Characteristics of bacteria in the forest soils under natural vegetation

Characteristics of the predominant bacteria isolated in November and May from the forest soils of both dry and wet types under natural vegetation were studied.

Although Gram-negative rods were the most abundant bacteria in both soil types and in both seasons, their contents were less and other bacteria especially spore-forming ones increased in May.

Among Gram-negative rods in the soil of the dry type in November, the most predominant was those with nonchromogenic rods motile with polar flagella which grew in a simple synthetic media containing glucose or p-hydroxybenzoate and ammonium as the sole carbon and nitrogen sources. In May, the ratio of the bacteria which require amino nitrogen or those with more chomplex nutritional requirement increased. In the soil of moderately wet type, the difference in kinds of bacteria between the two seasons was not so clear as that in the dry type.

Most of Bacillus species obtained in these soils were those requiring amino acids or other growth factors among which B. cereus was most abundant.     

DISTRIBUTION OF FORMS OF NITROGEN IN A PODZOLIC SOIL PROFILE FROM GARPENBERG, CENTRAL SWEDEN

The chemical nature and distribution patterns of the forms of N in a podzolic soil profile from central Sweden, developed under a stand of Norway spruce, were studied. Total N, native fixed NH₄, acid hydrolysable-N, and the amounts of ammonia, hexosamine, and amino-acid N in the hydrolysate were determined. From 17 to 27 per cent of the N was insoluble in 6N HC1, the highest percentage being in the A₂ horizon. Amino-acids in the acid hydrolysates decreased from 50 per cent of the total N content of the soil in the humus layer (A₀) to 24 per cent in the B horizon. Amino-acid composition varied little in samples from different horizons. Hexosamine-N was 11–14 per cent of the total soil N, tending to increase with depth. Approximately 15 per cent of the total soil N was found in the soil hydrolysate as NH₄. Values for native fixed NH₄ extracted by N HF: N HCl were 34–80 ppm but were reduced to 10–17 ppm when corrected for the NH₄ released by N HCl only. The figures thus obtained are considerably lower than those reported by other workers.     

Characterization of Cu-resistant bacterial communities in Cu-contaminated soils

Bacterial communities in a spoil heap in a copper mine, a forest soil with high Cu contamination, and an agricultural soil with low Cu contamination were characterized in terms of Gram-staining, plasmid frequency, pigmentation, Cu-resistance system, and predominant Cu-resistant bacterial species. Similarity existed in that the ratio of green colonies for sorbing Cu and Gram-negative bacteria increased with the increase of the Cu content of the medium regardless of the characteristics of the bacterial communities. It was found that the plasmid was not present in most of the Cu-resistant bacteria of the soils. Curesistant genera including Burkholderia, Alcaligenes, and Methylobacterium species were isolated from the Cu contaminated soils using YG agar plates treated with 2 mM Cu. Furthermore, the bacterium with the highest Cu resistance (MIC = 5.5 mm Cu) was identified as a Gram-positive bacterium Bacillus sp., though most of the Cu-resistant bacteria were Gram-negative.     

The distribution of PG (green fraction of P type humic acid) and the degree of humification of PB (brown fraction of P type humic acid) in soils of central Japan

Abstract

Pg contents of soils chosen from the major soil groups occurring in the mountain area of Central Japan were measured by the method presented by the author in a previous paper. The Pg contents of the soils ranged from 0 to 0.58 per cent of the dry soils. In podzolic soils, Pg contents were high in A horizons and gradually decreased with depth and in some cases of brown forest soils, Pg contents were highest in B horizons. The percentage of Pg in humic acid ranged from 0 to 8.6 per cent, and the highest value was observed in the C horizon of Dando Bo soil, Pg contents were high in humid and acidic soils containing much humic acid. Humidity, soil pH and humus content may affect the Pg accumulation by controlling the activity of Pg-producing fungi. ? log K values of Pb were calculated to estimate the degree of humification of P type humic acids and indicated that Pb's were relatively immature.     

THE INFLUENCE OF TEXTURE ON THE MOISTURE CHARACTERISTICS OF SOILS

The available-water capacity (AWC) of soil profiles in the field may be estimated by (a) measuring the thickness of each soil horizon; (b) assessing its texture; and (c) summing the products of the thickness of each horizon and the mean values of AWC for the relevant textural classes. (This mean value of AWC was calculated from the average particle-size composition and from a relationship between particle size composition and AWC.) Estimates of AWC using this method were compared with measured values for each of 39 soils. When a 21 textural-class system was used to describe the soils, the mean error (the error of the estimated AWC value relative to the measured value) was ±10 per cent and with a 12 class system the mean error was ±17 per cent.     

Moderately haloalkaliphilic actinomycetes in salt-affected soils

It was found that the population density of actinomycetes in solonchaks and saline desert soils varied from hundreds to tens of thousands of colony-forming units (CFUs) per 1 g of soil depending on soil type and was by 1–3 orders of magnitude lower than the number of mycelial bacteria in main soil types. Actinomycetes grow actively in saline soils, and the length of their mycelium reaches 140 m per 1 g of soil. Domination of moderately halophilic, alkaliphilic, and haloalkaliphilic actinomycetes, which grow well under 5% NaCl and pH 8–9, is a specific feature of actinomycetal complexes in saline soils. Representatives of Streptomyces and Micromonospora genera were found among the haloalkaliphilic actinomycetes. Micromonospores demonstrated lower (than streptomycetes) adaptability to high salt concentrations. Investigation of the phylogenetic position of isolated dominant haloalkaliphilic strains of streptomycetes performed on the basis of sequencing of the gene 16S rRNA enabled identifying these strains as Streptomyces pluricolorescens and S. prunicolor.     

Changes in weathering effectiveness and community of culturable mineral-weathering bacteria along a soil profile

Bacteria play important roles in mineral weathering, element mobilization, and soil formation. However, little is known about the mineral-weathering bacteria in subsurface soil environments. In this study, a total of 360 bacterial isolates were isolated from the different horizons of a soil profile and characterized for their mineral-weathering abilities and diversity along the soil profile. Among the 360 isolates, 226 isolates were found to have the ability to weather biotite. The average of released Fe, Si, and Al were significantly higher by the isolates from deeper horizons than from upper horizons. Although the proportion of the highly effective Fe solubilizers was not significantly different among the different horizons, the proportion of the highly effective Si and Al solubilizers was significantly higher in the deeper horizons than in the upper horizons. Furthermore, the element-releasing patterns of the mineral-weathering bacteria were different among the different horizons. Most of mineral-weathering bacteria from the soil profile could significantly lower the culture medium pH in the mineral-weathering process. The diversity of the mineral-weathering bacteria was higher in the upper horizons than in the deeper horizons. The weathering bacteria belonged to 12 bacterial genera, among which Burkholderia, Bacillus, and Lysinibacillus were the dominant and high-efficient weathering bacteria. The results showed the depth-related changes in the weathering capacity and community structures of the culturable mineral-weathering bacteria and suggested the possible roles of the bacteria in the mineral-weathering and element mobilization along the soil profile.     

Screening of soil bacteria for plasmids carrying antibiotic resistance

Summary To evaluate the role of plasmids in soil communities antibiotic-resistant bacteria have been isolated from soil. Among them, 419 l-aminopeptidase positive strains (Gram-negative) and 28 l-aminopeptidase negative strains (Gram-positive) were screened for the presence of plasmids. None of the Gram-negative organisms contained plasmids. Among the Gram-positive bacteria plasmid-harboring strains were detected.     

Micro-scale variation of solid-phase properties and soil solution chemistry in a forest podzol and its relation to soil horizons

In order to evaluate micro-scale heterogeneities 55 micro suction cups were placed in an array at 15 mm intervals in a profile face of a cambic podzol. The chemistry of soil solution (mineral anions, pH, UV absorption as a measure for DOC) was compared with solid-phase properties from soil samples (2 cm³ volume), which had surrounded the suction cups. Sequential extraction techniques (water, NF₄Cl, hydroxylamin-hydrochloride, citrate-bicarbonate, oxalate, dithionite-citrate-bicarbonate) and base titrations were applied to characterize the solid phase. Although the average soil solution concentrations between horizons often differed significantly, the spatial distributions of pH and SO₄^2? did not correlate with soil horizon borders. Even if concentration isolines and soil horizon borders were parallel, marked concentration gradients could be observed within individual soil horizons. The less intense the interaction between solute ion and soil matrix, the greater was the variation in solution concentration within a soil horizon. For the soil solid phase only a weak correlation of slow buffer reactions to soil horizons was found. The distribution of extractable Fe and Al was typical for a podzol profile, however, with very steep gradients within single soil horizons. Except for pH, which was related mainly to citrate-bicarbonate extractable aluminium, no solid-phase characteristic showed a clear correlation with soil solution chemistry.     

Long-term changes in microbial community structure in soils subjected to different fertilizing practices revealed by quinone profile analysis

Quinone profile analysis of stored air-dried soils gave an approximation of the long-term changes in the microbial community structure in four soils subjected to different types of fertilizer application from 1987 to 1997: unfertilized soil (NF-soil), soil amended with chemical fertilizers (CF-soil), soil amended with chemical fertilizers and 40 t ha^-1 y^-1 of farmyard manure (CF+ FYM-soil), and soil amended with 400 t ha^-1 y^-1 of farmyard manure (FYM-soil). The carbon content increased, and the soil pH remained higher in the soils receiving farmyard manure. Principal component analysis of the quinone profiles of the soils indicated that the microbial community structure showed a high similarity among the four soils before the onset of cultivation and changed to a different community structure specific to the respective fertilizing practices except for the NF-soil. The specific quinone profile became stable after two cropping seasons in the FYM-soil, after 10 cropping seasons in the CF+ FYM-soil and after 15 cropping seasons in the CF-soil, respectively. The quinone profile of the NF-soil did not become stable, and no specific profile was developed. The specific quinone profiles in the FYM- and CF+ FYM-soils were both characterized by large mole fractions of menaquinone with seven isoprenoid units (MK-7). Farmyard manure itself contained a large mole fraction of MK-7. It was suggested that the amount of MK-7 increased due to the application of farmyard manure. MK-7 indicates the presence of Gram-positive bacteria with low guanine plus cytosine contents such as Bacillus and Gram-negative bacteria of the Cytophaga-Flavobacterium complex. The specific quinone profile in the CF-soil was characterized by the presence of menaquinone with seven isoprenoid units dihydrated (MK-7(H₂)and MK-7(H₄). Although Brevibacterium and Kocuria contain MK-7(H₂), no microorganisms are known to have MK- 7(H.) as major quinone. The common major quinones were MK-8, MK-10(H₄) and a mixture of MK-8(H₄) and MK-9, suggesting the predominance of Grampositive bacteria in all the soils. Mole fractions of Ubiquinone with 8 isoprenoid units (Q-8) and Q-10 increased at various times in all the soils, indicating the sporadic growth of Gram-negative bacteria.     

Using pXRF and vis-NIR spectra for predicting properties of soils developed in loess

Visible near-infrared (vis-NIR) and portable X-ray fluorescence (pXRF) spectrometers have been increasingly utilized for predicting soil properties worldwide. However, only a few studies have focused on splitting the predictive models by horizons to evaluate prediction performance and systematically compare prediction performance for A, B, and combined A+B horizons. Therefore, we investigated the performance of pXRF and vis-NIR spectra, as individual or combined, for predicting the clay, silt, sand, total carbon (TC), and pH of soils developed in loess, and compared their prediction performance for A, B, and A+B horizons. Soil samples (176 in A horizon and 172 in B horizon) were taken from Mollisols and Alfisols in 136 pedons in Wisconsin, USA and analyzed for clay, silt, sand, pH, and TC. The pXRF and vis-NIR spectrometers were used to measure the pXRF and vis-NIR soil spectra. Data were separated into calibration (n=244, 70%) and validation (n=104, 30%) datasets. The Savitzky-Golay filter was applied to preprocess the pXRF and vis-NIR spectra, and the first 10 principal components (PCs) were selected through principal component analysis (PCA). Five types of predictor, i.e., PCs from vis-NIR spectra, pXRF of beams at 0-40 and 0-10 keV (XRF40 and XRF10, respectively) spectra, combined XRF40 and XRF10 (XRF40+XRF10) spectra, and combined XRF40, XRF10, and vis-NIR (XRF40+XRF10+vis-NIR) spectra, were compared for predicting soil properties using a machine learning algorithm (Cubist model). A multiple linear regression (MLR) model was applied to predict clay, silt, sand, pH, and TC using pXRF elements. The results suggested that pXRF spectra had better prediction performance for clay, silt, and sand, whereas vis-NIR spectra produced better TC and pH predictions. The best prediction performance for sand (R²=0.97), silt (R²=0.95), and clay (R²=0.84) was achieved using vis-NIR+XRF40+XRF10 spectra in B horizon, whereas the best prediction performance for TC (R²=0.93) and pH (R²=0.79) was achieved using vis-NIR+XRF40+XRF10 spectra in A+B horizon. For all soil properties, the best MLR model had a lower prediction accuracy than the Cubist model. It was concluded that pXRF and vis-NIR spectra can be successfully applied for predicting clay, silt, sand, pH, and TC with high accuracy for soils developed in loess, and that spectral models should be developed for different horizons to achieve high prediction accuracy.     

Significance of Silver Birch and Bushgrass for Establishment of Microbial Heterotrophic Community in a Metal-Mine Spoil Heap

Differences in the culturable fractions of total and metal-tolerant bacteria inhabiting bulk soil of a metal-mine spoil heap and the rhizosphere of silver birch (Betula pendula) or bushgrass (Calamagrostis epigejos), completed with changes in total microbial community structure in the soil, were assessed by MIDI-FAME (fatty acid methyl ester) profiling of whole-cell fatty acids. In addition, the abundance of metal-tolerant populations among the culturable bacterial communities and their identity and the metal-tolerance patterns were determined. The high proportions of Cu- and Zn-tolerant bacteria that ranged from 60.6% to 94.8% were ascertained in the heap sites. Within 31 bacterial isolates obtained, 24 strains were Gram-positive and Arthrobacter, Bacillus, Rathayibacter, Brochothrix, and Staphylococcus represented those identified. Minimum inhibitory concentration (MIC) data indicated that several strains developed multi-metal tolerance, and the highest tolerance to Cu (10 mM) and Zn (12 mM) was found for Pseudomonas putida TP3 and three isolated strains (BS3, TP12, and SL16), respectively. The analysis of FAME profiles obtained from the culturable bacterial communities showed that Gram-positive bacteria predominated in bulk soil of all heap sites. In contrast, the rhizosphere communities showed a lower proportion of the Gram-positive group, especially for silver birch. For the total microbial community, mostly Gram-negative bacteria (e.g., Pseudomonas) inhabited the heap sites. The results suggest that the quantitative and qualitative development of heterotrophic microbiota in the soil of the metal-mine spoil heap seems to be site-dependent (i.e., rhizosphere vs. bulk soil), according to differences in the site characteristics (e.g., enrichment of nutrients and total metal concentrations) and impact of plant species.     

Antagonists of Gaeumannomyces graminis from the rhizoplane of wheat in soils fertilized with ammonium- or nitrate-nitrogen

Take-all of wheat caused by Gaeumannomyces graminis var. tritici was less when soils in glasshouse pots were fertilized with NH₄⁺-N than with NO₃^?-N. The form of N did not alter countable populations of microorganisms in the rhizosphere or rhizoplane, but altered the numbers of bacteria and streptomycetes that inhibited the pathogen's growth in vitro. The pH of the medium used to isolate these microorganisms, whether similar or dissimilar to the pH of the rhizosphere, had some influence both upon countable populations and upon the proportions of antagonists. Highest counts of the rhizoplane microflora were on agar media with a pH similar to that of the soil. Most antagonists were isolated from a soil that is physically and chemically conducive to parasitism of wheat roots by Gaeumannomyces, but which contains a microflora suppressive toward the parasitic colonization of the roots. Isolates of the general bacterial flora, of Pseudomonas spp. and of streptomycetes, but not of Bacillus spp. inhibited the in vitro growth of G. graminis.     

Total lipid extracts from characteristic soil horizons in a podzol profile

The podzolization process is studied through lipids in nine characteristic podzol horizons. Organic matter accumulates particularly with aluminium in the Bh horizon, while the hard, cemented Bs horizon below this is formed mainly by iron oxides. The low soil pH seems to have no great influence on the preservation of lipids as reflected by the absolute amounts present and the presence of bacterial lipid markers throughout the profile. Independent of soil pH, lipids accumulate in organically enriched horizons. Albeit, high molecular weight organic compounds accumulate to a relatively greater extent than lipids in these horizons. A lipid signal related to the aerial parts, i.e. leaves and flowers, of Calluna is observed only in the O horizon. This ‘n‐alkane, steroid and triterpenoids’ signal is quickly lost in the underlying Ah horizon due to (bacterial) oxidation. The other total lipid extracts obtained are dominated by root‐derived compounds. In subsoil horizons rich in organic matter, i.e. the Ahb and Bh horizons, root‐derived friedooleanan and steroid compounds dominate the total lipid signal. Degraded horizons, poor in organic matter, i.e. the E2, Bhs, Bs and B/C horizons, are dominated by C₂₂ and C₂₄ω‐hydroxy acids, long‐chain (> C₂₀) n‐alkanoic acids with a strong even‐over‐odd predominance and C₂₂ and C₂₄n‐alkanols. Steroid and root‐derived triterpenoids with a friedooleanan structure have been removed from these horizons through degradation. Based on total organic carbon content and lipid composition, the formation of an E1 horizon has started, but is not yet complete. In the Ahb horizon, a contribution from buried vegetation to the total lipid signal is still present, although degradation and an input from roots have significantly altered the original signal. Overall, lipid data indicate that degradation (microbial oxidation) is an important process that should be taken into account, in addition to leaching, when describing podzolization processes in soils.     

CHANGES IN THE CHEMICAL NATURE OF SOIL ORGANIC PHOSPHATE DURING PEDOGENESIS

In two chronosequences of soils, total organic phosphate (P₀) accumulated rapidly during the first 50 years of soil development, when organic matter increased and pH decreased. The rate of P₀ accumulation then declined with age of soil until a ‘steady state’ was reached. The amounts of phospholipid, inositol phosphates and humic acid—P₀ followed the same trends as the total P₀. Parent materials and very young soils contained largely citric acid-soluble P₀, but after less than 50 years, surface horizons accumulated sufficient organic matter to complex a considerable proportion of the P₀. An upper limit of 20–5 per cent citric acid-soluble P₀ and 70–80 per cent NaOH-soluble P₀ was attained within 50 years of soil formation in the surface layers, and this slowly extended down the profile so that, after 10000 years, the soil had 20 per cent citric acid soluble-P₀ and 70 per cent NaOH-soluble P₀ to a depth of 1 m.     

Rehabilitation of desurfaced soils by afforestation in La Plata County,Argentina

Removal of topsoil, mainly for making bricks, is one of the main causes of soil loss around large urban centres of the Humid Pampa, Argentina. In about 7 per cent of La Plata County, the 20–40 cm thick A‐horizon has been removed for that purpose. Most of the affected areas were originally prime farmland; however, with removal of the A‐horizon they became unsuitable for agriculture, including grazing, since the exposed Bt‐horizon is unsuited for plant growth due to its high clay content (45–65 per cent) and the low nutrient levels. Since trees survive better on poor soils than do agricultural crops, the possibility of afforestating desurfaced soils has been studied. Eucalyptus are one of the major species used in tree planting programmes aimed at reclaiming degraded soils since they are fast growing and can grow to commercial size in a wide range of soils and climatic conditions. The work reported here was done in a desurfaced Vertic Argiudoll and a similar non‐desurfaced soil (control). Three Eucalyptus species were tested, i.e. E. camaldulensis, E. viminalis and E. dunnii. Their height and diameter (dbh) growth were 47.9 to 75.8 per cent less and timber volume 86.5 to 98.5 per cent less on the desurfaced soil. E. camaldulensis grew best in all the parameters in the desurfaced soil. Although tree growth was poor, afforestation may be an alternative use for desurfaced soils where agriculture and livestock breeding are not possible. Copyright © 2002 John Wiley & Sons, Ltd.     

MICROMORPHOLOGICAL QUANTIFICATION OF CLAY ILLUVIATION

Three concepts are introduced to describe the extent of clay illuviation phenomena quantitatively for pedogenic interpretations: (1) the degree of clay illuviation per thin section or (sub)horizon, subdivided into 5 classes, ranging from negligible (< 0.3 per cent by vol.) to very strong (> 7 per cent by vol.) clay illuviation; (2) the degree of reworking of the illuviated clay, subdivided into 3 classes, ranging from weak (< 30 per cent reworking) to strong (> 70 per cent); (3) the profile clay illuviation index: the sum of products of clay illuviation percentage per (sub)horizon and horizon thickness (in cm). The index ranges from very low (< 50 per cent cm) to very high (> 700 per cent cm). A distinction was made between the profile index based on the in situ illuviation features only and that based on all the illuviation features.     

Relationship between phosphatase active bacteria and phosphatase activities in forest soils

Acid phosphatase and alkaline phosphatase active colonies of bacteria, isolated from forest soils, were stained. The activity of acid and alkaline phosphatase and other soil properties (the number of aerobic bacteria, basal respiration, the level of ammonification, the number of bacteria active in ammonification, the level of nitrification, the number of micromycetes) were compared with the number of bacteria belonging to the genus Micrococcus. Soil samples were taken from the following horizons: F-AO1 (fermentative), H-AO2 (humic), and A (basic). The soil samples were taken from beneath forest stands in the Izera Mountains (North Bohemia, Czech Republic). The number of acid phosphatase active colonies correlated positively with the number of alkaline phosphatase active colonies in the F-AO1 horizon, and there was a high, positive correlation between the former and the level of ammonification in the H-AO2 horizon. The number of alkaline phosphatase active colonies correlated positively with organic carbon, the number of ammonification bacteria, and the number of micromycetes in the H-AO2 horizon. The A horizon was almost biologically inactive. Neither acid nor alkaline phosphatase activities correlated positively with the number of phosphatase active colonies of bacteria. Received: 6 December 1996     

Possible sources and compounds of aluminum in calcium chloride extract soil solutions in peat-podzolic-gleyed soil

Aluminum concentrations in aluminum compounds extracted with 0.001 M CaCl₂ from the main genetic horizons of a peat-podzolic-gleyed soil were determined experimentally and calculated from the equations. From the results of the calculations, the pAl values were plotted as functions of pH. In the Eih horizon, the main sources of Al in the CaCl₂ extract included organoaluminum compounds. In the E horizon, aluminum-organic matter complexes and sodium chloride were the main source of aluminum.     

Using support vector machines to predict cation exchange capacity of different soil horizons in Qingdao City,China

Agricultural, environmental and ecological modeling requires soil cation exchange capacity (CEC) that is difficult to measure. Pedotransfer functions (PTFs) are thus routinely applied to predict CEC from easily measured physicochemical properties (e.g., texture, soil organic matter, pH). This study developed the support vector machines (SVM)‐based PTFs to predict soil CEC based on 208 soil samples collected from A and B horizons in Qingdao City, Shandong Province, China. The database was randomly split into calibration and validation datasets in proportions of 3:1 using the bootstrap method. The optimal SVM parameters were searched by applying the genetic algorithm (GA). The performance of SVM models was compared to those of multiple stepwise regression (MSR) and artificial neural network (ANN) models. Results show that the accuracy of CEC predicted by SVM improves considerably over those predicted by MSR and ANN. The performance of SVM for B horizon (R² = 0.85) is slightly better than that for A horizon (R² = 0.81). The SVM is a powerful approach in the simulation of nonlinear relationship between CEC and physicochemical properties of widely distributed samples from different soil horizons. Sensitivity analysis was also conducted to explore the influence of each input parameter on the CEC predictions by SVM. The clay content is the most sensitive parameter, followed by soil organic matter and pH, while sand content has the weakest influence. This suggests that clay is the most important predictor for predicting CEC of both soil horizons.