchaea as well as uncultured soil Crenarchaea affiliated with group 1. In agreement, sequence comparison analyses showed that the majority of uncultured Crenarchaea group 1 had almost 100% sequence complementarity to the 3' end of the EK510R/(EURY498) primer. Therefore, we propose that EK510R/(EURY498R) is a universal archaeal primer rather than a Euryarchaea specific SSUrRNA primer. Hence, considerable care should be taken during application of this primer in studies of euryarchaeal biodiversity in soil environments.
No preview · Article · May 2007 · Journal of Microbiological Methods
[Show abstract][Hide abstract] ABSTRACT: A Gram-negative, rod-shaped, non-motile, non-spore-forming, pink-pigmented bacterium, SV97T, was isolated from a wetland soil near Ny-Alesund, Svalbard Islands, Norway (78 degrees N). On the basis of 16S rRNA gene sequence similarity, strain SV97T was shown to belong to the Alphaproteobacteria and was highly related to a number of non-characterized Methylocystis strains with GenBank accession nos AJ458507 and AJ458502 (100 %) and AF177299, AJ458510, AJ458467, AJ458471, AJ431384, AJ458475, AJ458484, AJ458501 and AJ458466 (99 %). The most closely related type strains were Methylocystis parvus OBBP(T) (97.2 %) and Methylocystis echinoides IMET 10491T (97%). The closest related recognized species within the genus Methylosinus was Methylosinus sporium NCIMB 11126T (96.0% similarity). Chemotaxonomic and phenotypic data (C(18:1)omega8 as the major fatty acid, non-motile, no rosette formation) supported the affiliation of strain SV97T to the genus Methylocystis. The results of DNA-DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain SV97(T) from the two recognized Methylocystis species. Strain SV97T therefore represents a novel species, for which the name Methylocystis rosea sp. nov. is proposed, with the type strain SV97T (= DSM 17261T = ATCC BAA-1196T).
Full-text · Article · Apr 2006 · International Journal of Systematic and Evolutionary Microbiology
[Show abstract][Hide abstract] ABSTRACT: A Gram-negative, rod-shaped, non-motile, non-spore forming bacterium (SV96T) was isolated from wetland soil near Ny-Alesund, Svalbard. On the basis of 16S rRNA gene sequence similarity, strain SV96T was shown to belong to the Gammaproteobacteria, related to Methylobacter psychrophilus Z-0021T (99.1 %), Methylobacter luteus ATCC 49878T (97.3 %), Methylobacter marinus A45T (97.0 %) and Methylobacter whittenburyi ATCC 51738T (95.8 %); the closest related species within the genus Methylomicrobium with a validly published name was Methylomicrobium album ATCC 33003T (95.0 %). Chemotaxonomic data (including the major fatty acids: 16 : 1omega8, 16 : 1omega7 and 16 : 1omega5t) supported the affiliation of strain SV96T to the genus Methylobacter. The results of DNA-DNA hybridization, physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain SV96T from the four Methylobacter species mentioned above. Strain SV96T therefore represents a novel species, for which the name Methylobacter tundripaludum sp. nov. is proposed (type strain SV96T = DSM 17260T = ATCC BAA-1195T).
Full-text · Article · Feb 2006 · International Journal of Systematic and Evolutionary Microbiology
[Show abstract][Hide abstract] ABSTRACT: The methanotrophic community in arctic soil from the islands of Svalbard, Norway (78 degrees N) was analysed by combining group-specific PCR with PCR of the highly variable V3 region of the 16S rRNA gene and then by denaturing gradient gel electrophoresis (DGGE). Selected bands were sequenced for identification. The analyses were performed with DNA extracted directly from soil and from enrichment cultures at 10 and 20 degrees C. The two genera Methylobacter and Methylosinus were found in all localities studied. The DGGE band patterns were simple, and DNA fragments with single base differences were separated. The arctic tundra is a potential source of extensive methane emission due to climatic warming because of its large reservoirs of stored organic carbon. Higher temperatures due to climatic warming can cause increased methane production, and the abundance and activity of methane-oxidizing bacteria in the arctic soil may be important regulators for methane emission to the atmosphere.
No preview · Article · Nov 2003 · Canadian Journal of Microbiology
[Show abstract][Hide abstract] ABSTRACT: Abstract A new method for isolation of methane oxidising bacteria (methanotrophs) is presented. Soil samples from a wetland area and a landfill were plated on polycarbonate membranes, which were incubated in a methane-air atmosphere using a non-sterile soil suspension as the medium. The membrane acted as a permeable growth support. The membrane method resulted in selective growth conditions, which allowed isolation of methane oxidising bacteria. The method resulted in isolation of both type I and type II methanotrophs from natural wetland and landfill soils. The isolates obtained from the landfill were dominated by type II methanotrophs and included several isolates carrying the gene for soluble methane monooxygenase (sMMO). Repetitive element sequence-based PCR fingerprinting documented genotypic diversity at the strain level. The presented method is a promising tool for easy and rapid isolation of different indigenous methanotrophs from an environment of interest.