Abstract:
:We re-evaluated PCR primers targeting nirS, nirK and nosZ genes for denaturing gradient gel electrophoresis as a tool to survey denitrifying community composition in environmental samples. New primers for both nirS and nosZ were combined with existing primers, while for nirK the previously published F1aCu:R3Cu set was chosen for denaturing electrophoresis. All three sets yielded amplicons smaller than 500 bp and amplified the correct fragment in all environmental samples. The denaturing gradient gel electrophoresis worked satisfactorily for nirK and nosZ, but not for nirS. This was probably due to the multiple melting domains in this particular nirS fragment. From the excised and sequenced bands, only sequences related to the target genes were detected and tree analysis showed that the selected primers acted as broad range primers for each of the three genes. By use of the new nirS primers it was demonstrated that agricultural soil harbours a substantial diversity of nirS denitrifiers.
journal_name
FEMS Microbiol Ecoljournal_title
FEMS microbiology ecologyauthors
Throbäck IN,Enwall K,Jarvis A,Hallin Sdoi
10.1016/j.femsec.2004.04.011subject
Has Abstractpub_date
2004-09-01 00:00:00pages
401-17issue
3eissn
0168-6496issn
1574-6941pii
FEM401journal_volume
49pub_type
杂志文章abstract::High-elevation lakes in the tropics are subject to extreme environmental fluctuations and microbes may harbor a unique genomic repertoire, but their composition and diversity are largely unknown. Here, we compared the planktonic bacterial community composition (BCC) and diversity of three tropical lakes located in the...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1093/femsec/fiy004
更新日期:2018-03-01 00:00:00
abstract::Many studies demonstrate the importance of the commensal microbiomes to animal health and development. However, the initial community assembly process is poorly understood. It is unclear to what extent the hosts select for their commensal microbiota, whether stochastic processes contribute, and how environmental condi...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1093/femsec/fiaa163
更新日期:2020-09-01 00:00:00
abstract::In eastern Canada, climate change-related warming and increased precipitation may alter winter snow cover, with potential consequences for soil conditions, nitrogen (N) cycling, and microbes. We conducted a 2-year field study aimed at determining the influence of snow removal, snow accumulation, and ambient snow in a ...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1093/femsec/fiz073
更新日期:2019-07-01 00:00:00
abstract::Abstract The 16S rRNA sequence diversity of the euryarchaeal community in a predominately freshwater sediment at East Hill Bridge (EHB) on the River Colne estuary, Essex, UK was investigated and compared to that from marine sediments at the mouth of the river (Colne Point). The East Hill Bridge sediments appear to sup...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/j.1574-6941.2002.tb00902.x
更新日期:2002-01-01 00:00:00
abstract::Epsilonproteobacteria are widely distributed in marine, freshwater, and terrestrial environments, although most well-studied groups are from hydrothermal vents and the human intestinal tract. The environmental variables that control epsilonproteobacterial communities in sulfidic terrestrial environments, however, are ...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/j.1574-6941.2011.01231.x
更新日期:2012-02-01 00:00:00
abstract::Arctic peatlands store large stocks of organic carbon which are vulnerable to the climate change but their fate is uncertain. There is increasing evidence that a part of it will be lost as a result of faster microbial mineralization. We studied the vulnerability of 3500-5900 years old bare peat uplifted from permafros...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1093/femsec/fiw140
更新日期:2016-09-01 00:00:00
abstract::Filamentous Chloroflexi species are often present in activated sludge wastewater treatment plants in relatively low numbers, although bulking incidences caused by Chloroflexi filaments have been observed. A new species-specific gene probe for FISH was designed and using phylum-, subdivision-, morphotype 1851- and spec...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/j.1574-6941.2006.00251.x
更新日期:2007-03-01 00:00:00
abstract::Soil microbes are essential to the continued productivity of sustainably managed agroecosystems. In shade coffee plantations, the relationship between soil microbial composition, soil nutrient availability and coffee productivity have been demonstrated, but the effects of management on the composition of the soil micr...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1093/femsec/fiaa164
更新日期:2020-09-01 00:00:00
abstract::Because methane-oxidizing bacteria (MOB) are the only biological sink for the greenhouse gas methane, knowledge of the functioning of these bacteria in various ecosystems is needed to understand the dynamics observed in global methane emission. The activity of MOB is commonly assessed by methane oxidation assays. The ...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/j.1574-6941.2009.00782.x
更新日期:2010-01-01 00:00:00
abstract::A major obstacle in the molecular investigation of natural, especially oceanic, microbial cells is their adequate preservation for further land-based molecular analyses. Here, we examined the use of microwaves for cell fixation before high-speed flow cytometric sorting to define the metaproteomes and metagenomes of ke...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/j.1574-6941.2010.00927.x
更新日期:2010-10-01 00:00:00
abstract::The colonization efficacies of salivaricin A (SalA)-producing Streptococcus salivarius strains 20P3 and 5 were compared when given in milk to 219 children, using either 2-day or 9-day dosing regimens. Colonization levels overall were superior for strain 5, and the 9-day dosing schedule resulted in higher levels of bot...
journal_title:FEMS microbiology ecology
pub_type: 临床试验,杂志文章
doi:10.1111/j.1574-6941.2006.00228.x
更新日期:2007-03-01 00:00:00
abstract::Marine macroalgae are subjected to large numbers of bacteria in their environment. These bacteria have the potential to affect the health and ecology of algae in a variety of ways and can be both beneficial and harmful to the algae. Therefore, algae have likely evolved mechanisms to differentially regulate the growth ...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/j.1574-6941.2010.01005.x
更新日期:2011-02-01 00:00:00
abstract::High-temperature (>/=60 degrees C) synthetic food waste compost was examined by cultivation-dependent and -independent methods to determine predominant microbial populations. Fluorescent direct counts totaled 6.4 (+/-2.5)x10(10) cells gdw(-1) in a freeze-dried 74 degrees C compost sample, while plate counts for thermo...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/j.1574-6941.2001.tb00805.x
更新日期:2001-04-01 00:00:00
abstract::Biodiversity patterns have been successfully linked to many ecosystem functions, and microbial communities have been suspected to harbour a large amount of functionally redundant taxa. We manipulated the diversity of stream and lake water column bacterial communities and investigated how the reduction in diversity aff...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/1574-6941.12101
更新日期:2013-07-01 00:00:00
abstract::Current strategies to protect groundwater sources from microbial contamination (e.g., wellhead protection areas) rely upon natural attenuation of microorganisms between wells or springs and potential sources of contamination and are determined using average (macroscopic) groundwater flow velocities defined by Darcy's ...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章,评审
doi:10.1016/j.femsec.2004.02.018
更新日期:2004-07-01 00:00:00
abstract::We hypothesized that apparently non-antagonistic soil bacteria may contribute to suppression of fungi during competitive interactions with other bacteria. Four soil bacteria (Brevundimonas sp., Luteibacter sp., Pedobacter sp. and Pseudomonas sp.) that exhibited little or no visible antifungal activity on different aga...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/j.1574-6941.2006.00197.x
更新日期:2007-01-01 00:00:00
abstract::The impact of heavy metal contamination on soil bacterial communities was studied in soils amended for many years with sewage sludge contaminated with heavy metals to varying extents. At the broad level of resolution, DNA reassociation analysis indicated a dramatic decrease in bacterial diversity from 16{ omitted}000 ...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/j.1574-6941.1999.tb00652.x
更新日期:1999-11-01 00:00:00
abstract::We report first insights into a representative genome of rice cluster I (RC-I), a major group of as-yet uncultured methanogens. The starting point of our study was the methanogenic consortium MRE50 that had been stably maintained for 3 years by consecutive transfers to fresh medium and anaerobic incubation at 50 degre...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1016/j.femsec.2004.12.004
更新日期:2005-07-01 00:00:00
abstract::Stolotermes ruficeps is a widespread, primitive, lower termite occupying dead and decaying wood of many tree species in New Zealand's temperate forests. We identified core bacterial taxa involved in gut processes through combined DNA- and RNA (cDNA)-based pyrosequencing analysis of the 16S nucleotide sequence from fiv...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/1574-6941.12424
更新日期:2014-12-01 00:00:00
abstract::The relative genetic diversity of microcystin-producing Microcystis in the water and sediment of the Daechung Reservoir, Korea, was investigated over an entire year, including the cyanobacterial bloom season. The cells of potentially toxic Microcystis strains containing mcyJ genotypes and cells containing the genus-sp...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/j.1574-6941.2010.00947.x
更新日期:2010-10-01 00:00:00
abstract::Host-associated microbiomes shape and are shaped by myriad processes that ultimately delineate their symbiotic functions. Whereas a host's stable traits, such as its lineage, relate to gross aspects of its microbiome structure, transient factors, such as its varying physiological state, relate to shorter term, structu...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1093/femsec/fiaa090
更新日期:2020-06-01 00:00:00
abstract::The Pseudomonas genus, which includes environmental and pathogenic species, is known to present antibiotic resistances, and can receive resistance genes from multi-resistant enteric bacteria released into the environment via faecal rejects. This study was aimed to investigate the resistome of Pseudomonas populations t...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1093/femsec/fiaa008
更新日期:2020-02-01 00:00:00
abstract::A dietary deficiency in polyunsaturated fatty acids (PUFAs) and/or sterols can severely constrain growth and reproduction of invertebrate consumers. Single nutrients are potentially assigned to different physiological processes, for example to support defence mechanisms; therefore, lipid requirements of healthy and pa...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/1574-6941.12407
更新日期:2014-11-01 00:00:00
abstract::Extreme acidophiles (microorganisms with pH optima of < 3) can colonize and exploit subterranean environments, such as abandoned metal sulfide mines, that have the potential for developing widespread or isolated pockets of acidity. Although acidophiles can utilize a wide range of electron donors, inorganic materials (...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章,评审
doi:10.1111/j.1574-6941.2011.01293.x
更新日期:2012-07-01 00:00:00
abstract::Mimosa caesalpiniifolia Benth. is a legume native to the semi-arid region of Brazil, in the Northeast. Its successful adaptation to other locations, such as the Atlantic Forest in the Southeast region, may be related to its ability to establish symbiosis with nitrogen-fixing bacteria, especially β-rhizobia of the genu...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1093/femsec/fiz109
更新日期:2019-08-01 00:00:00
abstract::The second step of nitrification, the oxidation of nitrite to nitrate, is vital for the functioning of the nitrogen cycle, but our understanding of the ecological roles of the involved microorganisms is still limited. The known diversity of Nitrospira, the most widely distributed nitrite-oxidizing bacteria, has increa...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1093/femsec/fiu031
更新日期:2015-03-01 00:00:00
abstract::Most plants form symbiotic associations with arbuscular mycorrhizal fungi (AMF). AMF increase the uptake of plant nutrients by extending their extra-radical mycelium (ERM) in the soil where other groups of microorganisms may suppress the activity of the ERM. However, little is known about such suppression in natural s...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1093/femsec/fiz020
更新日期:2019-03-01 00:00:00
abstract::Pressure-resistant circulating systems were constructed to enable the investigation of attached and unattached microbial populations under in situ pressure (2.5 MPa), diversity, dissolved gas and chemistry conditions. Three parallel flow cell cabinets were configured to allow observation of the effect on microbial met...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/j.1574-6941.2012.01370.x
更新日期:2012-07-01 00:00:00
abstract::The most widely used methods for the estimation of the living/dead fractions of bacterial cells involve specific stains that are able to reveal membrane integrity. Here, we have compared two different probes (propidium iodide and ethidium homodimer-2) that have different molecular weights and steric hindrance effects....
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/j.1574-6941.2005.00042.x
更新日期:2006-03-01 00:00:00
abstract::Ammonia oxidizers catalyze the first step of nitrification. Combined microbial nitrification-denitrification activities are essential for the removal of excess nitrogen from water bodies. In sandy streambeds, bed form structures are created by water flow and lead to the creation of heterogeneous microenvironments. The...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/1574-6941.12385
更新日期:2014-10-01 00:00:00