Improved isolation strategies allowed the phenotypic differentiation of two Nitrospira strains from widespread phylogenetic lineages.


: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 increased remarkably by analyses of 16S rRNA and functional gene sequences. However, only few representatives could be brought into laboratory cultures so far. In this study, two Nitrospira from activated sludge were isolated using novel approaches together with established methods. Highly enriched 'Candidatus Nitrospira defluvii' was separated from concomitant heterotrophs by taking advantage of its resistance against ampicillin and acriflavine. Beside this member of lineage I, a novel species of lineage II, named N. lenta, was initially enriched at 10°C and finally purified by using optical tweezers. The tolerance to elevated nitrite levels was much higher in N. defluvii than in the more fastidious N. lenta and was accompanied by pronounced biofilm formation. Phylogenetic classification of 12 additional enrichments indicated that Nitrospira lineage I is common in extreme and moderate ecosystems like lineage II. The new cultures will help to explore physiological and genomic differences affecting niche separation between members of this highly diverse genus.


FEMS Microbiol Ecol


Nowka B,Off S,Daims H,Spieck E




Has Abstract


2015-03-01 00:00:00












  • Identification of the bacterial community involved in methane-dependent denitrification in activated sludge using DNA stable-isotope probing.

    abstract::Methane is used as an alternative carbon source in the denitrification of wastewater lacking organic carbon sources because it is nontoxic and may be efficiently produced by anaerobic biological processes. Methane-dependent denitrification (MDD) in the presence of oxygen requires the co-occurrence of methanotrophy and...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章


    authors: Osaka T,Ebie Y,Tsuneda S,Inamori Y

    更新日期:2008-06-01 00:00:00

  • Complementary pathways of dissolved organic carbon removal pathways in clear-water Amazonian ecosystems: photochemical degradation and bacterial uptake.

    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


    authors: Amado AM,Farjalla VF,Esteves Fde A,Bozelli RL,Roland F,Enrich-Prast A

    更新日期:2006-04-01 00:00:00

  • On-board flow cytometric observation of picoplankton community structure in the East China Sea during the fall of different years.

    abstract::On-board flow cytometric determinations of picoplankton abundance (i.e. Synechococcus spp., Prochlorococcus spp., picoeukaryotes and also heterotrophic bacteria) were obtained in the East China Sea in fall of 2000 and 2003. The average abundances of Synechococcus, Prochlorococcus, picoeukaryotes and heterotrophic bact...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章


    authors: Pan LA,Zhang LH,Zhang J,Gasol JM,Chao M

    更新日期:2005-04-01 00:00:00

  • Endolithic photosynthetic communities within ancient and recent travertine deposits in Yellowstone National Park.

    abstract::Molecular and culture based methods were used to survey endolithic, photosynthetic communities from hot spring-formed travertine rocks of various ages, ranging from<10 to greater than 300,000 years. Much of this travertine contained a 1-3-mm-thick greenish band composed mainly of cyanobacteria 1-5 mm below the rock su...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章


    authors: Norris TB,Castenholz RW

    更新日期:2006-09-01 00:00:00

  • Community-specific pH response of denitrification: experiments with cells extracted from organic soils.

    abstract::Denitrifying prokaryotes are phylogenetically and functionally diverse. Little is known about the relationship between soil denitrifier community composition and functional traits. We extracted bacterial cells from three cultivated peat soils with contrasting native pH by density gradient centrifugation and investigat...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章


    authors: Dörsch P,Braker G,Bakken LR

    更新日期:2012-02-01 00:00:00

  • Growth, lipid accumulation, and fatty acid composition in obligate psychrophilic, facultative psychrophilic, and mesophilic yeasts.

    abstract::Obligate psychrophilic, facultative psychrophilic, and mesophilic yeasts were cultured in a carbon-rich medium at different temperatures to investigate whether growth parameters, lipid accumulation, and fatty acid (FA) composition were adaptive and/or acclimatory responses. Acclimation of facultative psychrophiles and...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章


    authors: Rossi M,Buzzini P,Cordisco L,Amaretti A,Sala M,Raimondi S,Ponzoni C,Pagnoni UM,Matteuzzi D

    更新日期:2009-09-01 00:00:00

  • Protective efficacy of probiotic alone or in conjunction with a prebiotic in Salmonella-induced liver damage.

    abstract::In view of the increasing interest in the bioecological and nutritional control of diseases, use of probiotics alone or in combination with prebiotics (synbiotics) appears as a therapeutic option for various diseases. In this study, an attempt was made to explore the protective potential of Lactobacillus acidophilus a...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章


    authors: Rishi P,Mavi SK,Bharrhan S,Shukla G,Tewari R

    更新日期:2009-08-01 00:00:00

  • Transcriptomics analysis of the metabolic mechanisms of iron reduction induced by sulfate reduction mediated by sulfate-reducing bacteria.

    abstract::Sulfate-reducing bacteria (SRB) play an important role in sulfur, iron, and carbon cycling. The majority of studies have illustrated the role of SRB in biogeochemical cycling in pure cultures. In this study, we established three SRB enrichment cultures (designated HL, NB, and WC) from different paddy soils and conduct...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章


    authors: Li GX,Bao P

    更新日期:2021-01-13 00:00:00

  • Fine-scale spatial patterns in microbial community composition in an acid mine drainage.

    abstract::Microbial community composition is essential for aquatic ecosystem functions and has been explored across diverse environments and various spatial scales. However, documented patterns are often based on samples from spatially/geographically separated locations or sites. Here, we define sampling volume as spatial scale...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章


    authors: Liang JL,Li XJ,Shu HY,Wang P,Kuang JL,Liu J,Zhang MM,Shu WS,Huang LN

    更新日期:2017-10-01 00:00:00

  • Whole genome sequencing and antibiotic diffusion assays, provide new insight on drug resistance in the genus Pedobacter.

    abstract::A total of four strains of the 'environmental superbug' Pedobacter isolated from sludge produced at Norwegian drinking water treatment plants, were characterized by whole genome sequencing and antibiotic susceptibility assays. As with previous studies on members of this genus, we found that the isolates were multi-dru...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章


    authors: Ullmann IF,Nygaard AB,Tunsjø HS,Charnock C

    更新日期:2020-06-01 00:00:00

  • Yeasts from Macrobrachium amazonicum: a focus on antifungal susceptibility and virulence factors of Candida spp.

    abstract::In the present study, it was sought to compare yeast microbiota of wild and captive Macrobrachium amazonicum and evaluate the antifungal susceptibility and production of virulence factors by the recovered isolates of Candida spp. Additionally, cultivation water was monitored for the presence of fungi. Overall, 26 yeas...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章


    authors: Brilhante RS,Paiva MA,Sampaio CM,Teixeira CE,Castelo-Branco DS,Leite JJ,Moreira CA,Silva LP,Cordeiro RA,Monteiro AJ,Sidrim JJ,Rocha MF

    更新日期:2011-05-01 00:00:00

  • Carbohydrate active enzymes are affected by diet transition from milk to solid food in infant gut microbiota.

    abstract::Infants experience a dramatic change in their food in the first year after birth when they shift from breast milk to solid food. This results in a large change in presence of indigestible polysaccharides, a primary energy resource of gut microbes. How the gut microbiota adapts to this dietary shift has not been well e...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章


    authors: Ye L,Das P,Li P,Ji B,Nielsen J

    更新日期:2019-11-01 00:00:00

  • Lysogens and free viruses in fresh, brackish, and marine waters: a Bayesian analysis.

    abstract::A yearlong study was conducted to determine factors that affect the abundance and distribution of lysogens and free viruses at fresh-, brackish-, and saltwater stations in Newport Bay, CA. The viral and bacterial abundance were highest in the freshwater (average 1.1 x 10(8) and 1.1 x 10(7) mL(-1), respectively) and lo...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章


    authors: Choi S,Jeliazkov I,Jiang SC

    更新日期:2009-08-01 00:00:00

  • Characterization and virulence retention of viable but nonculturable Vibrio harveyi.

    abstract::Vibrio harveyi has been reported to enter into a viable but nonculturable (VBNC) state. Two clinical V. harveyi strains, SF1 and CW2, and the type strain, VIB295(T), were incubated in sterilized seawater at 4 degrees C. Plate counts in these strains declined to undetectable levels (<0.1 CFU mL(-1)) within 69, 67 and 6...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章


    authors: Sun F,Chen J,Zhong L,Zhang XH,Wang R,Guo Q,Dong Y

    更新日期:2008-04-01 00:00:00

  • Thermus diversity and strain loss during enrichment.

    abstract::The diversity of Thermus strains isolated from each of two New Zealand hot pools was examined by isolating partial SSU (16S) rRNA genes and comparing their sequences. Although all of the sequences were similar, several variants were found in each pool. Standard methods for the enrichment of Thermus were then carried o...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章


    authors: Saul DJ,Reeves RA,Morgan HW,Bergquist PL

    更新日期:1999-10-01 00:00:00

  • Microform-related community patterns of methane-cycling microbes in boreal Sphagnum bogs are site specific.

    abstract::Vegetation and water table are important regulators of methane emission in peatlands. Microform variation encompasses these factors in small-scale topographic gradients of dry hummocks, intermediate lawns and wet hollows. We examined methane production and oxidization among microforms in four boreal bogs that showed m...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章


    authors: Juottonen H,Kotiaho M,Robinson D,Merilä P,Fritze H,Tuittila ES

    更新日期:2015-09-01 00:00:00

  • Factors influencing bacterial dynamics along a transect from supraglacial runoff to proglacial lakes of a high Arctic glacier [corrected].

    abstract::Bacterial production in glacial runoff and aquatic habitats along a c. 500 m transect from the ablation area of a Svalbard glacier (Midre Lovénbreen, 79 degrees N, 12 degrees E) down to a series of proglacial lakes in its forefield were assessed. In addition, a series of in situ experiments were conducted to test how ...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章


    authors: Mindl B,Anesio AM,Meirer K,Hodson AJ,Laybourn-Parry J,Sommaruga R,Sattler B

    更新日期:2007-02-01 00:00:00

  • Ecological physiology of the black band disease cyanobacterium Phormidium corallyticum.

    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


    authors: Richardson LL,Kuta KG

    更新日期:2003-04-01 00:00:00

  • In vitro suppression of fungi caused by combinations of apparently non-antagonistic soil bacteria.

    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


    authors: de Boer W,Wagenaar AM,Klein Gunnewiek PJ,van Veen JA

    更新日期:2007-01-01 00:00:00

  • Antibiotic resistance patterns of Pseudomonas spp. isolated from faecal wastes in the environment and contaminated surface water.

    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


    authors: Camiade M,Bodilis J,Chaftar N,Riah-Anglet W,Gardères J,Buquet S,Ribeiro AF,Pawlak B

    更新日期:2020-02-01 00:00:00

  • Structure and dynamics of microbiomes associated with the marine sponge Tedania sp. during its life cycle.

    abstract::Tedania sp. is a dominant sponge that is ubiquitous along the southeast coast of China. High-throughput sequencing and transmission electron microscopy were used to describe a detailed profile of sponge-associated microbiomes at seven life stages: adult, embryo-containing spawning adult, embryo, pre-competent larva at...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章


    authors: Wu S,Ou H,Liu T,Wang D,Zhao J

    更新日期:2018-05-01 00:00:00

  • Coral mucus-associated bacteria: a possible first line of defense.

    abstract::Interactions among microorganisms found in coral mucus can be either symbiotic or competitive. It has been hypothesized that microbial communities found on the surface of coral play a role in coral holobiont defense, possibly through production of antimicrobial substances. Selected microorganisms isolated from the muc...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章


    authors: Shnit-Orland M,Kushmaro A

    更新日期:2009-03-01 00:00:00

  • Biphasic kinetics of a methanotrophic community is a combination of growth and increased activity per cell.

    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


    authors: Steenbergh AK,Meima MM,Kamst M,Bodelier PL

    更新日期:2010-01-01 00:00:00

  • Linking changes in snow cover with microbial nitrogen cycling functional gene abundance and expression in agricultural soil.

    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


    authors: Brin LD,Goyer C,Zebarth BJ,Burton DL,Chantigny MH

    更新日期:2019-07-01 00:00:00

  • Drivers of richness and community composition of fungal endophytes of tree seeds.

    abstract::Recent studies revealed a high diversity of fungal endophytes in traded tree seeds, including potential plant pathogens. The factors determining richness and composition of seed mycobiomes are poorly understood, but might be an important determinant for tree health. We assessed the relative impact of host identity, si...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章


    authors: Franić I,Eschen R,Allan E,Hartmann M,Schneider S,Prospero S

    更新日期:2020-09-01 00:00:00

  • Temporal changes in the microbiome of stingless bee foragers following colony relocation.

    abstract::Maintaining beneficial interactions with microbial symbionts is vital for animal health. Yet, for social insects, the stability of microbial associations within and between cohorts is largely unknown. We investigated temporal changes in the microbiomes of nine stingless bee (Tetragonula carbonaria) colonies at seven t...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章


    authors: Hall MA,Brettell LE,Liu H,Nacko S,Spooner-Hart R,Riegler M,Cook JM

    更新日期:2020-12-30 00:00:00

  • Amoeba-resisting bacteria found in multilamellar bodies secreted by Dictyostelium discoideum: social amoebae can also package bacteria.

    abstract::Many bacteria can resist phagocytic digestion by various protozoa. Some of these bacteria (all human pathogens) are known to be packaged in multilamellar bodies produced in the phagocytic pathway of the protozoa and that are secreted into the extracellular milieu. Packaged bacteria are protected from harsh conditions,...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章


    authors: Paquet VE,Charette SJ

    更新日期:2016-03-01 00:00:00

  • Abundance and activity of nitrate reducers in an arable soil are more affected by temporal variation and soil depth than by elevated atmospheric [CO2].

    abstract::Elevated atmospheric carbon dioxide concentrations ([CO(2) ]) might change the abundance and the function of soil microorganisms in the depth profile of agricultural soils by plant-mediated reactions. The seasonal pattern of abundance and activity of nitrate-reducing bacteria was studied in a Mini-FACE experiment plan...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章


    authors: Marhan S,Philippot L,Bru D,Rudolph S,Franzaring J,Högy P,Fangmeier A,Kandeler E

    更新日期:2011-05-01 00:00:00

  • A cold-loving crenarchaeon is a substantial part of a novel microbial community in cold sulphidic marsh water.

    abstract::In this paper, we report the identification and first characterization of a novel, cold-loving, prokaryotic community thriving among white-greenish 'streamers' in the cold (c. 10 degrees C) sulphurous water of the marsh Sippenauer Moor near Regensburg, Bavaria, Germany. It consists of the bacterial genus Thiothrix, th...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章


    authors: Koch M,Rudolph C,Moissl C,Huber R

    更新日期:2006-07-01 00:00:00

  • Structure and activity of the denitrifying community in a maize-cropped field fertilized with composted pig manure or ammonium nitrate.

    abstract::One alternative to mineral fertilization is to use organic fertilizers. Our aim was to compare the impacts of 7-year applications of composted pig manure and ammonium nitrate on the structure and activity of the denitrifying community. Mineralization and organization of N, denitrification rates and N2O/N2 ratio were a...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章


    authors: Dambreville C,Hallet S,Nguyen C,Morvan T,Germon JC,Philippot L

    更新日期:2006-04-01 00:00:00