TY  - JOUR
AU  - Nelson, K.*
AU  - Schloter, M.
C1  - 71776
C2  - 56338
TI  - Special collection on pollution, bioremediation, and the environment.
JO  - Microb. Ecol.
VL  - 87
IS  - 1
PY  - 2024
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - Despite its enormous importance for ecosystem services, factors driving microbial recolonization of soils after disturbance are still poorly understood. Here, we compared the microbial recolonization patterns of a disturbed, autoclaved soil using different amounts of the original non-disturbed soil as inoculum. By using this approach, we manipulated microbial biomass, but did not change microbial diversity of the inoculum. We followed the development of a new soil microbiome after reinoculation over a period of 4 weeks using a molecular barcoding approach as well as qPCR. Focus was given on the assessment of bacteria and archaea. We could show that 1 week after inoculation in all inoculated treatments bacterial biomass exceeded the values from the original soil as a consequence of high dissolved organic carbon (DOC) concentrations in the disturbed soil resulting from the disturbance. This high biomass was persistent over the complete experimental period. In line with the high DOC concentrations, in the first 2 weeks of incubation, copiotrophic bacteria dominated the community, which derived from the inoculum used. Only in the disturbed control soils which did not receive a microbial inoculum, recolonization pattern differed. In contrast, archaeal biomass did not recover over the experimental period and recolonization was strongly triggered by amount of inoculated original soil added. Interestingly, the variability between replicates of the same inoculation density decreased with increasing biomass in the inoculum, indicating a deterministic development of soil microbiomes if higher numbers of cells are used for reinoculation.
AU  - Pinheiro Alves de Souza, Y.
AU  - Schloter, M.
AU  - Weisser, W.*
AU  - Schulz, S.
C1  - 67953
C2  - 54431
CY  - One New York Plaza, Suite 4600, New York, Ny, United States
SP  - 2882-2893
TI  - Deterministic development of soil microbial communities in disturbed soils depends on microbial biomass of the bioinoculum.
JO  - Microb. Ecol.
VL  - 86
IS  - 4
PB  - Springer
PY  - 2023
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - Nutrient turnover in soils is strongly driven by soil properties, including clay mineral composition. One main nutrient is phosphorus (P), which is known to be easily immobilized in soil. Therefore, the specific surface characteristics of clay minerals might substantially influence P availability in soil and thus the microbial strategies for accessing P pools. We used a metagenomic approach to analyze the microbial potential to access P after 842 days of incubation in artificial soils with a clay mineral composition of either non-expandable illite (IL) or expandable montmorillonite (MT), which differ in their surface characteristics like soil surface area and surface charge. Our data indicate that microorganisms of the two soils developed different strategies to overcome P depletion, resulting in similar total P concentrations. Genes predicted to encode inorganic pyrophosphatase (ppa), exopolyphosphatase (ppx), and the pstSCAB transport system were higher in MT, suggesting effective P uptake and the use of internal poly-P stores. Genes predicted to encode enzymes involved in organic P turnover like alkaline phosphatases (phoA, phoD) and glycerophosphoryl diester phosphodiesterase were detected in both soils in comparable numbers. In addition, P-o concentrations did not differ significantly. Most identified genes were assigned to microbial lineages generally abundant in agricultural fields, but some were assigned to lineages known to include oligotrophic specialists, such as Bacillaceae and Microchaetaceae.
AU  - Tanuwidjaja, I.
AU  - Vogel, C.*
AU  - Pronk, G.J.*
AU  - Schöler, A.
AU  - Kublik, S.
AU  - Vestergaard, G.
AU  - Kögel-Knabner, I.*
AU  - Mrkonjic Fuka, M.*
AU  - Schloter, M.
AU  - Schulz, S.
C1  - 60499
C2  - 49489
CY  - One New York Plaza, Suite 4600, New York, Ny, United States
SP  - 897–907
TI  - Microbial key players involved in P turnover differ in artificial soil mixtures depending on clay mineral composition.
JO  - Microb. Ecol.
VL  - 81
PB  - Springer
PY  - 2021
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - Biological soil crusts (biocrusts) play an important role in improving soil stability and resistance to erosion by promoting aggregation of soil particles. During initial development, biocrusts are dominated by bacteria. Some bacterial members of the biocrusts can contribute to the formation of soil aggregates by producing exopolysaccharides and lipopolysaccharides that act as "glue" for soil particles. However, little is known about the dynamics of "soil glue" producers during the initial development of biocrusts. We hypothesized that different types of initial biocrusts harbor distinct producers of adhesive polysaccharides. To investigate this, we performed a microcosm experiment, cultivating biocrusts on two soil substrates. High-throughput shotgun sequencing was used to obtain metagenomic information on microbiomes of bulk soils from the beginning of the experiment, and biocrusts sampled after 4 and 10 months of incubation. We discovered that the relative abundance of genes involved in the biosynthesis of exopolysaccharides and lipopolysaccharides increased in biocrusts compared with bulk soils. At the same time, communities of potential "soil glue" producers that were highly similar in bulk soils underwent differentiation once biocrusts started to develop. In the bulk soils, the investigated genes were harbored mainly by Betaproteobacteria, whereas in the biocrusts, the major potential producers of adhesive polysaccharides were, aside from Alphaproteobacteria, either Cyanobacteria or Chloroflexi and Acidobacteria. Overall, our results indicate that the potential to form exopolysaccharides and lipopolysaccharides is an important bacterial trait for initial biocrusts and is maintained despite the shifts in bacterial community composition during biocrust development.
AU  - Cania, B.
AU  - Vestergaard, G.
AU  - Kublik, S.
AU  - Köhne, J.M.*
AU  - Fischer, T.*
AU  - Albert, A.
AU  - Winkler, J.B.
AU  - Schloter, M.
AU  - Schulz, S.
C1  - 56701
C2  - 47228
CY  - One New York Plaza, Suite 4600, New York, Ny, United States
SP  - 326-341
TI  - Biological soil crusts from different soil substrates harbor distinct bacterial groups with the potential to produce exopolysaccharides and lipopolysaccharides.
JO  - Microb. Ecol.
VL  - 79
IS  - 2
PB  - Springer
PY  - 2020
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - Microorganisms play an essential role in nitrogen cycling and greenhouse gas emissions in soils and sediments. The recently discovered oxygenic denitrifiers are proposed to reduce nitrate and nitrite via nitric oxide dismutation directly to N-2 and O-2. So far, the ecological role of these microbes is not well understood. The only available tool for a targeted study of oxygenic denitrifiers is their respective maker gene, nitric oxide dismutase (nod). Here, we established the use of PacBio long-read sequencing of nod gene amplicons to study the diversity and community structure of oxygenic denitrifiers. Two distinct sets of environmental samples, agricultural soil and lake sediment, were investigated as examples. The circular consensus sequences (ca 1.0 kb) obtained covered most substitution characteristic of NO dismutase and allowed for reliable classification of oxygenic denitrifiers. Distinct nod gene pools and community structure were revealed for the different habitats, with most sequence types affiliated to yet unidentified environmental nod lineages. The abundance of nod genes ranged 2.2 x 10(6)-3.2 x 10(7) gene copies g(-1) soil or sediment, accounting for up to 3% of total bacterial 16S rRNA gene counts. This study indicates that nod-gene-targeted long-read sequencing can be a powerful tool for studying the ecology of these novel microbes, and the results also suggest that oxygenic denitrifiers are prevalent and abundant in different terrestrial samples, where they could play an important, but yet overlooked role in nitrogen transformations.
AU  - Zhu, B.*
AU  - Wang, Z.*
AU  - Kublik, S.
AU  - Ge, T.*
AU  - Casper, P.*
AU  - Schloter, M.
AU  - Lueders, T.*
C1  - 57995
C2  - 48250
CY  - One New York Plaza, Suite 4600, New York, Ny, United States
SP  - 243-247
TI  - Long-read amplicon sequencing of nitric oxide dismutase (nod) genes 
      reveal diverse oxygenic denitrifiers in agricultural soils and lake 
      sediments.
JO  - Microb. Ecol.
VL  - 80
IS  - 1
PB  - Springer
PY  - 2020
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - The development of the gut microbiome is influenced by several factors. It is acquired during and after birth and involves both maternal and environmental factors as well as the genetic disposition of the offspring. However, it is unclear if the microbiome development is directly triggered by the mode of delivery and very early contact with the mother or mostly at later stages of initial development mainly by breast milk provided by the mother. To investigate to what extent the gut microbiome composition of the offspring is determined by the nursing mother, providing breast milk, compared to the birth mother during early development, a cross-fostering experiment involving two genetically different mouse lines was developed, being prone to be obese or lean, respectively. The microbiome of the colon was analyzed by high-throughput 16S rRNA gene sequencing, when the mice were 3 weeks old. The nursing mother affected both α- and β-diversity of the offspring’s gut microbiome and shaped its composition. Especially bacterial families directly transferred by breast milk, like Streptococcaceae, or families which are strongly influenced by the quality of the breast milk like Rikenellaceae, showed a strong response. The core microbiome transferred from the obese nursing mother showed a higher robustness in comparison to the microbiome transferred from the lean nursing mother. Overall, the nursing mother impacts the gut microbial composition of the offspring during early development and might play an important role for health and disease of the animals at later stages of life.
AU  - Treichel, N.
AU  - Prevoršek, Z.*
AU  - Mrak, V.*
AU  - Kostric, M.
AU  - Vestergaard, G.
AU  - Fösel, B.
AU  - Pfeiffer, S.
AU  - Stres, B.*
AU  - Schöler, A.
AU  - Schloter, M.
C1  - 55115
C2  - 46331
SP  - 517–527
TI  - Effect of the nursing mother on the gut microbiome of the offspring during early mouse development.
JO  - Microb. Ecol.
VL  - 78
PY  - 2019
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - While root exudation follows diurnal rhythms, little is known about the consequences for the microbiome of the rhizosphere. In this study, we used a metatranscriptomic approach to analyze the active microbial communities, before and after sunrise, in the rhizosphere of barley. We detected increased activities of many prokaryotic microbial taxa and functions at the pre-dawn stage, compared to post-dawn. Actinomycetales, Planctomycetales, Rhizobiales, and Burkholderiales were the most abundant and therefore the most active orders in the barley rhizosphere. The latter two, as well as Xanthomonadales, Sphingomonadales, and Caulobacterales showed a significantly higher abundance in pre-dawn samples compared to post-dawn samples. These changes in taxonomy coincide with functional changes as genes involved in both carbohydrate and amino acid metabolism were more abundant in pre-dawn samples compared to post-dawn samples. This study significantly enhances our present knowledge on how rhizospheric microbiota perceives and responds to changes in the soil during dark and light periods.
AU  - Baraniya, D.*
AU  - Nannipieri, P.*
AU  - Kublik, S.
AU  - Vestergaard, G.
AU  - Schloter, M.
AU  - Schöler, A.
C1  - 52283
C2  - 43821
SP  - 830–833
TI  - The impact of the diurnal cycle on the microbial transcriptome in the rhizosphere of barley.
JO  - Microb. Ecol.
VL  - 75
IS  - 4
PY  - 2018
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - The lower respiratory tract has been previously considered sterile in a healthy state, but advances in culture-independent techniques for microbial identification and characterization have revealed that the lung harbors a diverse microbiome. Although research on the lung microbiome is increasing and important questions were already addressed, longitudinal studies aiming to describe developmental stages of the microbial communities from the early neonatal period to adulthood are lacking. Thus, little is known about the early-life development of the lung microbiome and the impact of external factors during these stages. In this study, we applied a barcoding approach based on high-throughput sequencing of 16S ribosomal RNA gene amplicon libraries to determine age-dependent differences in the bacterial fraction of the murine lung microbiome and to assess potential influences of differing "environmental microbiomes" (simulated by the application of used litter material to the cages). We could clearly show that the diversity of the bacterial community harbored in the murine lung increases with age. Interestingly, bacteria belonging to the genera Delftia and Rhodococcus formed an age-independent core microbiome. The addition of the used litter material influenced the lung microbiota of young mice but did not significantly alter the community composition of adult animals. Our findings elucidate the dynamic nature of the early-life lung microbiota and its stabilization with age. Further, this study indicates that even slight environmental changes modulate the bacterial community composition of the lung microbiome in early life, whereas the lung microbes of adults demonstrate higher resilience towards environmental variations.
AU  - Kostric, M.
AU  - Milger, K.
AU  - Krauss-Etschmann, S.*
AU  - Engel, M.
AU  - Vestergaard, G.
AU  - Schloter, M.
AU  - Schöler, A.
C1  - 51894
C2  - 43563
CY  - New York
SP  - 529-542
TI  - Development of a stable lung microbiome in healthy neonatal mice.
JO  - Microb. Ecol.
VL  - 75
IS  - 2
PB  - Springer
PY  - 2018
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - This study intended to elucidate the long-term effects of organic soil amendments on bacterial co-occurrence in bulk soil with and without addition of mineral fertiliser. Previous research mostly neglected the bacterial co-occurrence structure and focussed mainly on the parameters species diversity and abundance changes of species. Here we present a systematic comparison of two frequently used soil amendments, manure and straw, with regard to their impact on bacterial co-occurrence in a long-term field trial in Speyer, Germany. The approach involved 16S amplicon sequencing in combination with a bacterial network analysis, comparing the different fertiliser regimes. The results show an increase of bacterial diversity as well as an accumulation of bacteria of the order Bacillales in plots fertilised with manure compared to a control treatment. In the straw-amended plots neither an increase in diversity was found nor were indicative species detectable. Furthermore, network analysis revealed a clear impact of mineral fertiliser addition on bacterial co-occurrence structure. Most importantly, both organic amendments increased network complexity irrespective of mineral fertilisation regime. At the same time, the effects of manure and straw exhibited differences that might be explained by differences in their nutritional/chemical contents. It is concluded that bacterial interactions are a crucial parameter for the assessment of amendment effects regarding soil health and sustainability.
AU  - Schmid, C.
AU  - Schröder, P.
AU  - Armbruster, M.*
AU  - Schloter, M.
C1  - 52448
C2  - 43982
CY  - 233 Spring St, New York, Ny 10013 Usa
SP  - 226–239
TI  - Organic amendments in a long-term field trial-consequences for the bulk soil bacterial community as revealed by network analysis.
JO  - Microb. Ecol.
VL  - 76
IS  - 1
PB  - Springer
PY  - 2018
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - More than 50% of all anthropogenic N2O emissions come from the soil. Drained Histosols that are used for agricultural purposes are particularly potent sources of denitrification due to higher stocks of organic matter and fertiliser application. However, conditions that favour denitrification can vary considerably across a field and change significantly throughout the year. Spatial and temporal denitrifier dynamics were assessed in a drained, intensely managed Histosol by focusing on the genetic nitrite and N2O reduction potential derived from the abundance of nirK, nirS and nosZ genes. These data were correlated with soil properties at two different points in time in 2013. N2O emissions were measured every 2 weeks over three vegetation periods (2012-2014). Very low N2O emission rates were measured throughout the entire period of investigation in accordance with the geostatistical data that revealed an abundance of microbes carrying the N2O reductase gene nosZ. This, along with neutral soil pH values, is indicative of high microbial denitrification potential. While the distribution of the microbial communities was strongly influenced by total organic carbon and nitrogen pools in March, the spatial distribution pattern was not related to the distribution of soil properties in October, when higher nutrient availability was observed. Different nitrite reducer groups prevailed in spring and autumn. While nirS, followed by nosZ and nirK, was most abundant in March, the latter was the dominant nitrite reductase in October.
AU  - Schulz, S.
AU  - Kölbl, A.*
AU  - Ebli, M.*
AU  - Buegger, F.
AU  - Schloter, M.
AU  - Fiedler, S.*
C1  - 51104
C2  - 43090
CY  - New York
SP  - 765-770
TI  - Field-scale pattern of denitrifying microorganisms and N2O emission rates indicate a high potential for complete denitrification in an agriculturally used organic soil.
JO  - Microb. Ecol.
VL  - 74
IS  - 4
PB  - Springer
PY  - 2017
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - Soil microbial community responses to elevated atmospheric CO2 concentrations (eCO2) occur mainly indirectly via CO2-induced plant growth stimulation leading to quantitative as well as qualitative changes in rhizodeposition and plant litter. In order to gain insight into short-term, site-specific effects of eCO2 on the microbial community structure at the plant-soil interface, young beech trees (Fagus sylvatica L.) from two opposing mountainous slopes with contrasting climatic conditions were incubated under ambient (360 ppm) CO2 concentrations in a greenhouse. One week before harvest, half of the trees were incubated for 2 days under eCO2 (1,100 ppm) conditions. Shifts in the microbial community structure in the adhering soil as well as in the root rhizosphere complex (RRC) were investigated via TRFLP and 454 pyrosequencing based on 16S ribosomal RNA (rRNA) genes. Multivariate analysis of the community profiles showed clear changes of microbial community structure between plants grown under ambient and elevated CO2 mainly in RRC. Both TRFLP and 454 pyrosequencing showed a significant decrease in the microbial diversity and evenness as a response of CO2 enrichment. While Alphaproteobacteria dominated by Rhizobiales decreased at eCO2, Betaproteobacteria, mainly Burkholderiales, remained unaffected. In contrast, Gammaproteobacteria and Deltaproteobacteria, predominated by Pseudomonadales and Myxococcales, respectively, increased at eCO2. Members of the order Actinomycetales increased, whereas within the phylum Acidobacteria subgroup Gp1 decreased, and the subgroups Gp4 and Gp6 increased under atmospheric CO2 enrichment. Moreover, Planctomycetes and Firmicutes, mainly members of Bacilli, increased under eCO2. Overall, the effect intensity of eCO2 on soil microbial communities was dependent on the distance to the roots. This effect was consistent for all trees under investigation; a site-specific effect of eCO2 in response to the origin of the trees was not observed.
AU  - Gschwendtner, S.
AU  - Leberecht, M.*
AU  - Engel, M.
AU  - Kublik, S.
AU  - Dannenmann, M.*
AU  - Polle, A.*
AU  - Schloter, M.
C1  - 34366
C2  - 35265
CY  - New York
SP  - 867-878
TI  - Effects of elevated atmospheric CO2 on microbial community structure at the plant-soil interface of young beech trees (Fagus sylvatica L.) grown at two sites with contrasting climatic conditions.
JO  - Microb. Ecol.
VL  - 69
IS  - 4
PB  - Springer
PY  - 2015
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - Forest management practices (FMPs) significantly influence important ecological processes and services in Central European forests, such as leaf litter decomposition and nutrient cycling. Changes in leaf litter diversity, and thus, its quality as well as microbial community structure and function induced by different FMPs were hypothesized to be the main drivers causing shifts in decomposition rates and nutrient release in managed forests. In a litterbag experiment lasting 473 days, we aimed to investigate the effects of FMPs (even-aged timber management, selective logging and unmanaged) on bacterial and fungal communities involved in leaf litter degradation over time. Our results showed that microbial communities in leaf litter were strongly influenced by both FMPs and sampling date. The results from nonmetric multidimensional scaling (NMDS) ordination revealed distinct patterns of bacterial and fungal successions over time in leaf litter. We demonstrated that FMPs and sampling dates can influence a range of factors, including leaf litter quality, microbial macronutrients, and pH, which significantly correlate with microbial community successions.
AU  - Purahong, W.*
AU  - Kapturska, D.*
AU  - Pecyna, M.J.*
AU  - Jariyavidyanont, K.*
AU  - Kaunzner, J.*
AU  - Juncheed, K.*
AU  - Uengwetwanit, T.*
AU  - Rudloff, R.*
AU  - Schulz, E.*
AU  - Hofrichter, M.*
AU  - Schloter, M.
AU  - Kruger, D.*
AU  - Buscot, F.*
C1  - 43815
C2  - 36758
CY  - New York
SP  - 905-913
TI  - Effects of forest management practices in temperate beech forests on bacterial and fungal communities involved in leaf litter degradation.
JO  - Microb. Ecol.
VL  - 69
IS  - 4
PB  - Springer
PY  - 2015
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - In this study, we investigated the impact of soil pH on the diversity and abundance of archaeal ammonia oxidizers in 27 different forest soils across Germany. DNA was extracted from topsoil samples, the amoA gene, encoding ammonia monooxygenase, was amplified; and the amplicons were sequenced using a 454-based pyrosequencing approach. As expected, the ratio of archaeal (AOA) to bacterial (AOB) ammonia oxidizers’ amoA genes increased sharply with decreasing soil pH. The diversity of AOA differed significantly between sites with ultra-acidic soil pH (<3.5) and sites with higher pH values. The major OTUs from soil samples with low pH could be detected at each site with a soil pH <3.5 but not at sites with pH >4.5, regardless of geographic position and vegetation. These OTUs could be related to the Nitrosotalea group 1.1 and the Nitrososphaera subcluster 7.2, respectively, and showed significant similarities to OTUs described from other acidic environments. Conversely, none of the major OTUs typical of sites with a soil pH >4.6 could be found in the ultra- and extreme acidic soils. Based on a comparison with the amoA gene sequence data from a previous study performed on agricultural soils, we could clearly show that the development of AOA communities in soils with ultra-acidic pH (<3.5) is mainly triggered by soil pH and is not influenced significantly by the type of land use, the soil type, or the geographic position of the site, which was observed for sites with acido-neutral soil pH.
AU  - Stempfhuber, B.
AU  - Engel, M.
AU  - Fischer, D.
AU  - Neskovic-Prit, G.
AU  - Wubet, T.*
AU  - Schöning, I.*
AU  - Gubry-Rangin, C.*
AU  - Kublik, S.
AU  - Schloter-Hai, B.
AU  - Rattei, T.*
AU  - Welzl, G.
AU  - Nicol, G.W.*
AU  - Schrumpf, M.*
AU  - Buscot, F.*
AU  - Prosser, J.I.*
AU  - Schloter, M.
C1  - 42990
C2  - 35935
CY  - New York
SP  - 879-883
TI  - pH as a driver for ammonia-oxidizing Archaea in forest soils.
JO  - Microb. Ecol.
VL  - 69
IS  - 4
PB  - Springer
PY  - 2015
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - Three toluene-degrading microbial consortia were enriched under sulphate-reducing conditions from different zones of a benzene, toluene, ethylbenzene and xylenes (BTEX) plume of two connected contaminated aquifers. Two cultures were obtained from a weakly contaminated zone of the lower aquifer, while one culture originated from the highly contaminated upper aquifer. We hypothesised that the different habitat characteristics are reflected by distinct degrader populations. Degradation of toluene with concomitant production of sulphide was demonstrated in laboratory microcosms and the enrichment cultures were phylogenetically characterised. The benzylsuccinate synthase alpha-subunit (bssA) marker gene, encoding the enzyme initiating anaerobic toluene degradation, was targeted to characterise the catabolic diversity within the enrichment cultures. It was shown that the hydrogeochemical parameters in the different zones of the plume determined the microbial composition of the enrichment cultures. Both enrichment cultures from the weakly contaminated zone were of a very similar composition, dominated by Deltaproteobacteria with the Desulfobulbaceae (a Desulfopila-related phylotype) as key players. Two different bssA sequence types were found, which were both affiliated to genes from sulphate-reducing Deltaproteobacteria. In contrast, the enrichment culture from the highly contaminated zone was dominated by Clostridia with a Desulfosporosinus-related phylotype as presumed key player. A distinct bssA sequence type with high similarity to other recently detected sequences from clostridial toluene degraders was dominant in this culture. This work contributes to our understanding of the niche partitioning between degrader populations in distinct compartments of BTEX-contaminated aquifers.
AU  - Kuppardt, A.*
AU  - Kleinsteuber, S.*
AU  - Vogt, C.*
AU  - Lüders, T.
AU  - Harms, H.*
AU  - Chatzinotas, A.*
C1  - 30842
C2  - 33947
CY  - New York
SP  - 222-234
TI  - Phylogenetic and functional diversity within toluene-degrading, sulphate-reducing consortia enriched from a contaminated aquifer.
JO  - Microb. Ecol.
VL  - 68
IS  - 2
PB  - Springer
PY  - 2014
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - In the present study, the influence of the land use intensity on the diversity of ammonia oxidizing bacteria (AOB) and archaea (AOA) in soils from different grassland ecosystems has been investigated in spring and summer of the season (April and July). Diversity of AOA and AOB was studied by TRFLP fingerprinting of amoA amplicons. The diversity from AOB was low and dominated by a peak that could be assigned to Nitrosospira. The obtained profiles for AOB were very stable and neither influenced by the land use intensity nor by the time point of sampling. In contrast, the obtained patterns for AOA were more complex although one peak that could be assigned to Nitrosopumilus was dominating all profiles independent from the land use intensity and the sampling time point. Overall, the AOA profiles were much more dynamic than those of AOB and responded clearly to the land use intensity. An influence of the sampling time point was again not visible. Whereas AOB profiles were clearly linked to potential nitrification rates in soil, major TRFs from AOA were negatively correlated to DOC and ammonium availability and not related to potential nitrification rates.
AU  - Meyer, A.H.*
AU  - Focks, A.*
AU  - Radl, V.
AU  - Welzl, G.
AU  - Schöning, I.*
AU  - Schloter, M.
C1  - 27913
C2  - 32855
CY  - New York
SP  - 161-166
TI  - Influence of land use intensity on the diversity of ammonia oxidizing bacteria and archaea in soils from grassland ecosystems.
JO  - Microb. Ecol.
VL  - 67
IS  - 1
PB  - Springer
PY  - 2014
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - Mine wastes have been considered as a source of heavy metal (HM) contamination in the environment and negatively impact many important ecosystem services provided by soils. Plants like Miscanthus, which tolerate high HM concentrations in soil, are often used for phytoremediation and provide the possibility to use these soils at least for the production of energy crops. However, it is not clear if plant growth at these sites is limited by the availability of nutrients, mainly nitrogen, as microbes in soil might be affected by the contaminant. Therefore, in this study, we investigated in a greenhouse experiment the response of ammonia-oxidizing microbes in the root-rhizosphere complex of Miscanthus × giganteus grown in soils with different levels of long-term arsenic (As) and lead (Pb) contamination. Quantitative PCR of the ammonia monooxigenease gene (amoA) was performed to assess the abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) at two different points of plant growth. Furthermore, bulk soil samples before planting were analyzed. In addition, terminal restriction fragment length polymorphism (T-RFLP) analysis was used to investigate the diversity of archaeal amoA amplicons. Whereas high concentrations of As and Pb in soil (83 and 15 g/kg, respectively) resulted independent from plant growth in a clear reduction of AOA and AOB compared to the control soils with lower HM contents, in soils with contamination levels of 10 g/kg As and 0.2 g/kg Pb, only AOB were negatively affected in bulk soil samples. Diversity analysis of archaeal amoA genes revealed clear differences in T-RFLP patterns in response to the degree of HM contamination. Therefore, our results could clearly prove the different response patterns of AOA and AOB in HM-contaminated soils and the development of archaeal amoA phylotypes which are more tolerant towards HMs in soil samples from the areas that were impacted the most by mining waste, which could contribute to functional redundancy of ammonia-oxidizing microbes in soils and stability of nitrification pattern.
AU  - Ollivier, J.
AU  - Wanat, N.*
AU  - Austruy, A.*
AU  - Hitmi, A.*
AU  - Joussein, E.*
AU  - Welzl, G.
AU  - Munch, J.-C.*
AU  - Schloter, M.
C1  - 8513
C2  - 30154
SP  - 1038-1046
TI  - Abundance and diversity of ammonia-oxidizing prokaryotes in the root-rhizosphere complex of Miscanthus × giganteus grown in heavy metal-contaminated soils.
JO  - Microb. Ecol.
VL  - 64
IS  - 4
PB  - Springer
PY  - 2012
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - Unraveling functional genes related to biodegradation of organic compounds has profoundly improved our understanding of biological remediation processes, yet the ecology of such genes is only poorly understood. We used a culture-independent approach to assess the abundance and diversity of bacteria catalyzing the degradation of n-alkanes with a chain length between C(5) and C(16) at a forest site co-contaminated with mineral oil hydrocarbons and metals for nearly 60 years. The alkB gene coding for a rubredoxin-dependent alkane monooxygenase enzyme involved in the initial activation step of aerobic aliphatic hydrocarbon metabolism was used as biomarker. Within the area of study, four different zones were evaluated: one highly contaminated, two intermediately contaminated, and a noncontaminated zone. Contaminant concentrations, hydrocarbon profiles, and soil microbial respiration and biomass were studied. Abundance of n-alkane-degrading bacteria was quantified via real-time PCR of alkB, whereas genetic diversity was examined using molecular fingerprints (T-RFLP) and clone libraries. Along the contamination plume, hydrocarbon profiles and increased respiration rates suggested on-going natural attenuation at the site. Gene copy numbers of alkB were similar in contaminated and control areas. However, T-RFLP-based fingerprints suggested lower diversity and evenness of the n-alkane-degrading bacterial community in the highly contaminated zone compared to the other areas; both diversity and evenness were negatively correlated with metal and hydrocarbon concentrations. Phylogenetic analysis of alkB denoted a shift of the hydrocarbon-degrading bacterial community from Gram-positive bacteria in the control zone (most similar to Mycobacterium and Nocardia types) to Gram-negative genotypes in the contaminated zones (Acinetobacter and alkB sequences with little similarity to those of known bacteria). Our results underscore a qualitative rather than a quantitative response of hydrocarbon-degrading bacteria to the contamination at the molecular level.
AU  - Pérez-de-Mora, A.
AU  - Engel, M.
AU  - Schloter, M.
C1  - 6169
C2  - 29237
SP  - 959-972
TI  - Abundance and diversity of n-alkane-degrading bacteria in a forest soil co-contaminated with hydrocarbons and metals: A molecular study on alkB homologous genes.
JO  - Microb. Ecol.
VL  - 62
IS  - 4
PB  - Springer
PY  - 2011
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - Over the last few decades, the ability of rhizosphere bacteria to promote plant growth has been considered to be of scientific, ecological, and economic interest. The properties and mechanisms of interaction of these root-colonizing bacteria have been extensively investigated, and plant protection agents that are based on these bacterial strains have been developed for agricultural applications. In the present study, the root colonization of barley by Pseudomonas sp. DSMZ 13134, that is contained in the commercially available plant protection agent Proradix, was examined using the fluorescence in situ hybridization method with oligonucleotide probes and specific gfp-tagging of the inoculant strain in combination with confocal laser scanning microscopy. In the first phase of root colonization, the inoculant strain competed successfully with seed and soil-borne bacteria (including Pseudomonads) for the colonization of the rhizoplane. Pseudomonas sp. DSMZ 13134 could be detected in all parts of the roots, although it did not belong to the dominant members of the root-associated bacterial community. Gfp-tagged cells were localized particularly in the root hair zone, and high cell densities were apparent on the root hair surface. To investigate the impact of the application of Proradix on the structure of the dominant root-associated bacterial community of barley, T-RFLP analyses were performed. Only a transient community effect was found until 3 weeks post-application.
AU  - Buddrus-Schiemann, K.
AU  - Schmid, M.
AU  - Schreiner, K.
AU  - Welzl, G.
AU  - Hartmann, A.
C1  - 4745
C2  - 27987
SP  - 381-393
TI  - Root colonization by Pseudomonas sp. DSMZ 13134 and impact on the indigenous rhizosphere bacterial community of barley.
JO  - Microb. Ecol.
VL  - 60
IS  - 2
PB  - Springer
PY  - 2010
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - The objective of this study was to compare the microbial community composition and biomass associated with the rhizosphere of a perennial gramineous species (Lygeum spartum L.) with that of an annual (Piptatherum miliaceum L.), both growing in semiarid mine tailings. We also established their relationship with the contents of potentially toxic metals as well as with indicators of soil quality. The total phospholipid fatty acid (PLFA) amount was significantly higher in the rhizosphere soil of the annual species than in the rhizosphere soil of the perennial species. The fungal/bacterial PLFA ratio was significantly greater in the perennial species compared to the annual species. The fatty acid 16:1ω5c, the fungal/bacterial PLFA ratio and monounsaturated/saturated PLFA ratio were correlated negatively with the soluble contents of toxic metals. The cyc/prec (cy17:0 + cy19:0/16:1ω7 + 18:1ω7) ratio was correlated positively with the soluble contents of Pb, Zn, Al, Ni, Cd, and Cu. The results of the PLFA analysis for profiling microbial communities and their stress status of both the plant species indicate that perennial and annual gramineous species appear equally suitable for use in programmes of revegetation of semiarid mine tailings.
AU  - Carrasco, L.*
AU  - Gattinger, A.
AU  - Fliessbach, A.*
AU  - Roldan, A.*
AU  - Schloter, M.
AU  - Caravaca, F.*
C1  - 4782
C2  - 27514
SP  - 265-271
TI  - Estimation by PLFA of microbial community structure associated with the rhizosphere of Lygeum spartum and Piptatherum miliaceum growing in semiarid mine tailings.
JO  - Microb. Ecol.
VL  - 60
IS  - 2
PB  - Springer
PY  - 2010
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - Sulfadiazine (SDZ) is an antibiotic frequently used in agricultural husbandry. Via manuring of excrements of medicated animals, the drug reaches the soil and might impair important biochemical transformation processes performed by microbes, e.g., the nitrogen turnover. We studied the effect of pig manure and SDZ-spiked pig manure on denitrifying bacteria by quantifying nirK and nirS nitrite reductase genes in two arable soils. Addition of manure entailed mainly an increase of nirK-harboring denitrifiers in both soils, whereas in the SDZ-amended treatments, primarily the nirS denitrifiers increased in abundance after the bioavailable SDZ had declined. However, the community composition of nirS nitrite reducers investigated by denaturing gradient gel electrophoresis did not change despite the observed alterations in abundance.
AU  - Kleineidam, K.
AU  - Sharma, S.
AU  - Kotzerke, A.*
AU  - Heuer, H.*
AU  - Thiele-Bruhn, S.*
AU  - Smalla, K.*
AU  - Wilke, B.-M.*
AU  - Schloter, M.
C1  - 4115
C2  - 27652
SP  - 703-707
TI  - Effect of sulfadiazine on abundance and diversity of denitrifying bacteria by determining nirK and nirS genes in two arable soils.
JO  - Microb. Ecol.
VL  - 60
IS  - 4
PB  - Springer
PY  - 2010
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - Glacier forefields are an ideal playground to investigate the role of development stages of soils on the formation of plant-microbe interactions as within the last decades, many alpine glaciers retreated, whereby releasing and exposing parent material for soil development. Especially the status of macronutrients like nitrogen differs between soils of different development stages in these environments and may influence plant growth significantly. Thus, in this study, we reconstructed major parts of the nitrogen cycle in the rhizosphere soil/root system of Leucanthemopsis alpina (L.) HEYWOOD: as well as the corresponding bulk soil by quantifying functional genes of nitrogen fixation (nifH), nitrogen mineralisation (chiA, aprA), nitrification (amoA AOB, amoA AOA) and denitrification (nirS, nirK and nosZ) in a 10-year and a 120-year ice-free soil of the Damma glacier forefield. We linked the results to the ammonium and nitrate concentrations of the soils as well as to the nitrogen and carbon status of the plants. The experiment was performed in a greenhouse simulating the climatic conditions of the glacier forefield. Samples were taken after 7 and 13 weeks of plant growth. Highest nifH gene abundance in connection with lowest nitrogen content of L. alpina was observed in the 10-year soil after 7 weeks of plant growth, demonstrating the important role of associative nitrogen fixation for plant development in this soil. In contrast, in the 120-year soil copy numbers of genes involved in denitrification, mainly nosZ were increased after 13 weeks of plant growth, indicating an overall increased microbial activity status as well as higher concentrations of nitrate in this soil.
AU  - Töwe, S.
AU  - Albert, A.
AU  - Kleineidam, K.
AU  - Brankatschk, R.*
AU  - Dümig, A.*
AU  - Welzl, G.
AU  - Munch, J.-C.
AU  - Zeyer, J.*
AU  - Schloter, M.
C1  - 5992
C2  - 27760
SP  - 762-770
TI  - Abundance of microbes involved in nitrogen transformation in the rhizosphere of Leucanthemopsis alpina (L.) Heywood grown in soils from different sites of the Damma glacier forefield.
JO  - Microb. Ecol.
VL  - 60
IS  - 4
PB  - Springer
PY  - 2010
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - The genetic heterogeneity of neutral metalloprotease (npr) gene fragments from soil proteolytic bacteria was investigated at a cultivated field site with four different soil types and at three different depths in April, July, and October. Terminal restriction fragment length polymorphism (T-RFLP) analyses of polymerase chain reaction-amplified npr gene fragments were applied to study the dynamic of the npr gene pool with regard to environmental conditions. The aim of this study was to relate differences in npr community structure and richness to the vertical, site, and seasonal variations naturally occurring at the field site under investigation. T-RFLP analysis revealed a noticeable seasonal variability in the community structure of npr-containing bacteria. The data suggest that the composition of the npr proteolytic bacterial population in July differed from those at the other dates. Additionally, the diversity of npr genes decreased with increasing soil depth revealing the highest values in upper layers. The reasons behind the observed patterns in the community structure might be mainly seasonal and vertical variation of the quantity and heterogeneity of available substrates as well as spatial isolation caused by a varying water amount and the connectivity of soil particles among the soil profile. Sequencing and phylogenetical analysis of 120 npr clones from the top soils collected in July revealed that most of the clones exhibit only poor homology to npr genes of isolates previously obtained from various environments, indicating the presence of until now uncharacterized npr coding proteolytic bacteria at the study site.
AU  - Fuka, M.M.
AU  - Engel, M.
AU  - Hagn, A.
AU  - Munch, J.-C.
AU  - Sommer, M.*
AU  - Schloter, M.
C1  - 346
C2  - 26122
SP  - 391-401
TI  - Changes of diversity pattern of proteolytic bacteria over time and space in an agricultural soil.
JO  - Microb. Ecol.
VL  - 57
IS  - 3
PB  - Springer
PY  - 2009
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - Gaseous conditions at natural CO2 springs (mofettes) affect many processes in these unique ecosystems. While the response of plants to extreme and fluctuating CO2 concentrations ([CO2]) is relatively well documented, little is known on microbial life in mofette soil. Therefore, it was the aim of this study to investigate the abundance and diversity of CO2-fixing bacteria in grassland soils in different distances to a natural carbon dioxide spring. Samples of the same soil type were collected from the Stavesinci mofette, a natural CO2 spring which is known for very pure CO2 emissions, at different distances from the CO2 releasing vents, at locations that clearly differed in soil CO2 efflux (from 12.5 to over 200 mu mol CO2 m(-2) s(-1) yearly average). Bulk and rhizospheric soil samples were included into analyses. The microbial response was followed by a molecular analysis of cbbL genes, encoding for the large subunit of RubisCO, a carboxylase which is of crucial importance for C assimilation in chemolitoautotrophic microbes. In all samples analyzed, the "red-like" type of cbbL genes could be detected. In contrast, the "green-like" type of cbbL could not be measured by the applied technique. Surprisingly, a reduction of "red-like" cbbL genes copies was observed in bulk soil and rhizosphere samples from the sites with the highest CO2 concentrations. Furthermore, the diversity pattern of "red-like" cbbL genes changed depending on the CO2 regime. This indicates that only a part of the autotrophic CO2-fixing microbes could adapt to the very high CO2 concentrations and adverse life conditions that are governed by mofette gaseous regime.
AU  - Videmsek, U.*
AU  - Hagn, A.
AU  - Suhadolc, M.*
AU  - Radl, V.
AU  - Knicker, H.*
AU  - Schloter, M.
AU  - Vodnik, D.*
C1  - 1469
C2  - 26165
SP  - 1-9
TI  - Abundance and diversity of CO₂-fixing bacteria in grassland soils close to natural carbon dioxide springs.
JO  - Microb. Ecol.
VL  - 58
IS  - 1
PB  - Springer
PY  - 2009
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - Ozone is considered as the main factor in air pollution related to a decline of forest in North America and Europe. In the present study, the effect of changed litter quality, due to ozone stress to trees, on the microbial communities colonizing the subsequent litter was investigated. Litter bag technique using beech and spruce litter from ozone-stressed and control trees, was combined with 16S and 18S rRNA-based fingerprinting methods and cloning to characterize phylogenetic diversity. Litter bags were incubated for 2 and 8 weeks in a beech–spruce mixed forest. Differences between the structure of microbial communities colonizing control and ozone-exposed litter were evident by fingerprints of 16S and 18S rRNA RT-PCR products. RT-PCR products, from litter degraded for 8 weeks, were cloned to identify the bacterial and fungal groups. Clones similar to members of Actinobacteria dominated the bacterial libraries, whereas effects of changed litter quality were mainly observed for the Proteobacteria. Fungal libraries were dominated by clones similar to Ascomycota members. Reduced proportion of clones similar to Basidiomycota and Zygomycota in library from ozone-stressed spruce trees and Chytridiomycota from ozone-stressed beech trees was observed when compared to their control counterparts. As hypothesized, changed litter quality due to elevated O3 did influence the structure of litter-colonizing microbial communities. However, these differences were not as pronounced as those between the two plant species.
AU  - Aneja, M.K.
AU  - Sharma, S.
AU  - Fleischmann, F.*
AU  - Stich, S.
AU  - Heller, W.
AU  - Bahnweg, G.
AU  - Munch, J.-C.
AU  - Schloter, M.
C1  - 3432
C2  - 24525
SP  - 151-160
TI  - Influence of ozone on litter quality and its subsequent effects on the initial structure of colonizing microbial communities.
JO  - Microb. Ecol.
VL  - 54
IS  - 1
PB  - Springer
PY  - 2007
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - Despite the importance of peatlands as a major store of sequestered carbon and the role of fungi in releasing sequestered C, we know little about the community structure of fungi in peatlands. We investigated these across a gradient of naturally regenerating peatland vegetation using denaturing gradient gel electrophoresis (DGGE) and clone libraries of fragments of the fungal rRNA internal transcribed spacer (ITS) region. Significant changes in the fungal community structure of peat samples at different stages of regeneration were observed, which relate to the composition of the vegetation recolonizing these sites. Cloning and sequence analysis also demonstrated a potential shift in the relative abundance of the main fungal phyla. Some of the clones identified to genus level were highly related to fungi known to play a role in the degradation of plant litter or wood in similar ecosystems and/or form mycorrhizal associations. In addition, several fungal isolates highly related to peat clones were obtained, and their enzymic capacity to degrade structural plant tissues was assessed. Together, these results suggest that the fungal community composition of peat may be an important indicator of the status of regeneration and potential carbon sequestration of cutover peatlands.
AU  - Artz, R.R.*
AU  - Anderson, I.C.*
AU  - Chapman, S.J.*
AU  - Hagn, A.
AU  - Schloter, M.
AU  - Potts, J.M.*
AU  - Campbell, C.D.*
C1  - 3244
C2  - 24685
SP  - 508-522
TI  - Changes in fungal community composition in response to vegetational succession during the natural regeneration of cutover peatlands.
JO  - Microb. Ecol.
VL  - 54
IS  - 3
PB  - Springer
PY  - 2007
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - Lasiurus sindicus is a highly nutritive, drought-tolerant, perennial grass that is endemic to the Thar Desert of Rajasthan, India. Analysis of 16S rRNA coding genes of the bacterial isolates enriched in nitrogen-free semisolid medium, from the surface-sterilized roots of L. sindicus, showed predominance of Gram-negative over Gram-positive bacteria. According to comparative sequence analysis of 16S rDNA sequence data, Gram-positive bacteria with low GC content (Staphylococcus warneri and Bacillus sp.) and high GC content (Micrococcus luteus, Microbacterium sp.) were identified. Gram-negative bacteria included Azospirillum sp., Rhizobium sp., Agrobacterium tumefaciens, and Inquilinus limosus (alpha-proteobacteria); Ralstonia sp., Variovorax paradoxus, and Bordetella petrii (beta-proteobacteria); and Pseudomonas pseudoalcaligenes, Stenotrophomonas sp. (gamma-proteobacteria). The occurrence of nifH sequences in Azospirillum sp., Rhizobium sp., and P. pseudoalcaligenes showed the possibility of supplying biologically fixed nitrogen by the root-associated diazotrophs to the host plant.
AU  - Chowdhury, S.P.*
AU  - Schmid, M.
AU  - Hartmann, A.
AU  - Tripathi, A.K.*
C1  - 1197
C2  - 24833
SP  - 82-90
TI  - Identification of diazotrophs in the culturable bacterial community associated with roots of Lasiurus sindicus, a perennial grass of Thar Desert, India.
JO  - Microb. Ecol.
VL  - 54
IS  - 1
PB  - Springer
PY  - 2007
SN  - 0095-3628
ER  - 

TY  - JOUR
AU  - Aneja, M.K.
AU  - Sharma, S.
AU  - Fleischmann, F.*
AU  - Stich, S.
AU  - Heller, W.
AU  - Bahnweg, G.
AU  - Munch, J.-C.
AU  - Schloter, M.
C1  - 5351
C2  - 23751
SP  - 127-135
TI  - Microbial colonization of beech and spruce litter-influence of decomposition site and plant litter species on the diversity of microbial community.
JO  - Microb. Ecol.
VL  - 52
PY  - 2006
SN  - 0095-3628
ER  - 

TY  - JOUR
AU  - Herschkowitz, Y.*
AU  - Lerner, A.*
AU  - Davidov, Y.*
AU  - Rothballer, M.
AU  - Hartmann, A.
AU  - Okon, Y.*
AU  - Jurkevitch, E.*
C1  - 2822
C2  - 23309
SP  - 277-288
TI  - Inoculation with the plant-growth-promoting rhizobacterium Azospirillum brasilense causes little disturbance in the rhizosphere and rhizoplane of Maize (Zea mays).
JO  - Microb. Ecol.
VL  - 50
PY  - 2005
SN  - 0095-3628
ER  - 

TY  - JOUR
AU  - Sharma, S.
AU  - Aneja, M.K.
AU  - Mayer, J.*
AU  - Munch, J.-C.
AU  - Schloter, M.
C1  - 324
C2  - 22730
SP  - 1-9
TI  - Characterization of bacterial community structure in rhizosphere soil of grain legumes.
JO  - Microb. Ecol.
VL  - 49
PY  - 2005
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - Microbial biomass and community structure in paddy rice soil during the vegetation period of rice were estimated by analysis of their phospholipid fatty acids (PLFA), hydroxy fatty acids of lipopolysaccharides (LPS-HYFA), and phospholipid ether lipids (PLEL) directly extracted from the soil. A clear change in the composition of the community structure at different sampling periods was observed, indicated by the principal component analysis of the PLFA. A dramatic decline of ester-linked PLFA was observed in the soil samples taken at the second sampling time. In contrast to the ester-linked PLFA, the non-ester-linked PLFA composition did not change. The hydroxy fatty acids of lipopolysaccharides as well as ether lipids decreased consecutively during the observation period. Total microbial abundance was estimated to be (4.1-7.3) x 10(9) cells g(-1) soil (dry weight). About 44% account for aerobic and 32% for facultative anaerobic bacteria, and 24% for archaea, on average. According to the profile and patterns of PLFA in the soil sample, it may be suggested that the paddy soil at the August sampling period contained more abundant facultative anaerobic bacteria (ca. 36%) and archaea (ca. 37%), but the total microbial biomass was significantly lower than in the remaining sampling periods. As the plant approached maturity, the microbial community structure in the soil changed to contain more abundant Gram-negative bacteria and methanotrophs.
AU  - Bai, Q.*
AU  - Gattinger, A.
AU  - Zelles, L.
C1  - 21351
C2  - 19467
SP  - 273-281
TI  - Characterization of Microbial Consortia in Paddy Rice Soil by Phospholipid Analysis.
JO  - Microb. Ecol.
VL  - 39
IS  - 4
PY  - 2000
SN  - 0095-3628
ER  - 

TY  - JOUR
AB  - Fluorescence-labeled antibodies and oligonucleotides were used simultaneously for the in situ identification of bacteria in mixed cultures, as well as in the rhizosphere of inoculated plants. Counterstaining was performed with 4'-6-diamidino-2-phenylindole (DAPI), and scanning confocal laser microscopy or epifluoresence microscopy with a charge-coupled device (CCD) camera were used for detection of individual cells. This strategy gave insight into the relative abundance of an inoculated strain, enabled the exact localization of single cells, and allowed the estimation of the metabolic activity of the bacteria in a complex specimen. Using a strain-specific monoclonal antibody for Azospirillum brasilense Wa3, we could identify this particular strain in root samples of inoculated wheat plantlets. Strain Wa3, as well as other bacteria colonizing the rhizosphere, were stained simultaneously with rRNA-targeted, fluorescence-labeled oligonucleotide probes. In a co-inoculation experiment with A. brasilense strains Sp7 and Wa3, it was demonstrated by in situ identification and quantitative chemoluminescence ELISA that strain Sp7 outcompeted strain Wa3. The combined application of fluorescently labeled antibodies and oligonucleotides should be generally applicable for monitoring specific bacterial strains, within the background of the same species, in relation to the total microbiota.
AU  - Aßmus, B.
AU  - Schloter, M.
AU  - Kirchhof, G.
AU  - Hutzler, P.
AU  - Hartmann, A.
C1  - 23109
C2  - 36861
SP  - 32-40
TI  - Improved in situ tracking of rhizosphere bacteria using dual staining with fluorescence-labeled antibodies and rRNA-targeted oligonucleotides.
JO  - Microb. Ecol.
VL  - 33
IS  - 1
PB  - Springer
PY  - 1997
SN  - 0095-3628
ER  -