The biogeography of ammonia-oxidizing bacterial communities in soil.

Abstract:

:Although ammonia-oxidizing bacteria (AOB) are likely to play a key role in the soil nitrogen cycle, we have only a limited understanding of how the diversity and composition of soil AOB communities change across ecosystem types. We examined 23 soils collected from across North America and used sequence-based analyses to compare the AOB communities in each of the distinct soils. Using 97% 16S rRNA sequence similarity groups, we identified only 24 unique AOB phylotypes across all of the soils sampled. The majority of the sequences collected were in the Nitrosospira lineages (representing 80% of all the sequences collected), and AOB belonging to Nitrosospira cluster 3 were particularly common in our clone libraries and ubiquitous across the soil types. Community composition was highly variable across the collected soils, and similar ecosystem types did not always harbor similar AOB communities. We did not find any significant correlations between AOB community composition and measures of N availability. From the suite of environmental variables measured, we found the strongest correlation between temperature and AOB community composition; soils exposed to similar mean annual temperatures tended to have similar AOB communities. This finding is consistent with previous studies and suggests that temperature selects for specific AOB lineages. Given that distinct AOB taxa are likely to have unique functional attributes, the biogeographical patterns exhibited by soil AOB may be directly relevant to understanding soil nitrogen dynamics under changing environmental conditions.

journal_name

Microb Ecol

journal_title

Microbial ecology

authors

Fierer N,Carney KM,Horner-Devine MC,Megonigal JP

doi

10.1007/s00248-009-9517-9

subject

Has Abstract

pub_date

2009-08-01 00:00:00

pages

435-45

issue

2

eissn

0095-3628

issn

1432-184X

journal_volume

58

pub_type

杂志文章
  • Ectoparasite Activity During Incubation Increases Microbial Growth on Avian Eggs.

    abstract::While direct detrimental effects of parasites on hosts are relatively well documented, other more subtle but potentially important effects of parasitism are yet unexplored. Biological activity of ectoparasites, apart from skin injuries and blood-feeding, often results in blood remains, or parasite faeces that accumula...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/s00248-017-1140-6

    authors: Tomás G,Martín-Gálvez D,Ruiz-Castellano C,Ruiz-Rodríguez M,Peralta-Sánchez JM,Martín-Vivaldi M,Soler JJ

    更新日期:2018-08-01 00:00:00

  • Microbial production, enzyme activity, and carbon turnover in surface sediments of the Hudson River estuary.

    abstract::The detrital food web is a major nexus of energy flow in nearly all aquatic ecosystems. Energy enters this nexus by microbial assimilation of detrital carbon. To link microbiological variables with ecosystem process, it is necessary to understand the regulatory hierarchy that controls the distribution of microbial bio...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/BF00172569

    authors: Sinsabaugh RL,Findlay S

    更新日期:1995-09-01 00:00:00

  • Inhibition of the predatory activity ofBdellovibrio by various environmental pollutants.

    abstract::The predatory activity of bdellovibrios is affected by various environmental pollutants such as detergents, heavy metals, and pesticides. This was shown in a two-membered system ofBdellovibrio andPhotobacterium, in which the effect of the predator on the bioluminescence of the prey indicated the activity of the former...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/BF02032492

    authors: Varon M,Shilo M

    更新日期:1981-06-01 00:00:00

  • Microbial community structure and dynamics in the largest natural French lake (Lake Bourget).

    abstract::We investigated the dynamics and diversity of heterotrophic bacteria, autotrophic and heterotrophic flagellates, and ciliates from March to July 2002 in the surface waters (0-50 m) of Lake Bourget. The heterotrophic bacteria consisted mainly of "small" cocci, but filaments (>2 microm), commonly considered to be grazin...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/s00248-004-0230-4

    authors: Comte J,Jacquet S,Viboud S,Fontvieille D,Millery A,Paolini G,Domaizon I

    更新日期:2006-07-01 00:00:00

  • Comparisons of the fungal and protistan communities among different marine sponge holobionts by pyrosequencing.

    abstract::To date, the knowledge of eukaryotic communities associated with sponges remains limited compared with prokaryotic communities. In a manner similar to prokaryotes, it could be hypothesized that sponge holobionts have phylogenetically diverse eukaryotic symbionts, and the eukaryotic community structures in different sp...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/s00248-014-0393-6

    authors: He L,Liu F,Karuppiah V,Ren Y,Li Z

    更新日期:2014-05-01 00:00:00

  • PAH degradation capacity of soil microbial communities--does it depend on PAH exposure?

    abstract::Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous pollutants of the environment. But is their microbial degradation equally wide in distribution? We estimated the PAH degradation capacity of 13 soils ranging from pristine locations (total PAHs approximately 0.1 mg kg(-1)) to heavily polluted industrial sites (tot...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/s00248-005-0022-5

    authors: Johnsen AR,Karlson U

    更新日期:2005-11-01 00:00:00

  • A Polyphasic Approach for Assessing Eco-System Connectivity Demonstrates that Perturbation Remodels Network Architecture in Soil Microcosms.

    abstract::Network analysis was used to show changes in network attributes by analyzing the relations among the main soil microbial groups in a potted tomato soil inoculated with arbuscular mycorrhizal fungus, treated with low doses of Mentha spicata essential oil, or both, and then exposed to tenfold higher oil addition (stress...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/s00248-019-01367-x

    authors: Stamou GP,Monokrousos N,Gwynn-Jones D,Whitworth DE,Papatheodorou EM

    更新日期:2019-11-01 00:00:00

  • Fungi from Admiralty Bay (King George Island, Antarctica) Soils and Marine Sediments.

    abstract::Extreme environments such as the Antarctic can lead to the discovery of new microbial taxa, as well as to new microbial-derived natural products. Considering that little is known yet about the diversity and the genetic resources present in these habitats, the main objective of this study was to evaluate the fungal com...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/s00248-018-1217-x

    authors: Wentzel LCP,Inforsato FJ,Montoya QV,Rossin BG,Nascimento NR,Rodrigues A,Sette LD

    更新日期:2019-01-01 00:00:00

  • Haloarchaea from the Andean Puna: Biological Role in the Energy Metabolism of Arsenic.

    abstract::Biofilms, microbial mats, and microbialites dwell under highly limiting conditions (high salinity, extreme aridity, pH, and elevated arsenic concentration) in the Andean Puna. Only recent pioneering studies have described the microbial diversity of different Altiplano lakes and revealed their unexpectedly diverse micr...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/s00248-018-1159-3

    authors: Ordoñez OF,Rasuk MC,Soria MN,Contreras M,Farías ME

    更新日期:2018-10-01 00:00:00

  • On describing microbial growth kinetics from continuous culture data: Some general considerations, observations, and concepts.

    abstract::Analysis of continuous culture methodology suggests that this potentially powerful tool for kinetic analysis can be improved by minimizing several inherent shortcomings. Medium background substrates - organic carbon, phosphate, and manganese - were shown to dominate kinetic observations at concentrations below chemica...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/BF02011647

    authors: Law AT,Robertson BR,Dunker SS,Button DK

    更新日期:1975-12-01 00:00:00

  • Measurement of Electron Transport System (ETS) activity in soil.

    abstract::Electron transport system (ETS) activity was measured in amended and nonamended soil by measuring the reduction of 2-(p-iodophenyl)-3-(p-nitrophenyl)-5-phenyl tetrazolium chloride (INT) to iodonitrotetrazolium formazan (INT-formazan), which can be easily extracted with methanol without interference from other compound...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/BF02010449

    authors: Trevors JT,Mayfield CI,Inniss WE

    更新日期:1982-10-01 00:00:00

  • Response of induced perturbation on replicating β-proteobacterial ammonia-oxidizing populations in soil.

    abstract::The short-term response of induced perturbation by 4-ethylphenol on β-proteobacterial ammonia oxidizers (β-AOB) was investigated in two soils with initial differences in community structure. The hypotheses were that short-term effects of a disturbance of the AOB community is best monitored by specifically looking at t...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/s00248-011-9970-0

    authors: Nyberg KA,Enwall K,Schnürer A,Sundh I,Hallin S

    更新日期:2012-04-01 00:00:00

  • Bacterial population association with phytoplankton cultured in a bivalve hatchery.

    abstract::Bacterial populations association with phytoplankton cultures used as food for bivalve larvae were enumerated and identified from their partial 16S rDNA gene sequences. Microalgae were provided from different European hatcheries during the larval production season. Average concentration (direct counts) of bacteria ran...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/s00248-003-2031-6

    authors: Nicolas JL,Corre S,Cochard JC

    更新日期:2004-10-01 00:00:00

  • Effects of temperature and turbulence on the predator-prey interactions between a heterotrophic flagellate and a marine bacterium.

    abstract::Biotic and abiotic factors can influence interactions between microbial grazers and their prey, thus impacting both the cycling of biogenic carbon within the surface layer of the ocean and the export of carbon to the deep ocean and higher trophic levels. In this study, microcosm experiments were used to evaluate the c...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/s00248-002-1058-4

    authors: Delaney MP

    更新日期:2003-03-01 00:00:00

  • The significance of viruses to mortality in aquatic microbial communities.

    abstract::A variety of approaches including enumeration of visibly infected microbes, removal of viral particles, decay of viral infectivity, and measurements of viral production rates have been used to infer the impact of viruses on microbial mortality. The results are surprisingly consistent and suggest that, on average, abou...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/BF00166813

    authors: Suttle CA

    更新日期:1994-09-01 00:00:00

  • Shifts in microbial community composition following surface application of dredged river sediments.

    abstract::Sediment input to the Illinois River has drastically decreased river depth and reduced habitats for aquatic organisms. Dredging is being used to remove sediment from the Illinois River, and the dredged sediment is being applied to the surface of a brownfield site in Chicago with the goal of revegetating the site. In o...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/s00248-008-9410-y

    authors: Baniulyte D,Favila E,Kelly JJ

    更新日期:2009-01-01 00:00:00

  • Optimization of procedures for the recovery of heterotrophic bacteria from marine sediments.

    abstract::A study was undertaken of the various factors affecting the recovery of heterotrophic bacteria from marine sediments. The dilution medium and culture medium were found to be of great importance in the recovery of heterotrophic colony forming units (CFU). Statistical analysis of the total viable counts obtained under t...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/BF02512390

    authors: Litchfield CD,Rake JB,Zindulis J,Watanabe RT,Stein DJ

    更新日期:1974-12-01 00:00:00

  • Competition of two suspension-feeding protozoan populations for a growing bacterial population in continuous culture.

    abstract::Mathematical studies for ecosystems involving 2 predators competing for a growing prey population have shown that the 2 competitors can coexist in a state of sustained oscillations for a range of values of the system parameters. For the case of 1 suspension-feeding protozoan population, recent experimental observation...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/BF02011595

    authors: Baltzis BC,Fredrickson AG

    更新日期:1984-03-01 00:00:00

  • The Combined Effect of Temperature and Host Clonal Line on the Microbiota of a Planktonic Crustacean.

    abstract::Host-associated microbiota vary across host individuals and environmental conditions, but the relative importance of their genetic background versus their environment is difficult to disentangle. We sought to experimentally determine the factors shaping the microbiota of the planktonic Crustacean, Daphnia magna. We us...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/s00248-017-1126-4

    authors: Sullam KE,Pichon S,Schaer TMM,Ebert D

    更新日期:2018-08-01 00:00:00

  • Quantifying Ostreid herpesvirus (OsHV-1) genome copies and expression during transmission.

    abstract::Understanding the pathogenic potential of a new pathogen strain or a known pathogen in a new locale is crucial for management of disease in both wild and farmed animals. The Ostreid herpesvirus-1 (OsHV-1), a known pathogen of early-life-stage Pacific oysters, Crassostrea gigas, has been associated with mortalities of ...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/s00248-011-9937-1

    authors: Burge CA,Friedman CS

    更新日期:2012-04-01 00:00:00

  • Migration of Paraburkholderia terrae BS001 Along Old Fungal Hyphae in Soil at Various pH Levels.

    abstract::The movement of bacterial cells along with fungal hyphae in soil (the mycosphere) has been reported in several previous studies. However, how local soil conditions affect bacterial migration direction in the mycosphere has not been extensively studied. Here, we investigated the influence of two soil parameters, pH and...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/s00248-017-1137-1

    authors: Yang P,Oliveira da Rocha Calixto R,van Elsas JD

    更新日期:2018-08-01 00:00:00

  • Immunofluorescence detection of the denitrifying strain Pseudomonas stutzeri (ATCC 14405) in seawater and intertidal sediment environments.

    abstract::A strain-specific immunofluorescence assay for enumeration of a marine denitrifying bacterium was developed and applied in the marine environment. The polyclonal antiserum for Pseudomonas stutzeri (ATCC 14405) did not react with other pseudomonads, other heterotrophs, or autotrophic nitrifying strains. The abundance o...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/BF00171890

    authors: Ward BB,Cockcroft AR

    更新日期:1993-05-01 00:00:00

  • Vibrio harveyi associated with Aglaophenia octodonta (Hydrozoa, Cnidaria).

    abstract::A previously unknown association between a luminous bacterium, Vibrio harveyi, and a benthic hydrozoan, Aglaophenia octodonta, is described. Aglaophenia hydrocladia showed a clear fluorescence in the folds along the hydrocaulus and at the base of the hydrotheca, suggesting the presence of luminous bacteria. This hypot...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/s00248-006-9010-7

    authors: Stabili L,Gravili C,Piraino S,Boero F,Alifano P

    更新日期:2006-11-01 00:00:00

  • Year, Location, and Variety Impact on Grape-, Soil-, and Leaf-Associated Fungal Microbiota of Arkansas-Grown Table Grapes.

    abstract::With the recent advancement of next-generation sequencing methods, there has been an increase in studies on identification of vineyard microbiota, winery-associated microbiota, and microbiota in wine fermentation. However, there have been few studies investigating the fungal microbiota of table grapes which present di...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/s00248-021-01698-8

    authors: Cureau N,Threlfall R,Savin M,Marasini D,Lavefve L,Carbonero F

    更新日期:2021-01-29 00:00:00

  • Diversity of Geobacteraceae species inhabiting metal-polluted freshwater lake sediments ascertained by 16S rDNA analyses.

    abstract::The abundance, distribution, and phylogenetic diversity of members of the Fe(III)-reducing family Geobacteraceae were studied along a gradient of metal contaminants in Lake Coeur d'Alene, Idaho. Partial 16S rRNA gene fragments were amplified by PCR using primers directed toward conserved regions of the gene within the...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/s00248-005-8002-3

    authors: Cummings DE,Snoeyenbos-West OL,Newby DT,Niggemyer AM,Lovley DR,Achenbach LA,Rosenzweig RF

    更新日期:2003-08-01 00:00:00

  • The Microbial Food Web in the Recently Flooded Sep Reservoir: Diel Fluctuations in Bacterial Biomass and Metabolic Activity in Relation to Phytoplankton and Flagellate Grazers.

    abstract::The spatial distribution of the bacterial biomass and production and of potential heterotrophic activity (PHA) were measured every 4 h between 23 July (10:00 h) and 25 July (10:00 h) 1997 in a recently flooded oligo-mesotrophic reservoir (the Sep Reservoir, Puy-de-Dôme, France), in relation to temperature, the phytopl...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/s002480000056

    authors: Jugnia LB,Tadonléké RD,Sime-Ngando T,Devaux J

    更新日期:2000-12-01 00:00:00

  • Repression of Proteases and Hsp90 Chaperone Expression Induced by an Antiretroviral in Virulent Environmental Strains of Cryptococcus neoformans.

    abstract::This study evaluated the effect of the antiretroviral ritonavir on protease secretion in different strains of Cryptococcus neoformans isolated from the environment and investigated the expression of heat shock protein (Hsp90), classically described virulence factors in other yeast in the presence of the same antiretro...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/s00248-016-0900-z

    authors: Serafin CF,Paris AP,Paula CR,Simão RC,Gandra RF

    更新日期:2017-04-01 00:00:00

  • Short-term wavelike dynamics of bacterial populations in response to nutrient input from fresh plant residues.

    abstract::The objectives of the research were to investigate short-term dynamics of bacterial populations in soil after a disturbance in the form of fresh organic matter incorporation and to investigate how these dynamics are linked to those of some environmental parameters. To reach these objectives, soil bacterial populations...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/s00248-003-1054-3

    authors: Zelenev VV,van Bruggen AH,Semenov AM

    更新日期:2005-01-01 00:00:00

  • Rock phosphate solubilization and colonization of maize rhizosphere by wild and genetically modified strains of Penicillium rugulosum.

    abstract::Maize root colonization and phosphate solubilizing activity of the fungus Penicillium rugulosum were assessed in a greenhouse trial using soil-plant microcosms. The bacterial gene hph conferring resistance to hygromicin B was introduced by electroporation in the wild-type strain IR-94MF1 of P. rugulosum and one transf...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/s00248-002-1001-8

    authors: Reyes I,Bernier L,Antoun H

    更新日期:2002-07-01 00:00:00

  • Persistence of genetically engineeredErwinia carotovora in perturbed and unperturbed aquatic microcosms and effect on recovery of indigenous bacteria.

    abstract::Genetically engineeredErwinia carotovora persisted significantly longer in thermally perturbed microcosms (35 days) than in nonstressed microcosms (5 days). Decreased pressure of competitors and predators and increased nutrient availability were examined as the most probable reasons for greater vulnerability of pertur...

    journal_title:Microbial ecology

    pub_type: 杂志文章

    doi:10.1007/BF02543863

    authors: Scanferlato VS,Lacy GH,Cairns J Jr

    更新日期:1990-12-01 00:00:00