Statistical comparisons of community catabolic profiles

Glimm, Ekkehard; Heuer, Holger; Engelen, Bert; Smalla, Kornelia; Backhaus, Horst

doi:10.1016/s0167-7012(97)00046-8

Cited by 96 publications

(62 citation statements)

References 14 publications

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“…Each suspension of bacterial cells was diluted 1:10 and used to inoculate ECOlog plates (5) at 135 l per well; the plates were then incubated at 28°C in darkness. The optical density (OD) at 595 nm was measured with a microtiter plate reader (Tecan, Zurich, Switzerland) when a maximum of wells showed activity (66 h) (14). The raw OD values were corrected for the background color in the control well without a carbon source.…”

Section: Methodsmentioning

confidence: 99%

Changes in Bacterial Populations and in Biphenyl Dioxygenase Gene Diversity in a Polychlorinated Biphenyl-Polluted Soil after Introduction of Willow Trees for Rhizoremediation

Cárcer

Martín

Karlson

et al. 2007

Appl Environ Microbiol

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The aim of this study was to analyze the structural and functional changes occurring in a polychlorinatedbiphenyl (PCB)-contaminated soil ecosystem after the introduction of a suitable host plant for rhizoremediation (Salix viminalis). We have studied the populations and phylogenetic distribution of key bacterial groups (Alpha-and Betaproteobacteria, Acidobacteria, and Actinobacteria) and the genes encoding iron-sulfur protein ␣ (ISP␣) subunits of the toluene/biphenyl dioxygenases in soil and rhizosphere by screening gene libraries using temperature gradient gel electrophoresis. The results, based on the analysis of 415 clones grouped into 133 operational taxonomic units that were sequence analyzed (>128 kbp), show that the rhizospheric bacterial community which evolved from the native soil community during the development of the root system was distinct from the soil community for all groups studied except for the Actinobacteria. Proteobacteria were enriched in the rhizosphere and dominated both in rhizosphere and soil. There was a higher than expected abundance of Betaproteobacteria in the native and in the planted PCB-polluted soil. The ISP␣ sequences retrieved indicate a high degree of catabolic and phylogenetic diversity. Many sequences clustered with biphenyl dioxygenase sequences from gram-negative bacteria. A distinct cluster that was composed of sequences from this study, some previously described environmental sequences, and a putative ISP␣ from Sphingomonas wittichii RW1 seems to contain greater diversity than the presently recognized toluene/biphenyl dioxygenase subfamily. Moreover, the rhizosphere selected for two ISP␣ sequences that accounted for almost 60% of the gene library and were very similar to sequences harbored by Pseudomonas species.Soil contamination by organic compounds is a serious problem in most industrialized countries. Among pollutants, polychlorinated biphenyls (PCBs) are of special importance, and it is estimated that more than 300 million kg has been released to the environment (20). Remediation of PCB-contaminated soil has traditionally been carried out by incineration or burial of the soil in secure landfills. As a less-expensive removal strategy, rhizoremediation (53), the use of dual plant-microorganism systems in which the plant provides nutrients, support, and a greater availability of the substrate and the microorganisms drive the enzymatic remediation, has been proposed (26, 47).The soil compartment directly under the influence of living roots is designated the rhizosphere (25). It is a niche where complex microbial communities are supported by nutrients released by root exudates, mucilage, and decaying root cells (7), which induces a characteristic change in the distribution of the microorganisms associated with plant roots in comparison with their distribution in the bulk soil, designated the rhizosphere effect. Thus, in order to exploit the potential of the emerging rhizoremediation technology, a better understanding of the diverse microbial populations and catabolic ...

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Section: Methodsmentioning

confidence: 99%

Changes in Bacterial Populations and in Biphenyl Dioxygenase Gene Diversity in a Polychlorinated Biphenyl-Polluted Soil after Introduction of Willow Trees for Rhizoremediation

Cárcer

Martín

Karlson

et al. 2007

Appl Environ Microbiol

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“…PCA is an eigenvector analysis procedure (details described by Glimm et al (1997)) that attempts to maximize the amount of variance in the data set that can be explained by the first few principal components. Analyses of variance (ANOVA) were performed for each axis of the PCA.…”

Section: Plate Reading and Data Analysismentioning

confidence: 99%

“…Analyses of variance (ANOVA) were performed for each axis of the PCA. Subsequent to the ANOVA test, significant differences in the microbial communities were analysed with the Fisher LSD test (in the case of variance heterogeneity) or by the Scheffé test (in the case of variance homogeneity; Glimm et al 1997). All statistical analyses were performed using Statistica 6.1 (StatSoft, Inc.).…”

Section: Plate Reading and Data Analysismentioning

confidence: 99%

Bacterial community structure and carbon turnover in permafrost-affected soils of the Lena Delta, northeastern SiberiaThis article is one of a selection of papers in the Special Issue on Polar and Alpine Microbiology.

2009

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Arctic permafrost environments store large amounts of organic carbon. As a result of global warming, intensified permafrost degradation and release of significant quantities of the currently conserved organic matter is predicted for high latitudes. To improve our understanding of the present and future carbon dynamics in climate sensitive permafrost ecosystems, the present study investigates structure and carbon turnover of the bacterial community in a permafrost-affected soil of the Lena Delta (72822'N, 126828'E) in northeastern Siberia. 16S rRNA gene clone libraries revealed the presence of all major soil bacterial groups and of the canditate divisions OD1 and OP11. A shift within the bacterial community was observed along the soil profile indicated by the absence of Alphaproteobacteria and Betaproteobacteria and a simultaneous increase in abundance and diversity of fermenting bacteria like Firmicutes and Actinobacteria near the permafrost table. BIOLOG EcoPlates were used to describe the spectrum of utilized carbon sources of the bacterial community in different horizons under in situ temperature conditions in the presence and absence of oxygen. The results revealed distinct qualitative differences in the substrates used and the turnover rates under oxic and anoxic conditions. It can be concluded that constantly negative redox potentials as characteristic for the near permafrost table horizons of the investigated soil did effectively shape the structure of the indigenous bacterial community limiting its phylum-level diversity and carbon turnover capacity.Key words: active layer, soil organic carbon, microbial diversity, permafrost ecosystem. Résumé :Le pergélisol situé dans les zones arctiques constitue une vaste réserve de carbone organique. Le réchauffement climatique accroît la dégradation du pergélisol, ayant pour conséquence une libération massive de matière organique prévue dans les régions de hautes latitudes. De manière à améliorer notre compréhension de la dynamique présente et future du carbone dans les écosystèmes climatiques sensibles, telles que le pergélisol, cette étude examine la structure et le turnover du carbone de la communauté bactérienne contenue dans le sol sous influence directe du pergélisol, dans le delta de la Lena (72822'N, 126828'E) au nord de la Sibérie. Le clonage du gène 16S rRNA a révélé la présence de la totalité des groupes importants de bactéries du sol, ainsi que des divisions présumées OD1 et OP11. Un changement au sein de la communauté bactérienne a été observé le long du profil de sol, indiqué par l'absence des Alphaproteobacteria et des Betaproteobacteria et l'augmentation simultanée de l'abondance et de la diversité des bactéries fermentatives, comme par exemple les Firmicutes et les Actinobacteria, à proximité du pergélisol. Des plaques BIOLOG Eco ont été utilisées sous conditions de température contrôlées et en présence ou absence d'oxygène, afin de décrire le spectre des sources de carbone utilisées par la communauté bactérienne dans les différents horizo...

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“…While some authors advocate the analysis of presence/absence data in ordinations (4), we found no significantly different results from relativized peak height data and chose to present the latter. Only principal components with eigenvectors of Ͼ0.25 (9) were examined, and/or where principal components cumulatively explained 75% of the data variance (21). Sample outliers (Ͼ2 standard deviations from the mean) were removed from the analysis.…”

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

230

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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Statistical comparisons of community catabolic profiles

Cited by 96 publications

References 14 publications

Changes in Bacterial Populations and in Biphenyl Dioxygenase Gene Diversity in a Polychlorinated Biphenyl-Polluted Soil after Introduction of Willow Trees for Rhizoremediation

Changes in Bacterial Populations and in Biphenyl Dioxygenase Gene Diversity in a Polychlorinated Biphenyl-Polluted Soil after Introduction of Willow Trees for Rhizoremediation

Bacterial community structure and carbon turnover in permafrost-affected soils of the Lena Delta, northeastern SiberiaThis article is one of a selection of papers in the Special Issue on Polar and Alpine Microbiology.

Redox Fluctuation Structures Microbial Communities in a Wet Tropical Soil

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