Abstract:
:Molecular approaches have revealed considerable diversity and uncultured novelty in natural prokaryotic populations, but not direct links between the new genotypes detected and ecosystem processes. Here we describe the influence of the structure of communities of ammonia-oxidizing bacteria on nitrogen cycling in microcosms containing natural and managed grasslands and amended with artificial sheep urine, a major factor determining local ammonia concentrations in these environments. Nitrification kinetics were assessed by analysis of changes in urea, ammonia, nitrite and nitrate concentrations and ammonia oxidizer communities were characterized by analysis of 16S rRNA genes amplified from extracted DNA using ammonia oxidizer-specific primers. In natural soils, ammonia oxidizer community structure determined the delay preceding nitrification, which depended on the relative abundance of two Nitrosospira clusters, termed 3a and 3b. In batch cultures, pure culture and enrichment culture representatives of Nitrosospira 3a were sensitive to high ammonia concentration, while Nitrosospira cluster 3b representatives and Nitrosomonas europaea were tolerant. Delays in nitrification occurred in natural soils dominated by Nitrosospira cluster 3a and resulted from the time required for growth of low concentrations of Nitrosospira cluster 3b. In microcosms dominated by Nitrosospira cluster 3b and Nitrosomonas, no substantial delays were observed. In managed soils, no delays in nitrification were detected, regardless of initial ammonia oxidizer community structure, most probably resulting from higher ammonia oxidizer cell concentrations. The data therefore demonstrate a direct link between bacterial community structure, physiological diversity and ecosystem function.
journal_name
Environ Microbioljournal_title
Environmental microbiologyauthors
Webster G,Embley TM,Freitag TE,Smith Z,Prosser JIdoi
10.1111/j.1462-2920.2005.00740.xkeywords:
subject
Has Abstractpub_date
2005-05-01 00:00:00pages
676-84issue
5eissn
1462-2912issn
1462-2920pii
EMI740journal_volume
7pub_type
杂志文章abstract::Sensing potential nitrogen-containing respiratory substrates such as nitrate, nitrite, hydroxylamine, nitric oxide (NO) or nitrous oxide (N2 O) in the environment and subsequent upregulation of corresponding catabolic enzymes is essential for many microbial cells. The molecular mechanisms of such adaptive responses ar...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.13060
更新日期:2016-09-01 00:00:00
abstract::The Black Sea is the largest anoxic water basin on Earth and its stratified water column comprises an upper oxic, middle suboxic and a lower permanently anoxic, sulfidic zone. The abundance of sulfate-reducing bacteria (SRB) in water samples was determined by quantifying the copy number of the dsrA gene coding for the...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/j.1462-2920.2007.01413.x
更新日期:2007-12-01 00:00:00
abstract::Raphidiopsis raciborskii is an invasive bloom-forming cyanobacteria with the flexibility to utilize atmospheric and fixed nitrogen. Since nitrogen-fixation has a high requirement for iron as an ezyme cofactor, we hypothesize that iron availability would determine the success of the species under nitrogen-fixing condit...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.15328
更新日期:2021-01-01 00:00:00
abstract::Stable isotope labelling of amino acids in cell culture (SILAC) is a quantitative proteomic method that can illuminate new pathways used by cells to adapt to different lifestyles and niches. Archaea, while thriving in extreme environments and accounting for ∼20%-40% of the Earth's biomass, have not been analyzed with ...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.14014
更新日期:2018-01-01 00:00:00
abstract::The mqsRA operon encodes a toxin-antitoxin pair that was characterized to participate in biofilm and persister cell formation in Escherichia coli. Notably, the antitoxin MqsA possesses a C-terminal DNA-binding domain that recognizes the [5'-AACCT(N)2-4 AGGTT-3'] motif and acts as a transcriptional regulator controllin...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.14538
更新日期:2019-05-01 00:00:00
abstract::Stable carbon isotope signatures of diagnostic lipid biomarkers have suggested that Roseiflexus spp., the dominant filamentous anoxygenic phototrophic bacteria inhabiting microbial mats of alkaline siliceous hot springs, may be capable of fixing bicarbonate via the 3-hydroxypropionate pathway, which has been character...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/j.1462-2920.2007.01323.x
更新日期:2007-08-01 00:00:00
abstract::The role of archetypal ribonucleases (RNases) in the physiology and stress endurance of the soil bacterium and metabolic engineering platform Pseudomonas putida KT2440 has been inspected. To this end, variants of this strain lacking each of the most important RNases were constructed. Each mutant lacked either one exor...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.15291
更新日期:2021-01-01 00:00:00
abstract::The effect of the plasmid-encoded rulAB (resistance to ultraviolet radiation) determinant on responses of Pseudomonas syringae to ultraviolet-B (UV-B) radiation and the distribution of rulAB among pathovars of P. syringae were determined. The cloned rulAB determinant and the native rulAB+ plasmid pPSR1 both conferred ...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1046/j.1462-2920.1999.00008.x
更新日期:1999-02-01 00:00:00
abstract::How to explore protein sequence space efficiently and how to generate high-quality mutant libraries that allow to identify improved variants with current screening technologies are key questions for any directed protein evolution experiment. High-quality mutant libraries can be generated through improved random mutage...
journal_title:Environmental microbiology
pub_type: 杂志文章,评审
doi:10.1111/j.1462-2920.2007.01411.x
更新日期:2007-11-01 00:00:00
abstract::Most of the oil in low temperature, non-uplifted reservoirs is biodegraded due to millions of years of microbial activity, including via methanogenesis from crude oil. To evaluate stimulating additional methanogenesis in already heavily biodegraded oil reservoirs, oil sands samples were amended with nutrients and elec...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.14995
更新日期:2020-08-01 00:00:00
abstract::Fragilariopsis is a dominating psychrophilic diatom genus in polar sea ice. The two species Fragilariopsis cylindrus and Fragilariopsis curta are able to grow and divide below freezing temperature of sea water and above average sea water salinity. Here we show that antifreeze proteins (AFPs), involved in cold adaptati...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/j.1462-2920.2009.02149.x
更新日期:2010-04-01 00:00:00
abstract::Exopolysaccharide is a critical biofilm matrix component, yet little is known about how the synthesis of multiple exopolysaccharides is regulated. Pseudomonas aeruginosa can produce several biofilm matrix exopolysaccharides that include alginate, Psl and Pel. Here we demonstrated that AlgC, a key enzyme that provides ...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/j.1462-2920.2012.02753.x
更新日期:2012-08-01 00:00:00
abstract::A meromictic lake ecosystem (Mahoney Lake, BC, Canada) was investigated to elucidate the significance of chemocline bacteria in the total carbon cycle under natural conditions. In this lake, primary production by oxygenic phototrophs was insufficient to support the observed net secondary production of the calanoid cop...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1046/j.1462-2920.1999.00026.x
更新日期:1999-06-01 00:00:00
abstract::The factors that control the production of microcystins (hepatotoxins) during cyanobacterial blooms, and the function of these metabolites remain largely unknown. In an attempt to provide answers to these questions, we compared the fitness of microcystin (MC)-producing and non-MC-producing Planktothrix agardhii strain...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/j.1462-2920.2008.01730.x
更新日期:2008-12-01 00:00:00
abstract::We investigated to what extent a European songbird (Parus major) selectively transmits and amplifies Borrelia burgdorferi s.l. bacteria. Borrelia-naïve birds were recurrently exposed to Ixodes ricinus nymphs carrying a community of more than 34 5S-23S genotypes belonging to five genospecies (Borrelia garinii, Borrelia...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.12304
更新日期:2014-09-01 00:00:00
abstract::The genome of the soil bacterium Pseudomonas putida strain KT2440 has been erased of various determinants of resistance to antibiotics encoded in its extant chromosome. To this end, we employed a coherent genetic platform that allowed the precise deletion of multiple genomic segments in a large variety of Gram-negativ...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/j.1462-2920.2011.02538.x
更新日期:2011-10-01 00:00:00
abstract::In order to study the effect of different chloroethenes (electron acceptors) on the bacterial composition of dechlorinating communities, two reductive dechlorinating enrichment cultures were developed that were able to reduce trichloroethene (TCE) and cis-1,2-dichloroethene (cis-DCE) to ethene using hydrogen as electr...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1046/j.1462-2920.2003.00525.x
更新日期:2004-01-01 00:00:00
abstract::Bathycoccus and Ostreococcus are broadly distributed marine picoprasinophyte algae. We enumerated small phytoplankton using flow cytometry and qPCR assays for phylogenetically distinct Bathycoccus clades BI and BII and Ostreococcus clades OI and OII. Among 259 photic-zone samples from transects and time-series, Ostreo...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.13812
更新日期:2017-08-01 00:00:00
abstract::Although Escherichia coli is an important model organism for bacterial research, few studies have explored the nature of temporal variation in E. coli strains within the intestinal tracts of host individuals. In this study the E. coli strains of 54 mountain brushtail possums were sampled on four occasions during a yea...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.12088
更新日期:2013-08-01 00:00:00
abstract::The actinomycete Amycolatopsis japonicum produces the complexing agent ethylenediamine-disuccinate ([S,S]-EDDS), which is an isomer of the widely industrially applied ethylenediamine-tetraacetate (EDTA). In contrast to EDTA, [S,S]-EDDS is readily biodegradable and is therefore an alternative with a favourable environm...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.13159
更新日期:2016-04-01 00:00:00
abstract::Metapopulation theory developed in terrestrial ecology provides applicable frameworks for interpreting the role of local and regional processes in shaping species distribution patterns. Yet, empirical testing of metapopulation models on microbial communities is essentially lacking. We determined regional bacterioplank...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.13650
更新日期:2017-03-01 00:00:00
abstract::Pathogenic Vibrio parahaemolyticus strains producing either or both of a thermostable direct haemolysin (TDH) and a TDH-related haemolysin (TRH) encoded by tdh and trh genes, respectively, are isolated at a low rate from the environment. However, recently we observed that a considerable percentage of APW (alkaline pep...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/j.1462-2920.2006.00990.x
更新日期:2006-06-01 00:00:00
abstract::Phosphonoacetate is regarded as an antiviral xenobiotic whose mineralization can be catalysed by an enzyme, phosphonoacetate hydrolase, encoded by the phnA gene. To date the enzyme's activity has been detected in only a limited number of bacteria. Its expression has been shown to occur in a manner independent of the p...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/j.1462-2920.2005.00974.x
更新日期:2006-05-01 00:00:00
abstract::The sulfate-reducing culture N47 can utilize naphthalene or 2-methylnaphthalene as the sole carbon source and electron donor. Here we show that the initial reaction in the naphthalene degradation pathway is a methylation to 2-methylnaphthalene which then undergoes the subsequent oxidation to the central metabolite 2-n...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/j.1462-2920.2005.00900.x
更新日期:2006-02-01 00:00:00
abstract::Arctic marine microbes are affected by environmental changes that may ultimately influence their functions in carbon cycling. Here, we investigated in concert the structure and enzymatic activities of pelagic, particle-associated and benthic bacterial communities in the central Arctic Ocean, and used these data to eva...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.14304
更新日期:2018-08-01 00:00:00
abstract::Mas5, a yeast heat shock protein classified to the Hsp40 group, is homologous to bacterial archetype DnaJ but functionally unexplored in filamentous fungi. Here we identify a Mas5 homologue (46.86 kDa) in Beauveria bassiana and show its indispensability for host infection and environmental adaptation of the fungal ins...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.13197
更新日期:2016-03-01 00:00:00
abstract::When bacterial lineages make the transition from free-living to permanent association with hosts, they can undergo massive gene losses, for which the selective forces within host tissues are unknown. We identified here melanogenic clinical isolates of Pseudomonas aeruginosa with large chromosomal deletions (66 to 270 ...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.13336
更新日期:2016-10-01 00:00:00
abstract::The type VI secretion system (T6SS) of bacteria plays a key role in competing for specific niches by the contact-dependent killing of competitors. Recently, Rhs proteins with polymorphic C-terminal toxin-domains that inhibit or kill neighboring cells were identified. In this report, we identified a novel Rhs with an M...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.13621
更新日期:2017-01-01 00:00:00
abstract::Autophagy is a conserved degradation system in eukaryotic cells that includes non-selective and selective processes. Selective autophagy functions as a selective degradation mechanism for specific substrates in which autophagy-related protein 11 (ATG11) acts as an essential scaffold protein. In B. bassiana, there is a...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.14329
更新日期:2018-09-01 00:00:00
abstract::The roles of individual bacterioplankton species in the re-mineralization of algal biomass are poorly understood. Evidence from molecular data had indicated that a spring diatom bloom in the German Bight of the North Sea in 2009 was followed by a rapid succession of uncultivated bacterioplankton species, including mem...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.12479
更新日期:2015-10-01 00:00:00