Abstract:
:Riverine biofilms remain one of the least-studied habitats despite the significant increase in the examination of aquatic microbial communities in recent years. In this study, the dynamics of epilithic biofilm communities native on rocks from a low-order upland stream were examined over a period of 3 years. Spatial and temporal variations in bacterial communities were assessed using terminal restriction fragment length polymorphism, based on analysis of the 16S rRNA gene. In total, 108 epilithic biofilm samples were analysed and 170 different ribotypes were detected. A strong temporal gradient in ribotype composition was noticed, especially between samples collected in 2001 and those collected in 2002 and 2003, most likely reflecting interannual differences in weather conditions, such as temperature. A spatial gradient in ribotype composition, from upstream sites to the low-lying sites, was also evident and interpreted as an environmental variation gradient along the river course. Distinct biofilm communities consistently occurred at the first site along the river, which was significantly correlated to low pH. Temporal factors explained the highest degree of variation within the epilithic biofilms. Recurrent blooms of certain bacteria were noted within the system. Phylogenetic relationships of bacteria at one point in the river were determined using a cloning and sequencing approach, with Alphaproteobacteria dominating the community, followed by Cyanobacteria, Bacteroidetes and Betaproteobacteria.
journal_name
FEMS Microbiol Ecoljournal_title
FEMS microbiology ecologyauthors
Anderson-Glenna MJ,Bakkestuen V,Clipson NJdoi
10.1111/j.1574-6941.2008.00480.xsubject
Has Abstractpub_date
2008-06-01 00:00:00pages
407-18issue
3eissn
0168-6496issn
1574-6941pii
FEM480journal_volume
64pub_type
杂志文章abstract::Why should organisms cooperate with each other? Helping close relatives that are likely to share the same genes (kin selection) is one important explanation that is likely to apply across taxa. The production of metabolically costly extracellular iron-scavenging molecules (siderophores) by microorganisms is a cooperat...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章,评审
doi:10.1111/j.1574-6941.2007.00388.x
更新日期:2007-11-01 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::Nitrate reduction plays a key role in the biogeochemical dynamics and microbial ecology of coastal sediments. Potential rates of nitrate reduction were measured on undisturbed sediment slices from two eutrophic coastal environments using flow-through reactors (FTR). Maximum potential nitrate reduction rates ranged ove...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/j.1574-6941.2006.00155.x
更新日期:2006-11-01 00:00:00
abstract::Gradients in environmental conditions, including climate factors and resource availability, occur along mountain inclines, providing a 'natural laboratory' to explore their combined impacts on microbial distributions. Conflicting spatial patterns observed across elevation gradients in soil bacterial community structur...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1093/femsec/fiw253
更新日期:2017-03-01 00:00:00
abstract::Rice plants are the habitat for large and diverse populations of microbes, which play important roles on rice health and productivity. However, the response of microbiome on rice culm to water flooding is poorly understood. In this study, the bacterial community on non-flooded (RSA) and flooded (RSB) rice culms was in...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1093/femsec/fiz036
更新日期:2019-04-01 00:00:00
abstract::A total of 159 endophytic bacteria were isolated from surface-sterilized root nodules of wild perennial Glycyrrhiza legumes growing on 40 sites in central and northwestern China. Amplified fragment length polymorphism (AFLP) genomic fingerprinting and sequencing of partial 16S rRNA genes revealed that the collection m...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/j.1574-6941.2011.01198.x
更新日期:2012-01-01 00:00:00
abstract::Antimicrobial resistance is one of the most significant challenges facing the global medical community and can be attributed to the use and misuse of antibiotics. This includes use as growth promoters or for prophylaxis and treatment of bacterial infection in intensively farmed livestock from where antibiotics can ent...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1093/femsec/fiw159
更新日期:2016-10-01 00:00:00
abstract::Bacteria belonging to the genus Methylobacterium are characterized by being able to rely on methanol as a sole carbon and energy source and by presenting a more or less intense pink reddish pigmentation. These bacteria, also referred to as pink-pigmented methylotrophic bacteria (PPFMs), are common inhabitants of the p...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1016/S0168-6496(04)00003-0
更新日期:2004-03-01 00:00:00
abstract::Land plants directly contact soil through their roots. An enormous diversity of microbes dwelling in root-associated zones, including endosphere (inside root), rhizoplane (root surface) and rhizosphere (soil surrounding the root surface), play essential roles in ecosystem functioning and plant health. Rice is a staple...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1093/femsec/fiz040
更新日期:2019-05-01 00:00:00
abstract::Managed agricultural ecosystems are unique systems where crops and microbes are intrinsically linked. This study focuses on discerning microbiome successional patterns across all plant organs and tests for evidence of niche differentiation along temporal and spatial axes. Soybean plants were grown in an environmental ...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1093/femsec/fiaa206
更新日期:2021-01-08 00:00:00
abstract::Qualitative and quantitative changes of microbial communities in soil microcosms during bioremediation were determined throughout one year. The soil was contaminated with 0%, 2.5%, 5%, 10% (wt/wt) of petrochemical sludge containing polynuclear aromatic hydrocarbons. We analyzed the hydrocarbon concentration in the mic...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1016/j.femsec.2005.01.014
更新日期:2005-07-01 00:00:00
abstract::Microbial communities of ancient Mediterranean sapropels, buried sediment layers of high organic matter, were analyzed by most probable number (MPN) approaches. Mineral media containing different carbon sources in sub-millimolar concentrations were used. MPN numbers were elevated in sapropels and at the sediment surfa...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1016/j.femsec.2004.07.010
更新日期:2004-12-27 00:00:00
abstract::Plasmid pQBR55 ( approximately 149 kb) represents one of five (Groups I-V) genetically distinct transfer proficient, mercury resistance plasmid groups that have been observed in the phytosphere pseudomonad community at a single geographic location in Oxford, UK. A 4.9-kb HindIII fragment was cloned from pQBR55 (a Grou...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/j.1574-6941.2002.tb01010.x
更新日期:2002-11-01 00:00:00
abstract::Soil RNA and DNA were coextracted along a contamination gradient at a landfarming field with aged crude oil contamination to investigate pollution-dependent differences in 16S rRNA and rRNA gene pools. Microbial biomass correlated with nucleic acid yields as well as bacterial community change, indicating that the same...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/1574-6941.12376
更新日期:2014-10-01 00:00:00
abstract::A new fluorescence staining and flow cytometry protocol was developed to monitor several physiological states in biocontrol strain Pseudomonas fluorescens DR54 during storage survival in a stationary-phase culture, preparation of clay carrier for seed formulation, and establishment in a sugar beet spermosphere. The hi...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/j.1574-6941.2008.00631.x
更新日期:2009-03-01 00:00:00
abstract::The bacterium Pseudomonas aeruginosa is well known to have a remarkable adaptive capacity allowing it to colonise many environments. A recent study on environmental isolates from dental unit waterlines (DUWLs) hinted at a genetic clustering into two groups. Isolates from one of these groups, named cluster III, were sh...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1093/femsec/fix106
更新日期:2017-09-01 00:00:00
abstract::Methanogenic cultures were enriched from an air-dried rice field soil and incubated under anaerobic conditions at 30 degrees C with cellulose as substrate (ET1). The culture was then transferred and further incubated at either 15 degrees C (E15) or 30 degrees C (E30), to establish stable cultures that methanogenically...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/j.1574-6941.1999.tb00659.x
更新日期:1999-12-01 00:00:00
abstract::Investigations of the diversity of culturable yeasts at deep-sea hydrothermal sites have suggested possible interactions with endemic fauna. Samples were collected during various oceanographic cruises at the Mid-Atlantic Ridge, South Pacific Basins and East Pacific Rise. Cultures of 32 isolates, mostly associated with...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/j.1574-6941.2010.00881.x
更新日期:2010-07-01 00:00:00
abstract::Phytate-mineralizing rhizobacteria (PMR) perform an essential function for the mineralization of organic phosphorus but little is known about their ecology in soils and rhizosphere. In this study, PCR-based methods were developed for detection and quantification of the Bacillus β-propeller phytase (BPP) gene. Experime...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/j.1574-6941.2012.01480.x
更新日期:2013-02-01 00:00:00
abstract::The distribution of sulphate-reducing bacteria (SRBs) in three anaerobic sediments, one predominantly freshwater and low sulphate and two predominantly marine and high sulphate, on the River Tama, Tokyo, Japan, was investigated using 16S rRNA-targeted oligonucleotide probes. Hybridisation results and sulphate reductio...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/j.1574-6941.2001.tb00836.x
更新日期:2001-07-01 00:00:00
abstract::Rodent-associated Bartonella species are generally host-specific parasites in North America. Here evidence that Bartonella species can 'jump' between host species is presented. Northern grasshopper mice and other rodents were trapped in the western USA. A study of Bartonella infection in grasshopper mice demonstrated ...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/j.1574-6941.2007.00364.x
更新日期:2007-09-01 00:00:00
abstract::The physiological response of bacteria to temperature is critical for the regulation of biogeochemical processes on daily, seasonal, and inter-annual time scales. We investigated the temperature response of the marine sulfate-reducing bacterium Desulfobacterium autotrophicum strain HRM2. Growth experiments in a temper...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/j.1574-6941.2002.tb01030.x
更新日期:2002-12-01 00:00:00
abstract::Abstract Laboratory studies were carried out to assess the photosynthetic and nitrogen-fixing capabilities of the gliding, filamentous cyanobacterium Phormidium corallyticum. This species is found on coral reefs, and is one of the members of a pathogenic microbial consortium called black band disease of corals, a uniq...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1016/S0168-6496(03)00025-4
更新日期:2003-04-01 00:00:00
abstract::The aim of this work is to document the complex nutritional strategy developed by kleptoplastic intertidal foraminifera. We study the mixotrophic ability of a common intertidal foraminifer, Elphidium williamsoni, by (i) investigating the phylogenetic identity of the foraminiferal kleptoplasts, (ii) following their oxy...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1093/femsec/fiz046
更新日期:2019-05-01 00:00:00
abstract::The aim of this work was to relate depth profiles of prokaryotic community composition with geochemical processes in the deep subseafloor biosphere at two shallow-water sites on the Peru Margin in the Pacific Ocean (ODP Leg 201, sites 1228 and 1229). Principal component analysis of denaturing gradient gel electrophore...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/j.1574-6941.2006.00144.x
更新日期:2006-10-01 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::Metagenomics combined with 16S rRNA gene sequence analyses was applied to unveil the taxonomic composition and functional diversity of the farmed adult turbot gastrointestinal (GI) microbiome. Proteobacteria and Firmicutes which existed in both GI content and mucus were dominated in the turbot GI microbiome. 16S rRNA ...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/1574-6941.12174
更新日期:2013-12-01 00:00:00
abstract::Large amounts of epiphytic bacteria live on the leaf surfaces of submerged macrophytes in freshwater lakes. Despite their important roles in affecting host plant's health and biogeochemical cycling, knowledge about epiphytic bacteria assembly is not sufficient. We studied epiphytic bacteria on two cohabiting plant spe...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1093/femsec/fiaa025
更新日期:2020-04-01 00:00:00
abstract::Dissolved organic carbon (DOC) photochemical reactions establish important links between DOC and planktonic bacteria. We hypothesize that seasonal changes in DOC quality, related to the flood pulse, drive the effects of light-DOC interactions on uptake by planktonic bacteria uptake in clear-water Amazonian ecosystems....
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1111/j.1574-6941.2006.00028.x
更新日期:2006-04-01 00:00:00
abstract::The soil microbiome plays an important role in the establishment of weeds and invasive plants. They associate with microorganisms supporting their growth and health. Weed management strategies, like tillage and herbicide treatments, to control weeds generally alter soil structure going alongside with changes in the mi...
journal_title:FEMS microbiology ecology
pub_type: 杂志文章
doi:10.1093/femsec/fiw138
更新日期:2016-10-01 00:00:00