Improved Assessment of Denitrifying, N
            <sub>2</sub>
            -Fixing, and Total-Community Bacteria by Terminal Restriction Fragment Length Polymorphism Analysis Using Multiple Restriction Enzymes

Rösch, Christopher; Bothe, Hermann

doi:10.1128/aem.71.4.2026-2035.2005

Cited by 125 publications

(91 citation statements)

References 22 publications

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“…This and other in silico approaches (35) can generate putative identifications for uncultured members of a microbial community and has been successfully compared to clone libraries in characterizing samples from lakes (29), soils (45,46), and the human colon (36). The benefits of this technique are its capacity to rapidly generate phylogenetic assignments from submitted T-RFLP profiles; however, because experimental errors may occur in fragment size determination, these assignments may be less precise than those of a clone library (29,30).…”

Section: Vol 71 2005 Redox Fluctuation Structures Microbial Communimentioning

confidence: 99%

Redox Fluctuation Structures Microbial Communities in a Wet Tropical Soil

Pett‐Ridge

Firestone

2005

Appl Environ Microbiol

229

149

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Frequent high-amplitude redox fluctuation may be a strong selective force on the phylogenetic and physiological composition of soil bacterial communities and may promote metabolic plasticity or redox tolerance mechanisms. To determine effects of fluctuating oxygen regimens, we incubated tropical soils under four treatments: aerobic, anaerobic, 12-h oxic/anoxic fluctuation, and 4-day oxic/anoxic fluctuation. Changes in soil bacterial community structure and diversity were monitored with terminal restriction fragment length polymorphism (T-RFLP) fingerprints. These profiles were correlated with gross N cycling rates, and a Web-based phylogenetic assignment tool was used to infer putative community composition from multiple fragment patterns. T-RFLP ordinations indicated that bacterial communities from 4-day oxic/anoxic incubations were most similar to field communities, whereas those incubated under consistently aerobic or anaerobic regimens developed distinctly different molecular profiles. Terminal fragments found in field soils persisted either in 4-day fluctuation/aerobic conditions or in anaerobic/12-h treatments but rarely in both. Only 3 of 179 total fragments were ubiquitous in all soils. Soil bacterial communities inferred from in silico phylogenetic assignment appeared to be dominated by Actinobacteria (especially Micrococcus and Streptomycetes), "Bacilli," "Clostridia," and Burkholderia and lost significant diversity under consistently or frequently anoxic incubations. Community patterns correlated well with redox-sensitive processes such as nitrification, dissimilatory nitrate reduction to ammonium (DNRA), and denitrification but did not predict patterns of more general functions such as N mineralization and consumption. The results suggest that this soil's indigenous bacteria are highly adapted to fluctuating redox regimens and generally possess physiological tolerance mechanisms which allow them to withstand unfavorable redox periods.Oxygen is the primary terminal electron acceptor for the respiratory processes of most upland soil microorganisms (41); it is a critical determinant of both soil redox status and the physiological pathways available to bacteria and fungi mediating C and N cycles. As soil redox (pE) decreases, dominant element transformations are generally assumed to shift in a well-defined succession from high-energy-yield processes to those that release less energy for microbial growth. This idea, that biological metabolism should follow the electrochemical constraints of a system, is a relatively old concept; it was first described in 1960 (1) and later supported by studies of waterlogged sediments, aquifers (11, 32), and rice paddies (56). In all of these cases, changes in redox potential occur gradually over time and/or space.In upland humid tropical forests, soils have been found to experience rapid redox fluctuations (51). In these ecosystems, the combination of high C availability, warm temperatures, abundant rainfall, clay soils with high water-holding capacity, and high metaboli...

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Section: Vol 71 2005 Redox Fluctuation Structures Microbial Communimentioning

confidence: 99%

Redox Fluctuation Structures Microbial Communities in a Wet Tropical Soil

Pett‐Ridge

Firestone

2005

Appl Environ Microbiol

229

149

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“…Across all soil samples, total T-RF richnesses were nirS = 52, nirK = 53, nosZ = 47, which are typical values for T-RFLP studies of functional genes in soils (Deslippe et al, 2014;Rich and Myrold, 2004;Rösch and Bothe, 2005). While the minimum and maximum numbers of T-RFs varied among samples, the patterns of richness, evenness, and diversity among soils belonging to the three groups of soils were similar (see Table S4).…”

Section: Bacterial Denitrifiers In New Zealand Dairy-grazed Pasture Smentioning

confidence: 83%

Soil properties impacting denitrifier community size, structure, and activity in New Zealand dairy-grazed pasture

et al. 2017

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Abstract. Denitrification is an anaerobic respiration process that is the primary contributor of the nitrous oxide (N 2 O) produced from grassland soils. Our objective was to gain insight into the relationships between denitrifier community size, structure, and activity for a range of pasture soils. We collected 10 dairy pasture soils with contrasting soil textures, drainage classes, management strategies (effluent irrigation or non-irrigation), and geographic locations in New Zealand, and measured their physicochemical characteristics. We measured denitrifier abundance by quantitative polymerase chain reaction (qPCR) and assessed denitrifier diversity and community structure by terminal restriction fragment length polymorphism (T-RFLP) of the nitrite reductase (nirS, nirK) and N 2 O reductase (nosZ) genes. We quantified denitrifier enzyme activity (DEA) using an acetylene inhibition technique. We investigated whether varied soil conditions lead to different denitrifier communities in soils, and if so, whether they are associated with different denitrification activities and are likely to generate different N 2 O emissions. Differences in the physicochemical characteristics of the soils were driven mainly by soil mineralogy and the management practices of the farms. We found that nirS and nirK communities were strongly structured along gradients of soil water and phosphorus (P) contents. By contrast, the size and structure of the nosZ community was unrelated to any of the measured soil characteristics. In soils with high water content, the richnesses and abundances of nirS, nirK, and nosZ genes were all significantly positively correlated with DEA. Our data suggest that management strategies to limit N 2 O emissions through denitrification are likely to be most important for dairy farms on fertile or allophanic soils during wetter periods. Finally, our data suggest that new techniques that would selectively target nirS denitrifiers may be the most effective for limiting N 2 O emissions through denitrification across a wide range of soil types.

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“…Detection of enzyme activities was done using the API 20NE and API ZYM microtest systems (bioMérieux) according to the manufacturer's instructions (Table 2). The presence of the nifH gene was examined as described by Rosch & Bothe (2005). Test results and differential biochemical characteristics are listed in Table 2 In summary, data from the present study demonstrate that cluster B isolates belong to C. fungivorans and that cluster A and D isolates represent two novel Collimonas species, which can be differentiated from each other and from C. fungivorans by means of genotypic ( Fig.…”

mentioning

confidence: 88%

Collimonas arenae sp. nov. and Collimonas pratensis sp. nov., isolated from (semi-)natural grassland soils

Höppener-Ogawa

Boer

Leveau

et al. 2008

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

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Improved Assessment of Denitrifying, N ₂ -Fixing, and Total-Community Bacteria by Terminal Restriction Fragment Length Polymorphism Analysis Using Multiple Restriction Enzymes

Cited by 125 publications

References 22 publications

Redox Fluctuation Structures Microbial Communities in a Wet Tropical Soil

Redox Fluctuation Structures Microbial Communities in a Wet Tropical Soil

Soil properties impacting denitrifier community size, structure, and activity in New Zealand dairy-grazed pasture

Collimonas arenae sp. nov. and Collimonas pratensis sp. nov., isolated from (semi-)natural grassland soils

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Improved Assessment of Denitrifying, N 2 -Fixing, and Total-Community Bacteria by Terminal Restriction Fragment Length Polymorphism Analysis Using Multiple Restriction Enzymes

Cited by 125 publications

References 22 publications

Redox Fluctuation Structures Microbial Communities in a Wet Tropical Soil

Redox Fluctuation Structures Microbial Communities in a Wet Tropical Soil

Soil properties impacting denitrifier community size, structure, and activity in New Zealand dairy-grazed pasture

Collimonas arenae sp. nov. and Collimonas pratensis sp. nov., isolated from (semi-)natural grassland soils

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Improved Assessment of Denitrifying, N ₂ -Fixing, and Total-Community Bacteria by Terminal Restriction Fragment Length Polymorphism Analysis Using Multiple Restriction Enzymes