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.     

Halophilic and alkaliphilic streptomycetes in salt-affected soils

The number of streptomycetes isolated from salt-affected soils of the Caspian Lowland and desert soils of Mongolia comprises hundreds and thousands of colony-forming units (CFU) per one gram of soil. A complex of moderately halophilic streptomycetes is present in salt-affected soils. The factor of halophily (the ratio between the numbers of streptomycetes isolated from salt-affected soils on nutrient media with 5% NaCl and with 0.02% NaCl) has been calculated for the complex of streptomycetes. The streptomycetic complex of salt-affected soils is characterized by the presence of moderately haloalkaliphilic streptomycetes, whose optimum growth is observed in the medium containing 5% NaCl having pH 8.     

Biosynthetic potential of actinomycetes in brown forest soil on the eastern coast of the aegean sea

The taxonomic and functional structures of the actinomycetal complex in the litter and upper horizon of the brown forest soil was studied in a Pinus brutia var. pendulifolia forest on the eastern coast of the Aegean Sea. The complex of actinomycetes included representatives of the Streptomyces and Micromonospora genera and oligosporus forms. Streptomycetes predominated (73.8%) in the soil, and micromonospores (66.7%) were dominants in the litter. Thirty isolates of ten Streptomyces species from five series and three sections prevailed. In the upper soil horizon, species of the Helvolo-Flavus Helvolus section predominated (48%); the S. felleus species occurred most frequently. Among the isolated cultures, the S. globisporus and S. sindenensis species capable to produce antitumor antibiotics were found. The testing of the antimicrobial activity of the natural isolates showed that five strains inhibit the growth of pathogenic Fusarium sp., Alternaria sp., Acremonium sp., and Bipolaris sorokiniana fungi. When testing the effect of streptomycetes on the production of cellulases, a high-efficient strain belonging to the S. noboritoensis species was revealed. All the streptomycetes isolated from the brown forest soil produced auxins at the rate of 7.8 to 19.7 μg of indole acetic acid/mL of the liquid medium in the presence of 200 mg/L of tryptophan. Twelve isolates of streptomycetes were transferred to the collection of biotechnologically promising cultures for studying their properties.     

Actinomycetes in the rhizosphere of semidesert soils of Mongolia

The population density of actinomycetes in the desert-steppe soil, rhizosphere, and the above-ground parts of plants varies from tens to hundreds of thousands of colony-forming units (CFU) per gram of substrate. The actinomycetal complexes of the brown desert-steppe soil without plant roots are more diverse in their taxonomic composition than the actinomycetal complexes in the rhizosphere and the aboveground parts of plants. Additionally to representatives of the Streptomyces and Micromonospora genera, actinomycetes from the Nocardia, Saccharopolyspora, Thermomonospora, and Actinomadura genera were identified in the soil. The population density of actinomycetes in the rhizosphere and in the soil reached hundreds of thousand CFU/g; it considerably exceeded the population density of actinomycetes in the aboveground parts of plants. The maximum population density of actinomycetes was determined in the rhizosphere of Asparagus gobicus, Salsola pestifera, and Cleistogenes songorica.     

Actinomycetal complex of light sierozem on the Kopet-Dag piedmont plain

The population density of actinomycetes in the samples of light sierozem from the Kopet Dag piedmont plain (75 km from Ashkhabad, Turkmenistan) reaches hundreds of thousand CFU/g soil. The actinomycetal complex is represented by two genera: Streptomyces and Micromonospora. Representatives of the Streptomyces genus predominate and comprise 73 to 87% of the actinomycetal complex. In one sample, representatives of the Micromonospora genus predominated in the complex (75%). The Streptomyces genus in the studied soil samples is represented by the species from several sections and series: the species of section Helvolo-Flavus series Helvolus represent the dominant component of the streptomycetal complex; their portion is up to 77% of all isolated actinomycetes. The species of other sections and series are much less abundant. Thus, the percentage of the Cinereus Achromogenes section in the actinomycetal complex does not exceed 28%; representatives of the Albus section Albus series, Roseus section Lavendulae-Roseus series, and Imperfectus section belong to rare species; they have been isolated not from all the studied samples of light sierozem, and their portion does not exceed 10% of the actinomycetal complex.     

Changes in the structure of the rhizosphere complex of actinomycetes in the ontogenesis of winter rye

Changes in the taxonomic structure of actinomycetes in the rhizosphere of winter rye (Secale cereale L.) growing on acid soddy-podzolic soil were studied. During the first stages of ontogenesis of winter rye, the rhizosphere complex of mycelial prokaryotes was characterized by a relatively level generic structure (with respect to the indices of abundance and frequency of particular genera), low values of the species diversity, and low domination frequency of the species from the Streptomyces genus. The numbers and species diversity of the streptomycetes increased during the further growth of the winter rye, so that streptomycetes became a dominant group in the complex of the rhizosphere actinomycetes. According to the two-way ANOVA, the population density of the Micromonospora and the Streptosporangium genera in the rhizosphere was mainly dictated by the winter rye variety, whereas the population density of the streptomycetes depended on the particular stage of the winter rye development. The differences between the actinomycetal complexes characteristic of different varieties of winter rye at the early stages of its development was leveled by the end of the winter rye growth.     

Soil actinomycetes in the National Forest Park in northeastern China

The taxonomic and functional structure of actinomycete complexes in the litters and upper horizons of the soils under an artificial coniferous–broad-leaved forest located around the town of Chanchun (Tszilin province, PRС). The complex of actinomycetes included representatives of the Streptomyces, Micromonospora, Streptosporangium, and Streptoverticillium genera and oligosporous forms. In the actinomycete complexes, streptomycetes prevailed in the abundance (61–95%) and frequency of occurrence (100%). In the parcels of Korean pine (Pinus koraiensis) and Mongolian oak (Quercus mongolica), streptomycetes of 19 species from 8 series and 4 sections were isolated. The most representative, as in European forest biomes, was the Cinereus Achromogenes series. A distinguishing feature of the streptomycete complex in the biomes studied was the high participation of species from the Imperfectus series. The verification of the functional activity of natural isolates made it possible to reveal strains with high antagonistic and cellulolytic abilities. A high similarity of actinomycete complexes was found in Eurasian forest ecosystems remote from each other, probably due to the similarity of plant polymers decomposable by actinomycetes.     

The Magnetic Susceptibility and Iron Oxides of Aquic Soils in Southern Iran

An investigation of the effect of aquic conditions on Fe-oxides distribution and magnetic susceptibility (χ_lf) was conducted on selected soils from Southern Iran. Seven pairs of adjacent soil pedons with different soil moisture regimes (aquic and non-aquic), were selected. The average concentrations of poorly crystalline Fe (Fe_o) and total free Fe (Fe_d) in aquic soils were 0.2 and 0.07% respectively, and 0.45 and 0.9% in non-aquic soils, respectively. The ratio of Fe_o/Fe_d varied from 0.03 to 0.64. χ_lf ranged from 1.8 to 113 × 10^?8 m³ kg^?1 in the soil studied. The variation of χ_fd ranged from 0.0 to 9.65%. The χ_fd values observed in non-aquic soils were larger than in aquic soils (4.00% vs. 1.37%). Positive correlations were observed between χ and clay contents in both aquic and non-aquic soils; however, non-aquic soil samples showed a larger coefficient of determination. A positive correlation existed between χ_fd and χ in aquic and non-aquic soils. Higher values of χ_fd were observed at the soil surface of non-aquic soil samples than at deeper levels, suggesting a greater proportion of ultrafine grains. Of the soil properties that were assessed, clay, cation exchangeable capacity (CEC), Fe_d, Fe_o/Fe_d ratio, χ_lf and χ_fd contents, changed significantly in response to the aquic condition.     

Influence of moisture on the vital activity of actinomycetes in a cultivated low-moor peat soil

It was found that the actinomycetal complex of a cultivated low-moor peat soil is characterized by a high population density and diversity of actinomycetes; representatives of eleven genera were isolated from this soil: Streptomyces, Micromonospora, Actinomadura, Saccharopolyspora, Microbispora, Microtetraspora, Streptosporangium, Nocardioides, Saccharomonospora, Kibdelosporangium, and Thermomonospora. Some genera were isolated from the soil under all the studied levels of soil moisture. The so-called rare (rarely occurring) genera (Saccharomonospora, Kibdelosporangium, and Thermomonospora) were isolated upon the low level of soil moisture, which ensured an absence of competition from the more abundant actinomycetes. Spores of all the studied actinomycetes could germinate under the low moisture level (a _w = 0.67). The level of moisture a _w = 0.98 was found to be optimal for the development of the actinomycetes. The complete cycle of the development of all the actinomycetes up to spore formation occurring was only observed under the high moisture level (a _w = 0.98).     

Effect of biochar amendment on water infiltration in a coastal saline soil

Purpose

Increasing data have shown that biochar amendment can improve soil fertility and crop production, but there is little knowledge about whether biochar amendment can improve water infiltration in saline soils. We hypothesized that biochar amendment could promote water infiltration in saline soil. The aims of this study were to evaluate the effects of biochar amendment on water infiltration and find the suitable amendment rate and particle size of biochar as a saline soil conditioner.

Materials and methods

We measured water infiltration parameters in a coastal saline soil (silty loam) amended with non-sieved biochar at different rates (0.5, 1, 2, 5, and 10%, w/w) or sieved biochar of different particle sizes (≤?0.25 mm, 0.25–1 mm, and 1–2 mm) at 1 and 10% (w/w).

Results and discussion

Compared with the control, amending non-sieved biochar at 10% significantly decreased water infiltration into the saline soil (P?<?0.05). In contrast, sieved biochar of ≤?0.25 mm significantly improved water infiltration capacity, irrespective of the amendment rate. Sieved biochar of 1–2 mm was less effective to improve soil porosity and when amended at 10%, it even reduced the water infiltration capacity. The Philip model (R²?=?0.983–0.999) had a better goodness-of-fit than the Green-Ampt model (R²?=?0.506–0.923) for simulation of cumulative infiltration.

Conclusions

Amending biochar sieved to a small particle size improved water infiltration capacity of the coastal saline soil compared with non-sieved biochar irrespective of the amendment rate. This study contributes toward improving the hydrological property of coastal saline soil and rationally applying biochar in the field.

     

Specificity of actinomycetal complexes in urbanozems of the city of Kirov

The number and composition of the actinomycetal population was studied in urbanozems in the city of Kirov. It was shown that the total population of actinomycetes was an order of magnitude lower than that in the background territories, and the generic structure of the actinomycetal complex and the species composition of the streptomycetes were transformed under the influence of the urbanization factors. The obtained data were compared with the concentrations of the mobile forms of Pb, Zn, Cu, Fe, and Mn in different ecotopes (industrial, traffic, and recreation zones). The increase of the relative portion of micromonosporic actinomycetes in comparison with the background (reference) soils was observed in the complexes of the industrial and transport ecotopes mostly contaminated with heavy metals. It was found that the antibiotic potential of the streptomycetes in the contaminated soils was lower than in the soils of the background territories.     

Possibilities of using the Landau–Deryagin law to evaluate soil degradation as a result of its contamination with chlorides

The contamination of heavy loamy chernozem by iron, sodium, magnesium, calcium, and hydrogen chlorides (2% of soil mass) decreases soil moisture content (W, percent of soil mass) in the interval of the soil moisture pressure (Р) from 0.0 to–0.6 atm, which indicate soil degradation. In a range of P from–0.2 to–0.6 atm, there is a close correlation between the logarithm of Р module (log|P|) and W and, therefore, a regression relationship log|P _W | = |P ₀|–kW, where |P ₀| and k are empirically determined parameters. This relationship is similar to the Landau–Deryagin law. The parameters |P ₀| and k are also in a close correlation, which is described by the regression equation |P ₀| = 29.3k–0.557. At chernozem contamination by chlorides, the |P ₀| and k parameters become smaller, and so they may be used for the evaluation of degradation of chloride-contaminated soils.     

The effect of acidity on the distribution and symbiotic efficiency of rhizobia in Lithuanian soils

The distribution and symbiotic efficiency of nodule bacteria Rhizobium leguminosarum_bv. trifolii F., Sinorhizobium meliloti D., Rhizobium galegae L., and Rhizobium leguminosarum bv. viciae F. in Lithuanian soils as dependent on the soil acidity were studied in the long-term field, pot, and laboratory experiments. The critical and optimal pH values controlling the distribution of rhizobia and the symbiotic nitrogen fixation were determined for every bacterial species. The relationship was found between the soil pH and the nitrogen-fixing capacity of rhizobia. A positive effect of liming of acid soils in combination with inoculation of legumes on the efficiency of symbiotic nitrogen fixation was demonstrated.     

Assessing chemical soil tests for predicting nitrogen mineralization in paddy soils of the Dongting Lake region in China

Purpose

Developing routine methods that accurately predict soil nitrogen (N) mineralization is essential for fertilization recommendation; thus, chemical soil testing has received worldwide attention. However, the optimal chemical soil test for predicting soil N mineralization is region specific. This study aimed to determine suitable chemical soil tests for predicting N mineralization in paddy soils of the Dongting Lake region, China.

Materials and methods

Composite surface samples (0–20 cm) of soils (n?=?30) with diverse inherent properties were collected from representative paddy fields across the region. The benchmark indices for soil N mineralization were the net mineralization rate of soil N in a 112-day anaerobic incubation under waterlogged conditions (NMRN₁₁₂) and N mineralization potential (N _o ) estimated using a modified double exponential model. Laboratory-based measurements of soil labile organic N (SLON) were conducted using chemical fractionation methods including 0.01 M NaHCO₃ extraction, hot 2 M KCl hydrolysis, phosphate-borate (PB) buffer hydrolysis, acidic KMnO₄ oxidation, and alkaline KMnO₄ oxidation. These were compared with the benchmark indices to assess their suitability for use as indicators for N mineralization.

Results and discussion

Acidic KMnO₄-oxidative organic N (acidic KMnO₄-N) and PB buffer-hydrolysable organic N (PB_HYDR-N) correlated strongly with NMRN₁₁₂ and N _o (r?=?0.825–0.884, P?<?0.001, n?=?30). Grouping of soils based on soil texture generally provided no improvement in the relationships of chemical soil tests with NMRN₁₁₂ and N _o . Multiple stepwise regression analysis indicated that combining acidic KMnO₄-N and PB_HYDR-N yielded the best prediction of soil N mineralization, explaining 86.1 and 85.5 % of the variation in NMRN₁₁₂ and N _o , respectively, of the 30 tested paddy soils.

Conclusions

The results of acidic KMnO₄-N and PB_HYDR-N as indicators for soil N mineralization were promising, and the operations of acidic KMnO₄ oxidation and PB buffer hydrolysis procedures are simple and cost-effective. Therefore, a combination of acidic KMnO₄-N and PB_HYDR-N shows promise in predicting N mineralization in paddy soils of the Dongting Lake region. However, further calibration through field studies is required and the chemical characteristics of acidic KMnO₄-N and PB_HYDR-N needs to be further clarified.

     

Responses of soil nitrous oxide production and abundances and composition of associated microbial communities to nitrogen and water amendment

Soil moisture and nitrogen (N) are two important factors influencing N₂O emissions and the growth of microorganisms. Here, we carried out a microcosm experiment to evaluate effects of soil moisture level and N fertilizer type on N₂O emissions and abundances and composition of associated microbial communities in the two typical arable soils. The abundances and community composition of functional microbes involved in nitrification and denitrification were determined via quantitative PCR (qPCR) and terminal restriction length fragment polymorphism (T-RFLP), respectively. Results showed that N₂O production was higher at 90% water-filled pore (WFPS) than at 50% WFPS. The N₂O emissions in the two soils amended with ammonium were higher than those amended with nitrate, especially at relatively high moisture level. In both soils, increased soil moisture stimulated the growth of ammonia-oxidizing bacteria (AOB) and nitrite reducer (nirK). Ammonium fertilizer treatment increased the population size of AOB and nirK genes in the alluvial soil, while reduced the abundances of ammonia-oxidizing archaea (AOA) and denitrifiers (nirK and nosZ) in the red soil. Nitrate addition had a negative effect on AOA abundance in the red soil. Total N₂O emissions were positively correlated to AOB abundance, but not to other functional genes in the two soils. Changed soil moisture significantly affected AOA rather than AOB community composition in both soils. The way and extent of N fertilizers impacted on nitrifier and denitrifier community composition varied with N form and soil type. These results indicate that N₂O emissions and the succession of nitrifying and denitrifying communities are selectively affected by soil moisture and N fertilizer form in the two contrasting types of soil.     

Enhanced dissipation of DEHP in soil and simultaneously reduced bioaccumulation of DEHP in vegetable using bioaugmentation with exogenous bacteria

The widely used plastic film containing di(2-ethylhexyl) phthalate (DEHP) in agriculture has caused serious soil pollution and poses risks to human health through the food chain. An effective DEHP degradation bacteria, Microbacterium sp. J-1, was newly isolated from landfill soil. Response surface methodology was successfully employed for optimization resulting in 96% degradation of DEHP (200 mg L^?1) within 5 days. This strain degraded DEHP by hydrolysis of the ester bond and hydroxylation of the aromatic ring to form 2-ethyl hexanol, mono-(2-ethylhexyl) phthalate, phthalate acid, and protocatechuic acid, and subsequently transformed these compounds with a maximum specific degradation rate (q _max), half-saturation constant (K _s ), and inhibition constant (K _i ) of 1.46 day^?1, 180.2 mg L^?1, and 332.8 mg L^?1, respectively. Bioaugmentation of DEHP-contaminated soils with the strain J-1 greatly enhanced the DEHP dissipation rate (~88%). Moreover, this strain could efficiently colonize the rhizosphere soil of inoculated vegetables and further enhanced DEHP degradation (~97%), leading to a significant decrease (>70%) in DEHP accumulation in shoots and roots of the inoculated vegetables compared to uninoculated vegetables. The results highlighted the roles of the inoculated exogenous bacteria in simultaneously bioremediating contaminated soils and reducing bioaccumulation of DEHP in the edible part of the vegetable for food safety.     

Assessing the Antagonistic Potential and Antibiotic Resistance of Actinomycetes Isolated from Two Zheltozems of Southeastern China

Forty streptomycete strains have been isolated into pure culture from two eroded zheltozems (yellow soils) of the Fujian province. Their antagonistic activities and contributions to the formation of soil resistome have been characterized. The estimation of the antimicrobial effect of natural isolates allowed revealing 6 strains simultaneously inhibiting the growth of the fungi Fusarium oxisporum, Alternaria alternata, Paecilomyces sp., Trichoderma sp., and Candida albicans. One strain (Streptomyces aburaviensis F2-6) with a wide range of antifungal actions was also active against the bacteria Pseudomonas putuda, P. fluorescens, P. sepacia, Streptococcus sp., and Escherichia coli. It has been shown that the share of isolates with a wide range of antimicrobial effects (44%) and a high antagonistic activity (77%) in zheltozem of the urban Zhangzhou district is significantly higher than in the soil of the village of Hongkeng (22 and 39%, respectively). According to the resistome concept, determinants of resistance to antibiotics first appeared in their producers; they can be transmitted to other bacteria in the soil due to horizontal drift. Tests of streptomycetes for resistance to antibiotics with different acting mechanisms (inhibitors of the synthesis of cytoderm, protein, and metabolic pathways) has shown that the share of cultures with multiple resistance in zheltozems does not exceed 25–31%. No resistance to all of the studied antibiotics is characteristic of 15–16% of the strains isolated from zheltozems. The obtained data can be used for assessing the risks related to the transfer of antibiotic resistance genes from the environment to clinically valuable pathogenic species.     

Response of CaCl<Subscript>2</Subscript>-extractable heavy metals,polychlorinated biphenyls,and microbial communities to biochar amendment in naturally contaminated soils

Purpose

Biochar can be used to reduce the bioavailability and leachability of heavy metals, as well as organic pollutants in soils through adsorption and other physicochemical reactions. The objective of the study was to determine the response of microbial communities to biochar amendment and its influence on heavy metal mobility and PCBs (PCB52, 44, 101, 149, 118, 153, 138, 180, 170, and 194) concentration in application of biochar as soil amendment.

Materials and methods

A pot (macrocosm) incubation experiment was carried out with different biochar amendment (0, 3, and 6 % w/w) for 112 days. The CaCl₂-extractable concentration of metals, microbial activities, and bacterial community were evaluated during the incubation period.

Results and discussion

The concentrations of 0.01 M CaCl₂-extractable metals decreased (p?>?0.05) by 12.7 and 20.5 % for Cu, 5.0 and 15.6 % for Zn, 0.2 and 0.5 % for Pb, and 1.1 and 8.9 % for Cd, in the presence of 3 and 6 % of biochar, respectively, following 1 day of incubation. Meanwhile, the total PCB concentrations decreased from 1.23 mg kg^?1 at 1 day to 0.24 mg kg^?1 at 112 days after 6 % biochar addition, representing a more than 60 % decrease relative to untreated soil. It was also found out that biochar addition increased the biological activities of catalase, phosphatase, and urease activity as compared with the controls at the same time point. Importantly, the Shannon diversity index of bacteria in control soils was 3.41, whereas it was 3.69 and 3.88 in soils treated with 3 and 6 % biochar soil. In particular, an increase in the number of populations with the putative ability to absorb PCB was noted in the biochar-amended soils.

Conclusions

The application of biochar to contaminated soils decreased the concentrations of heavy metals and PCBs. Application of biochar stimulated Proteobacteria and Bacteroides, which may function to absorb soil PCB and alleviate their toxicity.

     

New processes of microbial transformation of nitrogen in soils as a source of greenhouse gases

DNA isolation from soil samples and amplification of fragment of a key gene of nitrification, archaeal and bacterial amoA, revealed presence of the product in all investigated soil samples. Characteristics of ammonia-oxidizing microbial communities in agrocenoses and undisturbed soil were determined. Bacteria were predominant in agrocenoses (at circum-neurtal pH), whereas the share of representatives of domain Archaea (phylum Thaumarchaeota) increased in prokaryotic ammonia-oxidizing complexes of undisturbed forest ecosystems (at low pH). It was demonstrated that the contribution of taumarhaea in nitrous oxide emission from gray forest soil may reach 20–25%.     

Application of compost and clay under water-stressed conditions influences functional diversity of rhizosphere bacteria

Applications of compost and clay to ameliorate soil constraints such as water stress are potential management strategies for sandy agricultural soils. Water repellent sandy soils in rain-fed agricultural systems limit production and have negative environmental effects associated with leaching and soil erosion. The aim was to determine whether compost and clay amendments in a sandy agricultural soil influenced the rhizosphere microbiome of Trifolium subterraneum under differing water regimes. Soil was amended with compost (2% w/w), clay (5% w/w) and a combination of both, in a glasshouse experiment with well-watered and water-stressed (70 and 35% field capacity) treatments. Ion Torrent 16S rRNA sequencing and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis of functional gene prediction were used to characterise the rhizosphere bacterial community and its functional component involved in nitrogen (N) cycling and soil carbon (C) degradation. Compost soil treatments increased the relative abundance of copiotrophic bacteria, decreased labile C and increased the abundance of recalcitrant C degrading genes. Predicted N cycling genes increased with the addition of clay (N₂ fixation, nitrification, denitrification) and compost + clay (N₂ fixation, denitrification) and decreased with compost (for denitrification) amendment. Water stress did not alter the relative abundance of phylum level taxa in the presence of compost, although copiotrophic Actinobacteria increased in relative abundance with addition of clay and with compost + clay. A significant role of compost and clay under water stress in influencing the composition of rhizosphere bacteria and their implications for N cycling and C degradation was demonstrated.