Population number, viability, and taxonomic composition of the bacterial nanoforms in iron-manganic concretions

It is shown for the first time that a significant part of the bacteria (up to 40%) in the iron-manganic concretions of soddy-podzolic and soddy meadow soils are represented by nanoforms; their number reaches 600–700 million cells/g. Judging from the specific luminescent coloration, the fraction of viable cells among the bacterial nanoforms is very high in the concretions and amounts up to 88–99%. For the first time, the following phyla were identified among the bacterial nanoforms in the concretions with the use of the FISH method: Alphaproteobacteria, Betaproteobacteria, Gammaproteobateria, Deltaproteobacteria, Acidobacteria, and Planctomycetes. The Gammaproteobacteria phylum predominated in the concretions from the soddy-podzolic soil, and the Deltaproteobacteria phylum predominated in the concretions from the soddy meadow soil. In the alluvial meadow soil, the Alphaproteobacteria, Betaproteobacteria, and Acidobacteria phyla were found. The significant number and portion of bacterial nanoforms in the concretions, their high vitality, and their taxonomic diversity allow us to conclude that the bacterial nanoforms play an important role in the processes taking place in the concretions.     

Population density and taxonomic composition of bacterial nanoforms in soils of Russia

The population density, physiological state, and taxonomic composition of bacterial nanoforms were first studied in soils of Russia. It was demonstrated with the help of fluorescent microscopy that the populations of nanoforms in the studied soils are very high and comprise tens and hundreds of millions of cells per 1 g of soil. The portion of cells with undamaged cell membranes was significantly higher in the nanoforms (95–98%) than in the cells of common size (about 50%), and this fact suggests the viability of the nanoforms. The taxonomic diversity of the nanoforms is great; the representatives of the main phylogenetic groups widespread in the soils were found among the nanoforms, namely, Archaea, Actinobacteria, Cytophaga, and Proteobacteria. The results allow assuming that the transformation of the cells into nanoforms is a relatively common event in the life of soil bacteria, allowing them to remain viable under unfavorable conditions and participate actively in soil processes.     

Study of ultramicrobacteria (Nanoforms) in soils and subsoil deposits by electron microscopy

The use of multiple centrifuging and filtration of water suspensions from different soils and subsoil deposits allowed revealing the ultrafine forms (nanosized, nanoforms) of bacteria. In the soils studied, the number of bacteria obtained by filtration using 0.2-??m filters was 20?C300 mln cells in 1 g soil; the share of these bacteria of their total population in the natural soils reached 5% and was higher (up to 15%) in the polluted urban soils. The study of bacterial nanoforms in situ by the methods of scanning and transmission microscopy has shown the presence of dividing cells, which testifies to their viability. The cells without signs of division were similar in their ultrastructural characteristics to dormant forms of nonspore-forming bacteria. They were observed in permafrost deposits. The data obtained attest that the bacterial nanoforms are widespread in soils and subsoil deposits. According to their morphological and cytological characteristics, they are represented by both active and dormant forms to survive unfavorable conditions.     

Viability of bacteria in peatlands

The viability of bacteria in oligotrofic bogs and fens was determined by the luminescent microscopy method with the help of a two-component fluorescent dye (L7012 LIVE/DEAD). Living bacterial cells were found in the entire peat profiles. Their portion was maximal (up to 60%) in the upper layers and did not exceed 25% in the lower layers. The portion of dead bacterial cells varied from 3 to 19%, and dormant cells constituted 25 to 95% of the total number of bacterial cells. The numbers of dormant cells increased down the profiles irrespectively of the peat type. The portion of nanoforms did not exceed 5% of the total. The cells of the nanoforms, unlike the bacteria of typical sizes, were characterized by their high viability (93–98%).     

Study of bacteria from manganese concretions. Precipitation of manganese by whole cells and cell-free extracts of isolated bacteria

A microbiological examination of manganese concretions which were found in an alfisol soil of West Peloponnese, Greece, is presented. Two new Mn²⁺ oxidizing bacteria identified as Pseudomonas sp. nov. (E₁) and Citrobacter freundii (E₄) were isolated from the core of the concretions. The Mn²⁺ oxidizing activity of the isolates was demonstrated on solidified media. The quantitative determination of Mn²⁺ precipitation was performed by activation analysis and atomic absorption spectrophotometry. The mechanism of Mn²⁺ precipitation was studied using whole cell, and cell-free extracts of both bacteria; a precipitation of 50% and 70%, respectively, occurred without any change in the pH. The precipitation of Mn²⁺ depended on the concentration of the whole cells and of the cell-free extracts and was independent of the presence of Mn during the growth of the cultures. The activity of cell-free extracts is heat sensitive and inhibited by HgCl₂.The porosity of the concretions and the presence of amorphous manganese oxides in them, together with the morphology and physiology of the bacteria isolated from the core of them, present good evidence that those bacteria play an important role in the formation of the examined concretions.     

The association of cobalt with easily reducible manganese in some acidic permanent grassland soils

The association of cobalt with manganese oxides was examined in some surface and sub-soils from areas of permanent grassland in England. Hydroquinone (0.2% in ammonium acetate at pH 7.0) was used to extract easily reducible Mn oxides from the soils. Two sequential extractions with this reagent removed significant proportions of the total Co along with the Mn; no significant amounts of iron were extracted. Mn-rich iron concretions were isolated from two of the soils and these contained from 230 to 880 μg g^?1 Co. Approximately 30% of the Co in the concretions was dissolved by two sequential extractions with hydroquinone with concurrent release of considerable amounts of Mn, but, as with the soils, not of Fe. The concretions contained 20–41 mg g^?1 Mn and 62–171 mg g^?1 Fe that were soluble in acidified H₂O₂. It was concluded that significant proportions of the Co in soils is associated with Mn oxides, and will show the same sensitivity to changes in acidity and redox potential as Mn.     

Gehalte an Haupt- und Nebenelementen in Konkretionen aus Oberböden von Marschen – Untersuchungen mit einer Mikrosonde

Contents of major and trace elements in concretions of surface samples from marsh soils – Electron microprobe analysis The amounts of 14 elements (Ti, Fe, Mn, Si, Al, Ca, and P, S, Co, Ni, Cu, Zn, Cd, Pb) in concretions of four A horizons of marsh soils were determined by electron microprobe analysis on thin sections. According to the major element compositions the following types of concretions can be distinguished: Ti-Fe(-Mn) concretions (31–39% Ti; 18–29% Fe; 0,3–5,5% Mn); Fe(-Mn) concretions (31–58% Fe; ≤ 1,8% Mn); Fe-Si(-Mn) concretions (6–28% Fe; 8–42% Si; ≤ 5% Mn); Mn-Fe and Mn-Fe-Si concretions (16–40% Mn; 2–9% Fe; 2–15% Si). The formation of Ti-Fe(-Mn) concretions can be explained by adsorption of Fe²⁺ ions under reducing conditions on surfaces of Ti minerals followed by oxidation to Fe(III) oxide. In this way pseudorutile may be formed. Concretions with high Fe and/or Mn content often contain occlusions of carbonates, silicates and/or SiO₂ (bioopal) which may act as nuclei for their growth. Redox processes in marsh soils result in the formation of concretions with dominating Fe or Mn accumulation. Among the group of trace elements, P and S (like Ti and Si) reach their highest concentrations in Fe rich concretions (up to 54.000 mg P/kg and 4.200 mg S/kg). The accumulation of these elements is obviously influenced by anion competition, especially of P and Si, and probably also Ti. Likewise, high amounts of Pb were found in Fe(-Mn) concretions (up to 12.000 mg/kg). Co, Ni, Zn, and Cd show the highest amounts in Mn rich concretions (Co up to 3.400; Ni 1.800; Zn 13.200; Cd 1.000 mg/kg). Cu is also accumulated in some concretions (up to 1140 mg/kg) but no clear affinity to one of the different types of concretions was found.     

Proto-imogolite allophane in podzol concretions in Australia: possible relationship to aluminous ferrallitic (lateritic) cementation

Proto-imogolite allophane was found in amounts ranging from 1% to 5% in concretions and ortstein from several sandy podzols in Australia. Micromorphological observations on concretions in which allophane was the dominant clay component indicated that it had been deposited in layers during successive drying episodes to form a yellow, glassy, weakly anisotropic, fluorescent cement around sand grains. Iron oxides and organic matter were minor components of the cement. It is proposed that a proto-imogolite sol is the mobile phase that deposits Al and Si in these concretions, and that the proto-imogolite allophane could be a precursor of kaolinite in older concretions, and of gibbsite in leaching environments. Proto-imogolite sols and allophane could play a similar role in the pedogenesis of kaolinite and gibbsite in concretions in freely drained ferrallitic soils.     

Estimation of Phosphorus Status of Soil Fe‐Enriched Concretions with the Acid Ammonium Oxalate Method

Abstract

Iron (Fe)‐enriched concretions, a complex natural matrix with high chemical heterogeneity and phosphate‐sorption capacity, is widespread in soils with restrictive drainage in Greece. However, the phosphorus (P) status and related characteristics of Fe‐enriched concretions in agricultural soils in areas where P fertilization is mainly inorganic are relatively unknown. Active noncrystalline Fe and aluminum (Al) oxides (Feox, Alox), oxalate extractable P (Pox), P sorption capacity (PSC), and the degree of P saturation (DPS) of Fe‐enriched concretions from agricultural imperfectly drained soils in central Greece were determined using the acid ammonium oxalate method. The concretions contain 13 times as much Feox, twice as much Alox, and almost 15 times as much Pox than the surrounding soil matrix. Pox accounted for 50–80% of total P of the soil concretions, indicating strong accumulation of noncrystalline P components (Al‐ and Fe‐P). The PSC, expressed as a 0.5 (Alox+Feox), ranged from 184.7 to 314 mmol kg^?1, demonstrating the strong affinity of the Fe‐enriched concretions for P. The DPS, which represents the fraction of concretion sorbent surface coverage by P, was computed as 100 (Pox/PSC) with values ranging from 6 to 13% (mean=8%). The results of this study indicate that the Fe‐enriched concretions, due to their high noncrystalline Fe and Al oxides content, act as major sink of phosphate, controlling the location, mobility, and dynamics of P in agricultural soils with restrictive drainage.     

Iron–manganese concretions contribute to benthic release of phosphorus and arsenic in anoxic conditions in the Baltic Sea

Purpose

Deposits of iron–manganese (Fe, Mn) concretions forming a large storage of phosphorus (P) and arsenic (As) are frequently under pressure of oscillating oxygen conditions in the eutrophic Gulf of Finland, the Baltic Sea. Yet, there is a poor understanding how anaerobic microbial processes regulate the cycling of elements in the concretions. The objective of this study was to highlight how the microbial processes control the release of elements from the concretions to brackish water during anoxia.

Materials and methods

Spherical concretions were collected from the oxic bottoms of the Gulf of Finland in the summer. Concretions and autoclaved controls were incubated in anoxic artificial brackish seawater with and without labile carbon, plus supplied with ammonium at 5, 10, and 20 °C for 15 weeks. Concentrations of Fe, Mn, P, and As were measured from the intact concretions and the ambient solutions during the experiment. Also, the consumption of the added ammonium and organic carbon and the formation of dissolved inorganic carbon were measured.

Results and discussion

At near-bottom temperature 5 °C, the concretions released at highest 0.12, 0.42, 0.02, and 0.0002 μmol g^?1 day^?1 of Fe, Mn, P, and As, respectively. The rates were significant only in the microcosms with added labile carbon, and only minor proportions (0.1–0.4 %) of their total contents were released during the incubations. The concretions removed completely the supplied ammonium only without carbon addition. We find that concretion deposit may form a local hot spot for the microbial reduction of Fe and Mn and release significant amounts of P and As, and participate in N cycling besides the bottom sediments of the Gulf of Finland during prolonged anoxia. However, the concretions may maintain their binding capacity for P and As longer than the fine-grained organic-rich sediment during anoxia.

Conclusions

During anoxia concretion deposits may form a temporal source of bioavailable P having ecological significance in the Gulf of Finland when concretions have access to labile organic carbon. Concretions from the Baltic Sea, the oceans, lakes, and soils contain high concentrations of Mn and Fe, but their proportions vary considerably. Anaerobic microbial processes may thus affect the stability of concretions from the different environments, but the outcome may depend on the ambient geochemical conditions.

     

Extraction of bacteria from soil: Efficiency of shaking or ultrasonication as indicated by direct counts and autoradiography

Blending, shaking with a mechanical wrist-action shaker or ultrasonication were compared for removing bacteria from a sandy soil and a silt loam soil. Bacteria were counted microscopically after staining with acridine orange. There was no significant difference in the numbers of bacteria released from the sandy soil by the different treatments but ultrasonication extracted more bacteria from the silt loam. Highest recoveries of bacteria were obtained with a combination of Tris buffer as extractant, and 25% Ringer's solution as diluent. Ultrasonication of an irradiated sandy soil containing added Bacillus cereus removed 97% of the bacteria from the sand grains, but lysed some cells. Members of the indigenous soil population were more firmly held by the soil than added bacteria. Optimum conditions for recovering soil bacteria by ultrasonication were either 10.5 μm for 30s or 5 μm for 2 min. With the natural population, the numbers of bacteria and the proportion of metabolizing bacteria increased a little after ultrasonication as shown by labelling cells with ³H-glucose and detecting uptake by autoradiography. However, three isolates of bacteria tested showed varying amounts of injury after ultrasonication, with 5 μm for 2 min causing more damage than 10.5 μm for 30s. Ultrasonication was a more efficient means of extracting the natural bacterial population of soil than shaking but the time and amplitude must be adjusted to avoid injury to cultured bacterial cells.     

Characterization of iron oxides in Fe-rich concretions from an imperfectly-drained Greek soil: a study by selective-dissolution techniques and X-ray diffraction

Fe-rich concretions commonly occur in Greek soils with alternating drying and waterlogging periods. This study was conducted to characterize the iron oxides in Fe-rich concretions from the upper solum of an Alfisol with seasonal perched water table by the combination of selective dissolution and X-ray diffraction (XRD) techniques. The results showed that more than 75% of the total iron (Fet) was associated with the crystalline and the amorphous Fe oxides, indicating a strong accumulation of free iron oxides (Fed) in concretions. Amorphous iron compounds (Feo) was present at high concentrations and fluctuated with profile depth. The active Fe ratio (Feo/Fed) values that ranged from 0.35 to 0.41 reflected an association of poorly crystalline goethite with some ferrihydrite. The XRD data showed that the Fe-rich concretions consisted of quartz, feldspars, illite and gypsum. The mineralogy of iron oxides in concretions was determined by comparison of XRD patterns for dithionite-citrate-bicarbonate (DCB) treated (deferrated) and untreated (non-deferrated) samples. Poorly crystalline goethite as demonstrated by broad lines in the diffraction patterns and ferrihydrite were the iron oxides detected in the concretions. This mineral assemblage appears to be related to the pedoenvironmental conditions in which the concretions were formed and indicates that the mechanisms governing the formation of crystalline Fe oxides from ferrihydrite are retarded by the presence of crystallization inhibitors.     

Soil bulk density corrections for providing a better relationship with root growth in gravelly soil

Abstract

Bulk density of a Tifton (Plinthitic Paleudult; fine loamy, siliceous, thermic) soil containing 5.8 to 11.0% of the sample weight as pebbles was 0.06–0.12 g/cc lower when corrections were made for presence of pebbles or concretions. A method for determining the bulk density of the soil matrix between pebbles or concretions is outlined. After adjustment, the bulk density at which root penetration was inhibited in this soil closely approximated that for soils which do not contain concretions. The proposed procedure reflects more nearly how bulk density changes where plant roots are growing than previously published procedures do.     

On some general regularities of the formation and changes in properties of mn‐fe concretions in soils of humid landscapes

An attempt is made to formulate general regularities of changes in the amount and composition of Mn‐Fe conoretions in soils of humid landscapes, confined to various soil‐forming rocks within the Russian platform. It is concluded, that the intensive formation of concretions is highly conditioned by waterlogging degree of soils and their hydrological regime. The content of concretions is always maximum in gley‐like soils (seldom in gley ones), independing on genesis of parent rocks; the fraction distribution of Mn‐Fe concretions proves to be stable in time; Mn amount is declined with increasing the waterloggiing degree of soils, while the content of Fe becomes increased; the highest accumulation of such microelements as Co, Pb, Cd is observed in concretions, which are rich in Mn. The concretions are characterized by a high amount of X‐ray‐amorphous Fe as well as by a low magnetic susceptibility. The chemical composition of concretions is shown to be preferable for quantitative diagnosis of the water‐logging degree in soils.     

Concretions in typical chernozem,gleyed chernozem-like,and solonetzic chernozem-like soils of the southern Tambov Lowland

A system for the diagnostics of chernozemic soils of the Tambov Lowland based on concretions is proposed for agricultural and reclamation purposes. The relationships between the structure and composition of the carbonate concretions, the long-term water regime of the soils, and the productivity of the crops have been established. The dense concretions in the typical chernozem testify to the depth of the seasonal wetting; the angular-rounded concretions in the deeply gleyed chernozem-like soil, to the upper boundary of the capillary fringe; and the angular concretions with sharp edges and cavities in the gleyic chernozem-like soils, to the groundwater table. In the chernozem-like soils that were waterlogged with bicarbonate-sodium water, the black angular concretions were formed in the solonetzic horizons, while the weakly compacted light-colored ones, in the zone of the capillary fringe. Humic acids were responsible for the color of the dark neoformations, and fulvic acids predominated in the light-colored ones. The appearance of black fine nodules indicated periodic surface water stagnation. Manganese predominantly accumulates in these nodules. The structure of the Mn-Fe concretions in the plow horizon observed at a magnification of 40–50 times has a diagnostic importance. The short-term (2–3 weeks) water stagnation leads to the formation of fine-stratified concretions, and the long-term (up to 1.5 months) stagnation promotes the formation of uniform porous ones. The solonetzic process induced by the bicarbonate-sodium water results in the appearance of mottled concretions.     

Composition of iron-manganese concretions from some New Zealand soils

A selection of iron-manganese concretions from five reference soil profiles and a buried loess deposit in New Zealand have been studied. Concretions appear to have developed by the precipitation of amorphous iron and manganese oxides among soil particles. X-ray fluorescence analysis shows that the concentrations of Fe, Mn, Co and Ba in the concretions are generally higher, and those of K, Ca, Si, and Al are generally lower, than in the soil materials surrounding the concretions, whereas Ti, Zn, S, and P show little variation. Other approximate analyses indicate that Cu, Ni, Mo, V, and Pb tend to be concentrated in concretions but for Ga, Zr, Sr, Li, and Rb there was no discernible trend. Electron probe microanalyses of some concretions show that Co and Ba are concentrated in Mn-rich phases rather than Fe-rich phases.Comparison with published results for concretions (Mn nodules) from the ocean floor and the floor of Lake Ontario indicates that, on average, marine concretions have higher Mn, and lower Si and Al concentrations than soil concretions, and that marine concretions have lower Fe concentrations than either Ontario or soil concretions.     

Composition and mineralogy of iron-manganese concretions from some soils of the Indo-Gangetic plain in Northwest India

Iron-manganese concretions from three reference soil series of the Indo-Gangetic plain of Punjab have been investigated for their composition, micromorphology and mineralogy. The data show that amounts of Fe, Mn, Co, Ni, Cu and Zn in the concretions are higher than in the surrounding soil matrix. The contents of Mn, Co and Ni increase and that of Fe decreases with the increasing size of concretions. Cu or Zn contents do not show any systematic differences with concretion size. A major portion of these elements is oxalate- and dithionite-extractable. A minor fraction is present in the silicate structure as well as in the pyrophosphate-extractable forms. The Fe and Mn compounds present in the concretions are x-ray amorphous. The concretions appear to have developed in situ.     

Microbial DNA extraction and analyses of soil iron–manganese nodules

Iron–manganese (Fe–Mn) nodules and concretions are soil new growth, reflecting soil environmental conditions during their formation. Bacteria play a dominant role in the oxidation of dissolved Mn(II) in aqueous systems and the formation of marine and freshwater Fe–Mn nodules. However, the role and significance of bacteria in soil Fe–Mn nodule formation have not been well recognized. In this paper, microbial DNA was directly extracted from two Fe–Mn nodule samples collected from Wuhan and Guiyang in central China. The extracted DNA was amplified by polymerase chain reaction (PCR) and cloned. The clones were then screened by amplified ribosomal DNA restriction analysis (ARDRA). Twenty patterns were obtained for Wuhan sample and Guiyang sample, respectively. DNA sequencing and phylogenetic analyses revealed that the bacterial compositions of the Fe–Mn nodules were mainly belonged to Firmicutes, β-proteobacteria, γ-proteobacteria branches of the domain bacteria. These divisions had close relativeness with Mn(II)-oxidizing bacteria identified from marine Fe–Mn nodules, implying the possible contributions of these bacteria to soil Fe–Mn nodule formation.     

Manganese, iron, and phosphorus in nodules of chernozem-like soils on the northern Tambov Plain and their importance for the diagnostics of gley intensity

Nodules (nodules) forming in the chernozem-like soils of flat-bottomed closed depressions on the northern part of the Tambov Plain differ in their morphology and chemical composition as related to the degree of hydromorphism of these soils. The highest are the coefficients of Mn, P, and Fe accumulation in the nodules from these soils. The Fe to Mn ratio grows with the increasing degree of hydromorphism. Under surface moistening, the maximal amounts of mobile Mn and Fe compounds were extracted from the nodules of the most hydromorphic podzolic chernozem-like soils; under the ground moistening, their greatest amounts were extracted from the least hydromorphic soil—the weakly gley soil. In the first case, the content of organic phosphates in concretions amounted to 30–50%; in the second one, 2–3% of their total content. Under surface moistening, the proportion of active mineral phosphates becomes higher with the increasing hydromorphism: from 30 (podzolized soil) to 70% (gleyic podzolic soil). Under ground moistening, on the contrary, their proportion decreases from 70–89% in the weakly gley soil to 40–50% in the gley chernozem-like soil. The possibility to determine the degree of hydromorphism of chernozem-like soils based on the coefficients of bogging is shown. The expediency of using Schvertmann’s criterion in these studies is assessed.     

Occurrence and transformations of iron and manganese in a colluvial terra rossa toposequence of northern Italy

A soil toposequence in NE Italy was studied, which consists of a terra rossa on Cretaceous limestone on the upper slope grading downwards into a colluvial fan with terra rossa material and finally into alluvial river sediments. It is postulated that the red colluviated terra rossa material has come under a moister hydroregime which provided reducing conditions. Because hematite of the terra rossa dissolved preferentially over goethite, as shown by quantitative Fe oxide mineralogy, soil color changed from 2.5YR to 7.5YR. The soils contained two types of concretions, red ones with a low Fe_o/Fe_d ratio and a high content of hematite and low content of Mn-oxides and black ones with a high Fe_o/Fe_d ratio, a small amount of hematite and abundant Mn oxides. The red concretions are therefore considered as inherited from an earlier period of pedogenesis whereas the black ones are neoformed in the present pedoenvironment. This is further supported by the lower Al-for-Fe substitution of goethite in the black concretions as compared to a higher Al substitution in the goethite inherited from the terra rossa.