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Jun Takada - One of the best experts on this subject based on the ideXlab platform.
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Two types of morphologically distinct fibers comprising Gallionella ferruginea twisted stalks.
Microbes and environments, 2012Co-Authors: Tomoko Suzuki, Nobuyuki Matsumoto, Hitoshi Kunoh, Hideki Hashimoto, Hiromichi Ishihara, Jun TakadaAbstract:Two morphologically distinct extracellular stalk fibers produced by Gallionella ferruginea were compared by electron microscopy and elemental analysis. The thick- and fine-fiber stalks were different in structure on a micrometer scale and in the site on the mother cell to which they were attached, but on a nanometer scale they were similar in ultrastructure and in the elemental composition of their basic fiber matrix.
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Silicon and phosphorus linkage with iron via oxygen in the amorphous matrix of Gallionella Ferruginea stalks
Applied and Environmental Microbiology, 2012Co-Authors: Tomoko Suzuki, Nobuyuki Matsumoto, Hitoshi Kunoh, Atsushi Itadani, Hideki Hashimoto, Jun TakadaAbstract:Bacterial species belonging to the genus Gallionella are Fe-oxidizing bacteria that produce uniquely twisted extracellular stalks consisting of iron-oxide-encrusted inorganic/organic fibers in aquatic environments. This paper describes the degree of crystallinity of Gallionella stalks and the chemical linkages of constituent elements in the stalk fibers. Transmission electron microscopy revealed that the matrix of the fiber edge consisted of an assembly of primary particles of approximately 3 nm in diameter. Scanning transmission electron microscopy revealed the rough granular surfaces of the fibers, which reflect the disordered assembly of the primary particles, indicating a high porosity and large specific surface area of the fibers. This may provide the surface with broader reactive properties. X-ray diffractometry, selected-area electron diffraction, and high-resolution transmission electron microscopy together showed that the primary particles had an amorphous structure. Furthermore, energy-dispersive X-ray analysis and Fourier transform infrared spectroscopy detected the bands characteristic of the vibrational modes assigned to O-H, Fe-O-H, P-O-H, Si-O-H, Si-O-Fe, and P-O-Fe bonds in the stalks, suggesting that the minor constituent elements P and Si could affect the degree of crystallinity of the fibers by linking with Fe via O. This knowledge about the mutual associations of these elements provides deeper insights into the unique inorganic/organic hybrid structure of the stalks.
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Structural and Spatial Associations between Fe, O, and C in the Network Structure of the Leptothrix ochracea Sheath Surface
Applied and environmental microbiology, 2011Co-Authors: Tomoko Suzuki, Hitoshi Kunoh, Hideki Hashimoto, Tomonari Kasai, Hiromichi Ishihara, Jun TakadaAbstract:The structural and spatial associations of Fe with O and C in the outer coat fibers of the Leptothrix ochracea sheath were shown to be substantially similar to the stalk fibers of Gallionella ferruginea, i.e., a central C core, probably of bacterial origin, and aquatic Fe interacting with O at the surface of the core.
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nanometer scale visualization and structural analysis of the inorganic organic hybrid structure of Gallionella ferruginea twisted stalks
Applied and Environmental Microbiology, 2011Co-Authors: Tomoko Suzuki, Nobuyuki Matsumoto, Hitoshi Kunoh, Hideki Hashimoto, Mitsuaki Furutani, Jun TakadaAbstract:The so-called Fe/Mn-oxidizing bacteria have long been recognized for their potential to form extracellular iron hydroxide or manganese oxide structures in aquatic environments. Bacterial species belonging to the genus Gallionella, one type of such bacteria, oxidize iron and produce uniquely twisted extracellular stalks consisting of iron oxide-encrusted inorganic/organic fibers. This paper describes the ultrastructure of Gallionella cells and stalks and the visualized structural and spatial localization of constitutive elements within the stalks. Electron microscopy with energy-dispersive X-ray microanalysis showed the export site of the stalk fibers from the cell and the uniform distribution of iron, silicon, and phosphorous in the stalks. Electron energy-loss spectroscopy revealed that the stalk fibers had a central carbon core of bacterial exopolymers and that aquatic iron interacted with oxygen at the surface of the carbon core, resulting in deposition of iron oxides at the surface. This new knowledge of the structural and spatial associations of iron with oxygen and carbon provides deeper insights into the unique inorganic/organic hybrid structure of the stalks.
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Nanometer-scale visualization and structural analysis of the inorganic/organic hybrid structure of Gallionella ferruginea twisted stalks.
Applied and environmental microbiology, 2011Co-Authors: Tomoko Suzuki, Nobuyuki Matsumoto, Hitoshi Kunoh, Hideki Hashimoto, Mitsuaki Furutani, Jun TakadaAbstract:The so-called Fe/Mn-oxidizing bacteria have long been recognized for their potential to form extracellular iron hydroxide or manganese oxide structures in aquatic environments. Bacterial species belonging to the genus Gallionella, one type of such bacteria, oxidize iron and produce uniquely twisted extracellular stalks consisting of iron oxide-encrusted inorganic/organic fibers. This paper describes the ultrastructure of Gallionella cells and stalks and the visualized structural and spatial localization of constitutive elements within the stalks. Electron microscopy with energy-dispersive X-ray microanalysis showed the export site of the stalk fibers from the cell and the uniform distribution of iron, silicon, and phosphorous in the stalks. Electron energy-loss spectroscopy revealed that the stalk fibers had a central carbon core of bacterial exopolymers and that aquatic iron interacted with oxygen at the surface of the carbon core, resulting in deposition of iron oxides at the surface. This new knowledge of the structural and spatial associations of iron with oxygen and carbon provides deeper insights into the unique inorganic/organic hybrid structure of the stalks.
Hendrikus J. Laanbroek - One of the best experts on this subject based on the ideXlab platform.
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The influence of human settlement on the distribution and diversity of iron-oxidizing bacteria belonging to the Gallionellaceae in tropical streams
Frontiers in microbiology, 2014Co-Authors: Mariana P. Reis, Marcelo P. Ávila, PatrÃcia S. Costa, Francisco A. R. Barbosa, Hendrikus J. Laanbroek, Edmar Chartone-souza, Andréa M. A. NascimentoAbstract:Among the neutrophilic iron-oxidizing bacteria (FeOB), Gallionella is one of the most abundant genera in freshwater environments. By applying qPCR and DGGE based on 16S rRNA gene-directed primers targeting Gallionellaceae, we delineated the composition and abundance of the Gallionellaceae-related FeOB community in streams differentially affected by metal mining, and explored the relationships between these community characteristics and environmental variables. The sampling design included streams historically impacted by mining activity and a non-impacted stream. The sediment and water samples harbored a distinct community represented by Gallionella, Sideroxydans, and Thiobacillus species. Sequences affiliated with Gallionella were exclusively observed in sediments impacted by mining activities, suggesting an adaptation of this genus to these environments. In contrast, Sideroxydans-related sequences were found in all sediments including the mining impacted locations. The highest and lowest relative frequencies of Gallionellaceae-related FeOB were associated with the lowest and highest concentrations of Fe, respectively. The data enclosed here clearly show distinct species-specific ecological niches, with Gallionella species dominating in sediments impacted by anthropogenic activities over Sideroxydans species.
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Spatial Patterns of Iron- and Methane-Oxidizing Bacterial Communities in an Irregularly Flooded, Riparian Wetland
Frontiers in microbiology, 2012Co-Authors: Juanjuan Wang, Hendrikus J. Laanbroek, Gerard Muyzer, Marion Meima-franke, Sascha Krause, Paul L E BodelierAbstract:Iron- and methane-cycling are important processes in wetlands with one connected to plant growth and the other to greenhouse gas emission, respectively. In contrast to acidic habitats, there is scarce information on the ecology of microbes oxidizing ferrous iron at circum-neutral pH. The latter is mainly due to the lack of isolated representatives and molecular detection techniques. Recently, we developed PCR-DGGE and QPCR assays to detect and enumerate Gallionella-related neutrophilic iron-oxidisers (FeOB) enabling the assessment of controlling physical as well as biological factors in various ecosystems. In this study, we investigated the spatial distribution of Gallionella-related FeOB in co-occurrence with methane-oxidizing bacteria (MOB) in a riparian wetland. Soil samples were collected at different spatial scales (ranging from meters to centimeters) representing a hydrological gradient. The diversity of FeOB was assessed using PCR-DGGE and the abundance of both FeOB and MOB by QPCR. Geostatistical methods were applied to visualize the spatial distribution of both groups. Spatial distribution as well as abundance of FeOB and MOB was clearly correlated to the hydrological gradient as expressed in moisture content of the soil. Gallionella-related numbers of FeOB outnumbered the MOB subgroups indicating their competitiveness or the prevalence of Fe2+ over CH4 oxidation in this floodplain.
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Distribution and Diversity of Gallionella-Like Neutrophilic Iron Oxidizers in a Tidal Freshwater Marsh
Applied and environmental microbiology, 2011Co-Authors: Juanjuan Wang, Gerard Muyzer, Paul L E Bodelier, S. Vollrath, Thilo Behrends, Marion Meima-franke, Frank Den Oudsten, Philippe Van Cappellen, Hendrikus J. LaanbroekAbstract:Microbial iron oxidation is an integral part of the iron redox cycle in wetlands. Nonetheless, relatively little is known about the composition and ecology of iron-oxidizing communities in the soils and sediments of wetlands. In this study, sediment cores were collected across a freshwater tidal marsh in order to characterize the iron-oxidizing bacteria (FeOB) and to link their distributions to the geochemical properties of the sediments. We applied recently designed 16S rRNA primers targeting Gallionella-related FeOB by using a nested PCR-denaturing gradient gel electrophoresis (DGGE) approach combined with a novel quantitative PCR (qPCR) assay. Gallionella-related FeOB were detected in most of the samples. The diversity and abundance of the putative FeOB were generally higher in the upper 5 to 12 cm of sediment than in deeper sediment and higher in samples collected in April than in those collected in July and October. Oxygen supply by macrofauna appears to be a major force in controlling the spatial and temporal variations in FeOB communities. The higher abundance of Gallionella-related FeOB in April coincided with elevated concentrations of extractable Fe(III) in the sediments. Despite this coincidence, the distributions of FeOB did not exhibit a simple relationship to the redox zonation inferred from the geochemical depth profiles.
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EXPLORING MICROBIAL IRON OXIDATION IN WETLAND SOILS
2010Co-Authors: Juanjuan Wang, Gerard Muyzer, Paul L E Bodelier, S. Vollrath, Marion Meima-franke, F. Den Oudsten, Hendrikus J. LaanbroekAbstract:The release of oxygen by the roots of wetland plants creates suboxic conditions that may favour the growth of iron-oxidizing bacteria (FeOB). Given their importance in iron cycling, little is known about the diversity or distribution of these bacteria. This is largely due to the lack of efficient methods to study them and the difficulty in isolating them in pure culture. Our study is focussing at the ecology of FeOB by developing molecular and microbiological methods to investigate them in situ. Firstly, gradient tubes were used to enrich and isolate iron-oxidizing bacteria. A novel iron-oxidizing strain related to Gallionella spp. was isolated from an irregularly flooded grassland soil. Secondly, a specific primer set 122f/998r targeting the 16S rRNA gene was developed on the basis of the isolate. The primer set was applied to community DNA obtained from three contrasting wetland environments, followed by DGGE analysis. The PCR products were also used to construct a 16S rRNA gene library. The cloned sequences all represented novel iron oxidizers most closely related to Gallionella spp., and were comparable to the PCR-DGGE result. Thirdly, a SYBR Green qPCR assay was developed. Together with the previously mentioned nested PCR-DGGE method, the qPCR assay was used to quantify the distribution of FeOB in the tidal freshwater marsh. The effects of plant niches, soil depth, elevation gradient and season were investigated. The results showed that the composition of the FeOB community varied with sediment depth, elevation gradient and season, while no influence was observed from plant species. A strong correlation between relative abundance and Fe(III) concentration indicated that the bacterial distribution might be influenced by the iron dynamics. Moreover, oxygen availability and moisture content could serve other steering factors.
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Diversity of iron oxidizers in wetland soils revealed by novel 16S rRNA primers targeting Gallionella-related bacteria
The ISME Journal, 2009Co-Authors: Juanjuan Wang, Gerard Muyzer, Paul L E Bodelier, Hendrikus J. LaanbroekAbstract:Neutrophilic iron-oxidizing bacteria (FeOB) are important catalysts of iron cycling in wetland environments. However, little is known about their diversity and distribution in various environments. The aim of this study was to develop a PCR-DGGE assay enabling the detection of neutrophilic iron oxidizers in wetland habitats. Gradient tubes were used to enrich FeOB. From these enrichments, a clone library was established on the basis of the almost complete 16S rRNA gene using the universal bacterial primers 27f and 1492r. This clone library consisted of mainly α- and β- Proteobacteria , among which two major clusters were closely related to Gallionella spp. Specific probes and primers were developed on the basis of this 16S rRNA gene clone library. The newly designed Gallionella -specific 16S rRNA gene primer set 122f/998r was applied to community DNA obtained from three contrasting wetland environments, followed by Denaturing Gradient Gel Electrophoresis (DGGE) analysis. A second 16S rRNA gene clone library was constructed using the PCR products from one of our sampling sites amplified with the newly developed primer set 122f/998r. The cloned 16S rRNA gene sequences all represented novel culturable iron oxidizers most closely related to Gallionella sp. On the basis of their nucleotide sequences, four groups could be identified that were comparable to the DGGE banding pattern obtained before with the same PCR products as used for the second clone library. Using these Gallionella -specific 16S rRNA gene-based primers, in combination with DGGE, first insights into the diversity and distribution of these bacteria in wetland soils were obtained.
Tomoko Suzuki - One of the best experts on this subject based on the ideXlab platform.
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Two types of morphologically distinct fibers comprising Gallionella ferruginea twisted stalks.
Microbes and environments, 2012Co-Authors: Tomoko Suzuki, Nobuyuki Matsumoto, Hitoshi Kunoh, Hideki Hashimoto, Hiromichi Ishihara, Jun TakadaAbstract:Two morphologically distinct extracellular stalk fibers produced by Gallionella ferruginea were compared by electron microscopy and elemental analysis. The thick- and fine-fiber stalks were different in structure on a micrometer scale and in the site on the mother cell to which they were attached, but on a nanometer scale they were similar in ultrastructure and in the elemental composition of their basic fiber matrix.
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Silicon and phosphorus linkage with iron via oxygen in the amorphous matrix of Gallionella Ferruginea stalks
Applied and Environmental Microbiology, 2012Co-Authors: Tomoko Suzuki, Nobuyuki Matsumoto, Hitoshi Kunoh, Atsushi Itadani, Hideki Hashimoto, Jun TakadaAbstract:Bacterial species belonging to the genus Gallionella are Fe-oxidizing bacteria that produce uniquely twisted extracellular stalks consisting of iron-oxide-encrusted inorganic/organic fibers in aquatic environments. This paper describes the degree of crystallinity of Gallionella stalks and the chemical linkages of constituent elements in the stalk fibers. Transmission electron microscopy revealed that the matrix of the fiber edge consisted of an assembly of primary particles of approximately 3 nm in diameter. Scanning transmission electron microscopy revealed the rough granular surfaces of the fibers, which reflect the disordered assembly of the primary particles, indicating a high porosity and large specific surface area of the fibers. This may provide the surface with broader reactive properties. X-ray diffractometry, selected-area electron diffraction, and high-resolution transmission electron microscopy together showed that the primary particles had an amorphous structure. Furthermore, energy-dispersive X-ray analysis and Fourier transform infrared spectroscopy detected the bands characteristic of the vibrational modes assigned to O-H, Fe-O-H, P-O-H, Si-O-H, Si-O-Fe, and P-O-Fe bonds in the stalks, suggesting that the minor constituent elements P and Si could affect the degree of crystallinity of the fibers by linking with Fe via O. This knowledge about the mutual associations of these elements provides deeper insights into the unique inorganic/organic hybrid structure of the stalks.
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Structural and Spatial Associations between Fe, O, and C in the Network Structure of the Leptothrix ochracea Sheath Surface
Applied and environmental microbiology, 2011Co-Authors: Tomoko Suzuki, Hitoshi Kunoh, Hideki Hashimoto, Tomonari Kasai, Hiromichi Ishihara, Jun TakadaAbstract:The structural and spatial associations of Fe with O and C in the outer coat fibers of the Leptothrix ochracea sheath were shown to be substantially similar to the stalk fibers of Gallionella ferruginea, i.e., a central C core, probably of bacterial origin, and aquatic Fe interacting with O at the surface of the core.
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nanometer scale visualization and structural analysis of the inorganic organic hybrid structure of Gallionella ferruginea twisted stalks
Applied and Environmental Microbiology, 2011Co-Authors: Tomoko Suzuki, Nobuyuki Matsumoto, Hitoshi Kunoh, Hideki Hashimoto, Mitsuaki Furutani, Jun TakadaAbstract:The so-called Fe/Mn-oxidizing bacteria have long been recognized for their potential to form extracellular iron hydroxide or manganese oxide structures in aquatic environments. Bacterial species belonging to the genus Gallionella, one type of such bacteria, oxidize iron and produce uniquely twisted extracellular stalks consisting of iron oxide-encrusted inorganic/organic fibers. This paper describes the ultrastructure of Gallionella cells and stalks and the visualized structural and spatial localization of constitutive elements within the stalks. Electron microscopy with energy-dispersive X-ray microanalysis showed the export site of the stalk fibers from the cell and the uniform distribution of iron, silicon, and phosphorous in the stalks. Electron energy-loss spectroscopy revealed that the stalk fibers had a central carbon core of bacterial exopolymers and that aquatic iron interacted with oxygen at the surface of the carbon core, resulting in deposition of iron oxides at the surface. This new knowledge of the structural and spatial associations of iron with oxygen and carbon provides deeper insights into the unique inorganic/organic hybrid structure of the stalks.
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Nanometer-scale visualization and structural analysis of the inorganic/organic hybrid structure of Gallionella ferruginea twisted stalks.
Applied and environmental microbiology, 2011Co-Authors: Tomoko Suzuki, Nobuyuki Matsumoto, Hitoshi Kunoh, Hideki Hashimoto, Mitsuaki Furutani, Jun TakadaAbstract:The so-called Fe/Mn-oxidizing bacteria have long been recognized for their potential to form extracellular iron hydroxide or manganese oxide structures in aquatic environments. Bacterial species belonging to the genus Gallionella, one type of such bacteria, oxidize iron and produce uniquely twisted extracellular stalks consisting of iron oxide-encrusted inorganic/organic fibers. This paper describes the ultrastructure of Gallionella cells and stalks and the visualized structural and spatial localization of constitutive elements within the stalks. Electron microscopy with energy-dispersive X-ray microanalysis showed the export site of the stalk fibers from the cell and the uniform distribution of iron, silicon, and phosphorous in the stalks. Electron energy-loss spectroscopy revealed that the stalk fibers had a central carbon core of bacterial exopolymers and that aquatic iron interacted with oxygen at the surface of the carbon core, resulting in deposition of iron oxides at the surface. This new knowledge of the structural and spatial associations of iron with oxygen and carbon provides deeper insights into the unique inorganic/organic hybrid structure of the stalks.
Juanjuan Wang - One of the best experts on this subject based on the ideXlab platform.
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Revealing the microbial community structure of clogging materials in dewatering wells differing in physico-chemical parameters in an open-cast mining area.
Water research, 2014Co-Authors: Juanjuan Wang, Maren Sickinger, Valerian Ciobota, Martina Herrmann, Helfried Rasch, Petra Rösch, Jürgen Popp, Kirsten KüselAbstract:Abstract Iron rich deposits cause clogging the pumps and pipes of dewatering wells in open-cast mines, interfering with their function; however, little is known about either the microbial community structure or their potential role in the formation of these deposits. The microbial diversity and abundance of iron-oxidizing and -reducing bacteria were compared in pipe deposit samples with different levels of encrustation from 16 wells at three lignite mining sites. The groundwater varied in pH values from slightly acidic (4.5) to neutral (7.3), Fe(II) concentrations from 0.48 to 7.55 mM, oxygen content from 1.8 to 5.8 mg L −1 , and dissolved organic carbon (DOC) from 1.43 to 12.59 mg L −1 . There were high numbers of bacterial 16S rRNA gene copies in deposits, up to 2.5 × 10 10 copies g −1 wet weight. Pyrosequencing analysis of bacterial 16S rRNA genes revealed that Proteobacteria was the most abundant phylum (63.3% of the total reads on average), followed by Actinobacteria (10.2%) and Chloroflexi (6.4%). Gallionella -related sequences dominated the bacterial community of pipe deposits and accounted for 48% of total sequence reads. Pipe deposits with amorphous ferrihydrite and schwertmannite mostly contained Gallionella (up to 1.51 × 10 10 16S rRNA gene copies g −1 wet weight), while more crystalline deposits showed a higher bacterial diversity. Surprisingly, the abundance of Gallionella was not correlated with groundwater pH, oxygen, or DOC content. Sideroxydans- related 16S rRNA gene copy numbers were one order of magnitude less than Gallionella , followed by acidophilic Ferrovum -related groups. Iron reducing bacteria were detected at rather low abundance, as was expected given the low iron reduction potential, although they could be stimulated by lactate amendment. The overall high abundance of Gallionella suggests that microbes may make major contributions to pipe deposit formation irrespective of the water geochemistry. Their iron oxidation activity might initiate the formation of amorphous iron oxides, potentially providing niches for other microorganisms later after crystallization, and leading to higher bacterial diversity along with deposit accumulation in later stages of clogging.
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Spatial Patterns of Iron- and Methane-Oxidizing Bacterial Communities in an Irregularly Flooded, Riparian Wetland
Frontiers in microbiology, 2012Co-Authors: Juanjuan Wang, Hendrikus J. Laanbroek, Gerard Muyzer, Marion Meima-franke, Sascha Krause, Paul L E BodelierAbstract:Iron- and methane-cycling are important processes in wetlands with one connected to plant growth and the other to greenhouse gas emission, respectively. In contrast to acidic habitats, there is scarce information on the ecology of microbes oxidizing ferrous iron at circum-neutral pH. The latter is mainly due to the lack of isolated representatives and molecular detection techniques. Recently, we developed PCR-DGGE and QPCR assays to detect and enumerate Gallionella-related neutrophilic iron-oxidisers (FeOB) enabling the assessment of controlling physical as well as biological factors in various ecosystems. In this study, we investigated the spatial distribution of Gallionella-related FeOB in co-occurrence with methane-oxidizing bacteria (MOB) in a riparian wetland. Soil samples were collected at different spatial scales (ranging from meters to centimeters) representing a hydrological gradient. The diversity of FeOB was assessed using PCR-DGGE and the abundance of both FeOB and MOB by QPCR. Geostatistical methods were applied to visualize the spatial distribution of both groups. Spatial distribution as well as abundance of FeOB and MOB was clearly correlated to the hydrological gradient as expressed in moisture content of the soil. Gallionella-related numbers of FeOB outnumbered the MOB subgroups indicating their competitiveness or the prevalence of Fe2+ over CH4 oxidation in this floodplain.
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Ecology of neutrophilic iron-oxidizing bacteria in wetland soils
2011Co-Authors: Juanjuan WangAbstract:Wetland ecosystems are important as sites of rapid biogeochemical cycling of bioactive elements, among which iron features prominently. The redox cycling of iron exerts a strong influence on soil chemistry and the metabolism of plants and microorganisms. Studies have shown that bacteria play an important role in the process of iron oxidation in wetlands. This study explores the diversity and distribution of iron-oxidizing bacteria (FeOB) in soils and sediments of freshwater and brackish wetlands of circum-neutral pH, and analyzes the potential environmental factors influencing them. Gradient tubes were used to enrich FeOB from soil and sediment samples. From these enrichments, a clone library was established on the basis of the almost complete 16S rRNA gene. Specific probes and primers were developed using Gallionella-related sequences from this library. The newly designed Gallionella-specific 16S rRNA gene primer set was applied to community DNA obtained from three contrasting wetland environments, followed by Denaturing Gradient Gel Electrophoresis (DGGE) analysis and cloning. The retrieved 16S rRNA gene sequences yielded novel iron oxidizers most closely related to Gallionella spp. A novel quantitative PCR (qPCR) assay was developed. In combination with the nested PCR-DGGE approach, it was used to delineate the spatial and temporal distributions of FeOB at a number of locations characterized by different plant species in a tidal freshwater marsh (Appels, Belgium). The presence of Gallionella-related FeOB was confirmed in vegetated and non-vegetated sediments of the tidal marsh. A high temporal variability of the composition of the iron-oxidizing community was observed. Iron-oxidizing bacteria flourished especially in early spring. The simultaneous accumulation of iron (hydr)oxides further indicated increased iron oxidizing activity. Overall, the results implied a highly dynamic FeOB community structure. The spatial distribution of FeOB communities was also analyzed along a flooding gradient in an irregularly flooded riparian wetland (Ewijk, Netherlands). In addition, the co-occurrence of methane-oxidizing bacteria (MOB) was investigated, as MOB represent a biological component that may affect the distribution of FeOB under conditions of oxygen limitation. A clear trend of increasing abundance of FeOB was observed with increasing elevation and, hence, decreasing flooding intensity and soil moisture content. The abundance of FeOB exceeded that of MOB. With the modified gradient tube method, we successfully isolated a novel FeOB strain, representing a new genus. This neutrophilic iron-oxidizing bacterium, Ferrocurvibacter nieuwersluisensis gen. nov., sp. nov., was isolated from an iron-rich grassland. This isolate belongs to the same group as detected by the specific primers. In conclusion, this thesis describes novel findings about the occurrence of neutrophilic iron-oxidizing bacteria in a number of wetland ecosystems in the delta area of the Netherlands and Belgium, by characterizing the distribution of FeOB in various wetlands and by enriching and isolating these organisms. This work opens up new opportunities for using molecular tools to study microbial iron oxidation at circum-neutral pH and contributes to the knowledge of iron cycling in redox-stratified environments. Future work should focus on the spatial and temporal distributions of FeOB in additional environment settings, the mechanism of bacterial iron oxidation, and its interactions with other key biotic and abiotic processes, in particular microbial iron reduction
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Distribution and Diversity of Gallionella-Like Neutrophilic Iron Oxidizers in a Tidal Freshwater Marsh
Applied and environmental microbiology, 2011Co-Authors: Juanjuan Wang, Gerard Muyzer, Paul L E Bodelier, S. Vollrath, Thilo Behrends, Marion Meima-franke, Frank Den Oudsten, Philippe Van Cappellen, Hendrikus J. LaanbroekAbstract:Microbial iron oxidation is an integral part of the iron redox cycle in wetlands. Nonetheless, relatively little is known about the composition and ecology of iron-oxidizing communities in the soils and sediments of wetlands. In this study, sediment cores were collected across a freshwater tidal marsh in order to characterize the iron-oxidizing bacteria (FeOB) and to link their distributions to the geochemical properties of the sediments. We applied recently designed 16S rRNA primers targeting Gallionella-related FeOB by using a nested PCR-denaturing gradient gel electrophoresis (DGGE) approach combined with a novel quantitative PCR (qPCR) assay. Gallionella-related FeOB were detected in most of the samples. The diversity and abundance of the putative FeOB were generally higher in the upper 5 to 12 cm of sediment than in deeper sediment and higher in samples collected in April than in those collected in July and October. Oxygen supply by macrofauna appears to be a major force in controlling the spatial and temporal variations in FeOB communities. The higher abundance of Gallionella-related FeOB in April coincided with elevated concentrations of extractable Fe(III) in the sediments. Despite this coincidence, the distributions of FeOB did not exhibit a simple relationship to the redox zonation inferred from the geochemical depth profiles.
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EXPLORING MICROBIAL IRON OXIDATION IN WETLAND SOILS
2010Co-Authors: Juanjuan Wang, Gerard Muyzer, Paul L E Bodelier, S. Vollrath, Marion Meima-franke, F. Den Oudsten, Hendrikus J. LaanbroekAbstract:The release of oxygen by the roots of wetland plants creates suboxic conditions that may favour the growth of iron-oxidizing bacteria (FeOB). Given their importance in iron cycling, little is known about the diversity or distribution of these bacteria. This is largely due to the lack of efficient methods to study them and the difficulty in isolating them in pure culture. Our study is focussing at the ecology of FeOB by developing molecular and microbiological methods to investigate them in situ. Firstly, gradient tubes were used to enrich and isolate iron-oxidizing bacteria. A novel iron-oxidizing strain related to Gallionella spp. was isolated from an irregularly flooded grassland soil. Secondly, a specific primer set 122f/998r targeting the 16S rRNA gene was developed on the basis of the isolate. The primer set was applied to community DNA obtained from three contrasting wetland environments, followed by DGGE analysis. The PCR products were also used to construct a 16S rRNA gene library. The cloned sequences all represented novel iron oxidizers most closely related to Gallionella spp., and were comparable to the PCR-DGGE result. Thirdly, a SYBR Green qPCR assay was developed. Together with the previously mentioned nested PCR-DGGE method, the qPCR assay was used to quantify the distribution of FeOB in the tidal freshwater marsh. The effects of plant niches, soil depth, elevation gradient and season were investigated. The results showed that the composition of the FeOB community varied with sediment depth, elevation gradient and season, while no influence was observed from plant species. A strong correlation between relative abundance and Fe(III) concentration indicated that the bacterial distribution might be influenced by the iron dynamics. Moreover, oxygen availability and moisture content could serve other steering factors.
M. R. Carvalho - One of the best experts on this subject based on the ideXlab platform.
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Bioconstructions in ochreous speleothems from lava tubes on Terceira Island (Azores)
Sedimentary Geology, 2011Co-Authors: A. De Los Ríos, Mª Ángeles Bustillo, Carmen Ascaso, M. R. CarvalhoAbstract:Abstract The ochreous speleothems examined here were obtained from a lava tube on Terceira Island (Azores) and show compact mineralized areas intermixed with zones in which bacterial structures are evident. Bacterial layers of filament-like structures are common throughout the deposits but differences in microstructure among the different speleothems were observed, reflecting a broad morphological range of deposits. The structures and minerals detected in the speleothems betray their biogenic origin. Gallionella and Leptothrix were the two most frequently observed morphotypes and probably the main contributors to speleothem formation. However, DGGE analysis indicated the presence of another bacterial population (with a predominance of proteobacteria) that could also contribute to iron hydroxide–oxide precipitation. The sheaths of Leptothrix cells and stalks of Gallionella cells were associated with large amounts of extrapolymeric substances (EPS), which play a role in biomineralization processes. Independently of the taxa present, mineral deposits were composed of poorly ordered Si-rich ferrihydrite, a typical mineral phase of biogenic Fe precipitates. In this microscopy study of interrelationships between mineral precipitates and associated microorganisms and their structures, we attribute bacteria to have an important role in constructing these speleothems. Through their metabolic activity, these bacteria cause the precipitation of ferrihydrite but their mineral structures could also act as nucleation points for passive mineral precipitation. Finally, the build-up of bacterial mineral structures and later cementation processes seems responsible for the formation of mineral layers that confer consistency to the speleothem. Our findings point to bacterial activity as the main factor determining speleothem structure and formation.
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Bioconstructions in ochreous speleothems from lava tubes on Terceira Island (Azores)
Sedimentary Geology, 2011Co-Authors: A. De Los Ríos, Mª Ángeles Bustillo, Carmen Ascaso, M. R. CarvalhoAbstract:13 pages, figures and tables statistics.The ochreous speleothems examined here were obtained from a lava tube on Terceira Island (Azores) and\ud show compact mineralized areas intermixed with zones in which bacterial structures are evident. Bacterial\ud layers of filament-like structures are common throughout the deposits but differences in microstructure\ud among the different speleothems were observed, reflecting a broad morphological range of deposits.\ud The structures and minerals detected in the speleothems betray their biogenic origin. Gallionella and\ud Leptothrix were the two most frequently observed morphotypes and probably the main contributors to\ud speleothem formation. However, DGGE analysis indicated the presence of another bacterial population (with\ud a predominance of proteobacteria) that could also contribute to iron hydroxide–oxide precipitation. The\ud sheaths of Leptothrix cells and stalks of Gallionella cells were associated with large amounts of extrapolymeric\ud substances (EPS), which play a role in biomineralization processes. Independently of the taxa present, mineral\ud deposits were composed of poorly ordered Si-rich ferrihydrite, a typical mineral phase of biogenic Fe\ud precipitates.\ud In this microscopy study of interrelationships between mineral precipitates and associated microorganisms\ud and their structures, we attribute bacteria to have an important role in constructing these speleothems.\ud Through their metabolic activity, these bacteria cause the precipitation of ferrihydrite but their mineral\ud structures could also act as nucleation points for passive mineral precipitation. Finally, the build-up of\ud bacterial mineral structures and later cementation processes seems responsible for the formation of mineral\ud layers that confer consistency to the speleothem. Our findings point to bacterial activity as the main factor\ud determining speleothem structure and formation.Peer reviewe
