Isolation of bacterial DNA from soil

DNA has been isolated from the bacterial fraction of two soils. Numbers of bacteria, determined by fluorescence microscopy were 1.1 and 2.2·10¹⁰ cells g^?1 dry wt. The total amounts of bacterial DNA in these soils were 90 and 187 μg g^?1 dry wt respectively.A modification of Marmur's method was used to isolate DNA, but difficulties in separating DNA from humic substances gave low yields and impure DNA.DNA could be partly separated from humic material in the presence of 8 m urea by ion-exchange chromatography on DEAE-Sepharose CL-6B. Final purification was obtained by chromatography on a hydroxyapatite column. When lowering the EDTA concentration in the saline-EDTA solution used for lysis, the amount of humic substances in the cell-free lysate after centrifugation was considerably decreased. The lysate could then be chromatographed directly on hydroxyapatite. Quantities up to 1.5 mg DNA high purity was isolated from 90 g wet soil (37 g dry wt).The isolated DNA was characterized by treatment with DNAse and absorption spectra. No uncommon bases were revealed by thin layer chromatography of the DNA hydrolysates. Melting curves of the isolated DNA showed a relatively broad melting profile, with half maximum hyperchromicity (T_m) near 90°C. Sedimentation coefficients determined by analytical ultracentrifugation showed that the isolated DNA had a high molecular weight, ranging from 2.3 to 10.1·10⁵ daltons.     

Soil microorganisms antagonistic towards Rhizobium japonicum

Success in introducing Rhizobium japonicum strains into soil is related to their interaction with native microorganisms including some that are antagonistic. Actinomycetes, bacteria, fungi and rhizobiophages antagonistic towards strains of R. japonicum were counted directly using soil samples from field plots under different crop and soil management systems. The antagonistic actinomycete population varied from 1.3 × 10³ to 4.5 × 10⁵ g^?1 dry soil and ranged up to 90% of total actinomycetes. Soybean rhizosphere soil samples included antagonistic actinomycetes ranging up to 70% of total actinomycetes. The antagonistic bacterial population was less than 10% of total bacteria and the proportion did not vary significantly with crop or soil management practices. Antagonistic fungi were observed for many of the soils examined but they could not be counted. There were few rhizobiophages and they were found most frequently in soybean rhizospheres. Occasional bacterial and actinomycete colonies that stimulated growth of R. japonicum were randomly observed among the soil samples tested.     

Response of soil microbial diversity to land-use conversion of natural forests to plantations in a subtropical mountainous area of southern China

Land-use conversion can affect the soil microbial community diversity, soil organic matter and nutrient cycling. In this study, soils within a representative land-use sequence were sampled in a subtropical region of China, including four natural forests, Altingia gracilipes Hemsl. (ALG), Cinnamomum chekiangense Nakai (CIC), Castanopsis fargesii Franch. (CAF), and Tsoongiodendron odorum Chun (TSO), and two plantations, Cunninghamia lanceolata (Lamb.) Hook. (CUL) and a citrus orchard (Citrus reticulata Blanco). The soil microbial diversity was investigated by phospholipid fatty acid (PLFA) analysis, denaturing gradient gel electrophoresis (DGGE) and real-time quantitative polymerase chain reaction (PCR). Results showed that microbial community diversity exhibited distinct patterns among land-use types. After conversion of natural forests to plantations, the amount of PLFA and the number of bacterial 16?S rRNA gene copies were reduced significantly, as well as the number of DGGE bands. The average quantity of PLFA was lower by 31% in the CUL plantation and 57% in the citrus orchard, respectively, than in natural forests. Simultaneously, the average copy numbers of the bacterial 16?S rRNA gene were significantly decreased from 8.1?×?10^10?g^?1?dry weight (DW) in natural forest to 4.9?×?10^10?g^?1 DW in CUL plantation, and 3.1?×?10^10?g^?1 DW in the citrus orchard. Such negative responses of soil microbes to conversion of natural forests to plantations could mainly result from decreases in soil organic carbon and necessary elements for growth during land-use conversion, as revealed by statistical analysis. Our results suggested that the soil microbial diversity was indirectly in?uenced by land-use types in the mid-subtropical mountainous area of southern China. Changes in the amount of litterfall and the soil nutrient status that resulted from land-use conversion drove these indirect changes. Furthermore, deliberate management brought negative effects on soil microbes, which is not beneficial to the sustainability of the ecosystem.     

Selective isolation and occurrence of nocardiae in soil

Nocardiae were isolated from 15 out of 47 soils using Diagnostic Sensitivity Test Agar supplemented with antibiotics. Up to 7.3 × 10⁴ g^?1 dry wt. soil were counted, indicating that these bacteria might be more widespread and important than previously thought. Study of randomly selected isolates showed that they formed fragmenting mycelium, contained arabinose, galactose, meso-diaminopimelic acid and nocardomycolic acids. They clustered with Nocardia asteroides markers in a numerical taxonomic analysis.     

Effects of Silver Nanoparticles on Soil Ammonia-Oxidizing Microorganisms Under Temperatures of 25 and 5℃

The excellent bactericidal performance of silver nanoparticles (Ag NPs) has led to their wide applications, resulting in increasing concerns about their potential environmental impacts. This study evaluated the influences of different concentrations of Ag NPs (0, 1, 10, and 100 μg g^-1 dry soil) on the ammonia-oxidizing microorganisms in soil at cultivation temperatures of 25 and 5℃ for 37 d. The results showed that 1 μg g^-1 dry soil of Ag NPs had no acute effects on the ammonia-oxidizing microorganisms. However, 10 and 100 μg g^-1 dry soil of Ag NPs levels were found to significantly inhibit the activities of soil nitrification, with a decrease of 69.89% and 94.55%, respectively, at 25℃ and 61.65% and 83.79%, respectively, at 5℃ compared to the control (0 μg g^-1 dry soil of Ag NPs). These levels of Ag NPs also obviously decreased soil urease activity from about 380.47 ±0.07 (at 5℃) and 529.76 ±13.44 (at 25℃) mg N g^-1 dry soil d^-1 to 61.70 ±2.97 and 68.29 ±8.22 mg N g^-1 dry soil d^-1, respectively, after 37 d of cultivation. Quantitative polymerase chain reaction showed the abundance of ammonia-oxidizing archaea and bacteria. For the same exposure time, the effects of Ag NPs on the activities of ammonia-oxidizing microorganisms and urease decreased with decreasing temperature. The threshold concentration of Ag NPs that induced negative effects on ammonia-oxidizing microorganisms was higher at 5℃ than at 25℃. Therefore, the temperature has a major impact on the toxicity of Ag NPs to ammonia-oxidizing microorganisms and on the urease activity, with toxicity being reduced with decreasing temperature.     

覆盖模式及小麦根系对土壤微生物区系的影响

采用平皿分离培养法研究了5种栽培模式和小麦根系对土壤细菌、真菌及放线菌数量的影响。连续2年的定位测定结果表明:覆膜有利于土壤微生物数量增加。5种栽培模式中,小麦根区、根外土壤细菌数量均以覆膜模式下最高,分别为116.8×106cfu·g-1和86.7×106cfu·g-1;土壤真菌和放线菌数量均以垄沟覆膜(垄上覆膜、垄沟播种)模式下最高,分别为3.0×103cfu·g-1、1.4×103cfu·g-1和18.9×105cfu·g-1、19.7×105cfu·g-1。不同模式下小麦根系对土壤细菌和真菌数量影响较大,表现为根区高于根外;而根系对放线菌影响较小,只有补灌和覆膜2种模式为根区高于根外。多重比较结果显示,覆膜与其他模式之间细菌数量差异极显著,根区土壤细菌和真菌数量与根外存在显著差异。覆盖和根系能大幅度增加根区细菌、真菌和放线菌的数量,强化小麦根区根外细菌和真菌的数量差异。     

Effect of 7-year application of a nitrification inhibitor, dicyandiamide (DCD), on soil microbial biomass, protease and deaminase activities, and the abundance of bacteria and archaea in pasture soils

Purpose

The nitrification inhibitor dicyandiamide (DCD) has been shown to be highly effective in reducing nitrate (NO₃ ^?) leaching and nitrous oxide (N₂O) emissions when used to treat grazed pasture soils. However, there have been few studies on the possible effects of long-term DCD use on other soil enzyme activities or the abundance of the general soil microbial communities. The objective of this study was to determine possible effects of long-term DCD use on key soil enzyme activities involved in the nitrogen (N) cycle and the abundance of bacteria and archaea in grazed pasture soils.

Materials and methods

Three field sites used for this study had been treated with DCD for 7 years in field plot experiments. The three pasture soils from three different regions across New Zealand were Pukemutu silt loam in Southland in the southern South Island, Horotiu silt loam in the Waikato in the central North Island and Templeton silt loam in Canterbury in the central South Island. Control and DCD-treated plots were sampled to analyse soil pH, microbial biomass C and N, protease and deaminase activity, and the abundance of bacteria and archaea.

Results and discussion

The three soils varied significantly in the microbial biomass C (858 to 542 μg C g^?1 soil) and biomass N (63 to 28 μg N g^?1), protease (361 to 694 μg tyrosine g^?1 soil h^?1) and deaminase (4.3 to 5.6 μg NH₄ ⁺ g^?1 soil h^?1) activity, and bacteria (bacterial 16S rRNA gene copy number: 1.64?×?10⁹ to 2.77?×?10⁹ g^?1 soil) and archaea (archaeal 16S rRNA gene copy number: 2.67?×?10⁷ to 3.01?×?10⁸ g^?1 soil) abundance. However, 7 years of DCD use did not significantly affect these microbial population abundance and enzymatic activities. Soil pH values were also not significantly affected by the long-term DCD use.

Conclusions

These results support the hypothesis that DCD is a specific enzyme inhibitor for ammonia oxidation and does not affect other non-target microbial and enzyme activities. The DCD nitrification inhibitor technology, therefore, appears to be an effective mitigation technology for nitrate leaching and nitrous oxide emissions in grazed pasture soils with no adverse impacts on the abundance of bacteria and archaea and key enzyme activities.     

Phenoxy herbicide degradation in soils: Quantitative studies of 2,4-D- and MCPA-degrading microbial populations

Microbial populations able to degrade 2,4-D (2,4-dichlorophenoxyacetate) and MCPA (4-chloro-2-methylphenoxyacetate) were enumerated by means of a most probable number (MPN) procedure in eight Natal soils not previously treated with these herbicides. Estimated 2,4-D-degrading populations ranged from 1.26 to 245.2 and MCPA-degrading populations from 0.34 to 1377 g^?1 dry soil; in seven of the soils the populations of these organisms were less than 40 and 30 g^?1, respectively. Such counts indicate that for the successful isolation of 2,4-D- or MCPA-degrading microorganisms from soil, at least 1 g dry weight of soil should be used for enrichment cultures. The 2,4-D-degrading organisms occurred among the aerobic soil bacteria detectable by plate count, at frequencies of only 1 in 30 × 10³ to 1 in 36 × 10⁶ and the MCPA-degrading organisms at frequencies of 1 in 5 × 10³ to 1 in 133 × 10⁶; the ease with which the herbicide-degrading organisms can be isolated from enriched soil cultures treated with 2,4-D or MCPA is evidence of their massive preferential proliferation in response to the herbicides.Log 2,4-D- and MCPA-degrading populations did not differ significantly in four soil samples, but in the others either the 2,4-D- or the MCPA-degrading population was dominant. The longer persistence of MCPA compared with that of 2,4-D could therefore not be ascribed to quantitative differences in the populations of MCPA- and 2,4-D-degrading soil microorganisms.No relationship was evident between the soil populations of 2,4-D- or MCPA-degrading microorganisms and aerobic soil bacteria, and variations of the three populations among the soil samples were not associated in any obvious way with the soil physical and chemical characteristics, except perhaps an association of the highest counts of herbicide-degrading organisms with a sugar cane soil of sandy texture and high C: N ratio.     

Mechanisms of persistence of low numbers of bacteria preyed upon by protozoa

Tetrahymena pyriformis cultures were maintained when transferred serially in solutions containing 10⁵ to 10⁷Klebsiella pneumoniae cells.ml^?1, bacterial numbers that were observed to persist in the presence of protozoa. The number of cells of one strain of K. pneumoniae surviving predation in solution was essentially the same in the absence of an alternative prey as in the presence of a second K. pneumoniae strain. Toxins deleterious to protozoa did not appear as the animal consumed the bacteria. T. pyriformis reduced the abundance of Escherichia coli from about 10⁸ to 10⁶.ml^?1. but the latter number persisted for 15 days; however, in solutions containing chloramphenicol, the abundance of E. coli fell to 590 cells. ml^?1 in 15 days. In solutions containing the antibiotic, T. pyriformis reduced the Rhizobium sp. population from more than 10⁶ to less than 10³ cells in 10 days and K. pneumoniae from more than 10⁸.ml^?1 to zero in 18 days. An appreciable decline in abundance of these bacteria did not occur in the antibiotic-amended liquid free of protozoa. T. pyriformis did not greatly reduce Rhizobium sp. numbers when both were added to irradiated soil, but the predator caused the bacterial population to decline from 4 × 10⁸ to fewer than 10⁵.g^?1 in 16 days in chloramphenicol-treated soil. Colpoda sp. inoculated with Rhizobium sp. into soil sterilized by autoclaving only reduced the prey abundance from 10⁹ to 10⁸.g^?1, but the protozoan caused the bacterial population to fall to about 100.g^?1 in 15 days in the presence of the antibiotic. The population of Rhizobium sp. added to nonsterile soil dropped from in excess of 10⁸ to 6 × 10⁶.g^?1 in 29 days. but it declined to 550. g^?1 in the same period when chloramphenicol was also introduced. It is concluded that the ability of these bacteria to maintain themselves in solution and in soil is governed by their capacity to reproduce and replace the cells consumed by predation.     

cry1Ac/cpti转基因大米水稻土中微生物群落的多样性研究

Two types of cry1Ac/cpti transgenic rice(GM1 and GM2)and their parental non-cry1Ac/cpti rice(CK1 and CK2)were planted in the field at Wufeng,Fujian Province,China for four years to investigate the influence of genetically modified rice on diversity of bacterial and fungal community in the paddy soil.The community composition and abundance of bacteria or fungi in the paddy soil were assessed at different growth stages of rice by denaturing gradient gel electrophoresis and real-time polymerase chain reaction based on 16S rRNA gene or SSU rRNA gene in the 4th year after the experimental establishment.The composition of bacterial or fungal community changed during rice growth,while no significant differences were observed between the fields cultivated with GM1and CK1,or between the fields cultivated with GM2 and CK2 in either bacterial or fungal community composition.The copy numbers of bacterial 16S rRNA gene in the soils with CK1,CK2,GM1 and GM2 ranged from 5.64×1011to 6.89×1011copies g-1dry soil at rice growth stages,and those of fungal SSU rRNA gene from 5.24×108to 8.68×108copies g-1dry soil.There were no marked differences in the copies of bacterial 16S rRNA gene or fungal SSU rRNA gene between CK1 and GM1 or between CK2 and GM2at any growth stage of rice.Planting cry1Ac/cpti transgenic rice had no significant effect on composition and abundance of bacterial and fungal community in paddy soil during the rice growing season at least in the short term.     

Quantitative and qualitative aspects of a developing rhizosphere microflora of hydroponically grown maize seedlings

The roots of 7-day-old hydroponically grown maize seedlings inoculated with a soil suspension 2 days after sowing are mostly inhabited by shorter rods and occasionally by actinomycete-like filaments, as seen by scanning electron microscopy. The density of the bacterial cover increases from 39 × 10³ bacteria/mm² in the region where root hairs are just emerging to 63 × 10³ in the root hair zone 10 mm below the emerging secondary roots, and 188 × 10³ in the oldest part 10 mm below the grain. In this region the bacterial cover can locally form a coherent multilayer. The average area covered by 1 bacterium is 1.04μm² as measured by means of an image analyser. The percentage of the root area covered by its microflora, presuming a monolayer, is therefore 4%, 7% and 20%, respectively, of the three root zones under investigation. With an average dry weight of 0.64pg/cell all the 1.2 × 10⁹ rhizoplane bacteria/g root dry matter only account for less than 0.1% of the root weight. The microbial population adapted to the rhizosphere has very simple nutritional demands. Whereas 65% of the soil microflora isolated on yeast extract grows on the simple aforementioned medium, the value is 92% for the rhizosphere organisms. In spite of appreciable amounts of vitamins found in the inoculated nutrient solution, the growth of vitamin requiring species is not stimulated compared to the soil population. The same is true for amino acids.     

Dynamics and stratification of bacteria and fungi in the organic layers of a scots pine forest soil

The abundance and micro-stratification of bacteria and fungi inhabiting the organic layers of a Scots pine forest (Pinus sylvestris L.) were investigated. An experiment using stratified litterbags, containing organic material of four degradation stages (fresh litter, litter, fragmented litter and humus) was performed over a period of 2.5 years. Dynamics and stratification of fluorescent stained bacteria and fungi, ratios between bacterial and fungal biomass, and relationships with moisture and temperature are described. Average bacterial counts in litter and fragmented litter were similar, i.e., approximately 5×10⁹ bacteriag^–1 (dry weight) organic matter, and significantly exceeded those in humus. The mean bacterial biomass ranged from 0.338 to 0.252mg carbon (C) g^–1 (dry weight) organic matter. Lengths of mycelia were significantly below the usually recorded amounts for comparable temperate coniferous forests. The highest average hyphal length, 53mg^–1 (dry weight) organic matter, was recorded in litter and decreased significantly with depth. The corresponding mean fungal biomass ranged from 0.050 to 0.009mg Cg^–1 (dry weight). The abundance of bacteria and fungi was influenced by water content, that of fungi also by temperature. A litterbag series with freshly fallen litter of standard quality, renewed bimonthly, revealed a clear seasonal pattern with microbial biomass peaks in winter. The mean hyphal length was 104mg^–1 (dry weight) and mean number of bacteria, 2.40×10⁹ bacteria g^–1 (dry weight). Comparable bacterial and fungal biomass C were found in the freshly fallen litter [0.154 and 0.132mgCg^–1 (dry weight) organic material, respectively]. The ratio of bacterial-to-fungal biomass C increased from 1.2 in fresh litter to 28.0 in humus. The results indicate the existence of an environmental stress factor affecting the abundance of fungi in the second phase of decomposition. High atmospheric nitrogen deposition is discussed as a prime factor to explain low fungal biomass and the relatively short lengths of fungal hyphae in some of the forest soil layers under study. Received: 26 June 1997     

Short-term bacterial growth,nutrient uptake,and ATP turnover in sterilized,inoculated and C-amended soil: The influence of N availability

Bacteria, Pseudomonas paucimobilis, were inoculated at two concentrations (6.56 × 10⁴ g^?1 and 6.56 × 10⁶g^?1) into sterilized soil amended with 700 μg glucose-C g^?1. Two levels of NH⁺₄-N (11.0μg g^?1 and 81.0 μg g^?1) were used. The subsequent development was followed for three days by measurement of several biological, chemical and physiological parameters.The amount of bacterial biomass-C (μg g^?1 soil) became twice as great in high as in low N treatments, and significantly decreased between 39.5 and 63.5 h for the high inoculum, high N level treatment due to decreasing cell size. By the end of the experiment the cumulative respired carbon was twice as great and more inorganic P was immobilized for high compared to low N treatments and all available NH⁺₄-N was taken up by the final sample time. Soil ATP concentrations were twice as large in high N treatments but the turnover times were twice as long compared to low N systems. The yield coefficient (Y), calculated from respiration and biomass-C values, equalled 0.61 while substrate was plentiful. Nitrogen limitation did not alter the efficiencey with which glucose was transformed into biomass, but rather controlled the total amount of glucose used and biomass produced.     

Rhizobacteria: Influence of cultivar and soil type on plant growth and yield of potato

The influence of potato cultivar and soil type on effectiveness of plant growth-promoting rhizobacteria (PGPR) was examined. Rhizobacteria were isolated from potato roots and tubers obtained from fields with a history of high potato yields. Fluorescent pigment-producing rhizobacteria. identified as strains of Pseudomonas putida and P. fluorescens, were selected for their antibiosis against Erwinia carovotora ssp. carotovora and growth-promoting activity on potatoes. In greenhouse tests, treatments of potato seedpieces and stem cuttings increased shoot dry weight from 1.23- to 2.00-fold and root dry weight from 1.27- to 2.78-fold. Survival of PGPR in the rhizosphere was monitored using antibioticresistant strains. Populations of these strains decreased from 3.6 × 10⁹ cgu g^?1 dry root weight to 4.5 × 10⁵ cfu g^?1 dry root weight 4 weeks after treatment. In field trials, PGPR strains were applied to seedpieces of cultivars Kennebec, Pungo, Red Pontiac and Superior and planted in Cape Fear loam. Plymouth loamy sand or Delanco sandy loam. Significant yield increases of 1.17–1.37-fold over controls were observed in two of three field trials. Variability in plant growth-promoting activity was observed between greenhouse and field trials, and no given treatment combination of PGPR strain, potato cultivar and soil type was consistently better than another.     

中国西北干旱土壤中固定二氧化碳的RuBisCO基因丰度及其多样性研究

Arid soils where water and nutrients are scarce occupy over 30% of the Earth's total surface. However, the microbial autotrophy in the harsh environments remains largely unexplored. In this study, the abundance and diversity of autotrophic bacteria were investigated, by quantifying and profiling the large subunit genes of ribulose-1,5-bisphosphate carboxylase/oxygenase(Ru Bis CO) form I(cbb L) responsible for CO2 fixation, in the arid soils under three typical plant types(Haloxylon ammodendron, Cleistogenes chinensis,and Reaumuria soongorica) in Northwest China. The bacterial communities in the soils were also characterized using the 16 S r RNA gene. Abundance of red-like autotrophic bacteria ranged from 3.94 × 105 to 1.51 × 106 copies g-1dry soil and those of green-like autotrophic bacteria ranged from 1.15 × 106 to 2.08 × 106 copies g-1dry soil. Abundance of both red- and green-like autotrophic bacteria did not significantly differ among the soils under different plant types. The autotrophic bacteria identified with the cbb L gene primer were mainly affiliated with Alphaproteobacteria, Betaproteobacteria and an uncultured bacterial group, which were not detected in the 16 S r RNA library. In addition, 25.9% and 8.1% of the 16 S r RNA genes were affiliated with Cyanobacteria in the soils under H. ammodendron and R. soongorica, respectively. However, no Cyanobacteria-affiliated cbb L genes were detected in the same soils. The results suggested that microbial autotrophic CO2 fixation might be significant in the carbon cycling of arid soils, which warrants further exploration.     

Effect of land use on the abundance and diversity of autotrophic bacteria as measured by ribulose-1,5-biphosphate carboxylase/oxygenase (RubisCO) large subunit gene abundance in soils

Elucidating the biodiversity of CO₂-assimilating bacterial communities under different land uses is critical for establishing an integrated view of the carbon sequestration in agricultural systems. We therefore determined the abundance and diversity of CO₂ assimilating bacteria using terminal restriction fragment length polymorphism and quantitative PCR of the cbbL gene (which encodes ribulose-1,5-biphosphate carboxylase/oxygenase). These analyses used agricultural soils collected from a long-term experiment (Pantang Agroecosystem) in subtropical China. Soils under three typical land uses, i.e., rice–rice (RR), upland crop (UC), and paddy rice–upland crop rotation (PU), were selected. The abundance of bacterial cbbL (0.04 to 1.25?×?10⁸ copies g^?1 soil) and 16S rDNA genes (0.05–3.00?×?10¹⁰ copies g^?1 soil) were determined in these soils. They generally followed the trend RR?>?PU?>?UC. The cbbL-containing bacterial communities were dominated by facultative autotrophic bacteria such as Mycobacterium sp., Rhodopseudomonas palustris, Bradyrhizobium japonicum, Ralstonia eutropha, and Alcaligenes eutrophus. Additionally, the cbbL-containing bacterial community composition in RR soil differed from that in upland crop and paddy rice–upland crop rotations soils. Soil organic matter was the most highly statistically significant factor which positively influenced the size of the cbbL-containing population. The RR management produced the greatest abundance and diversity of cbbL-containing bacteria. These results offer new insights into the importance of microbial autotrophic CO₂ fixation in soil C cycling.     

Depth-specific distribution and importance of nitrite-dependent anaerobic ammonium and methane-oxidising bacteria in an urban wetland

Anaerobic ammonium oxidation (anammox) and nitrite-dependent anaerobic methane oxidation (n-damo) are two recently discovered processes in the nitrogen cycle that are catalysed by anammox bacteria and n-damo bacteria, respectively. Here, the depth-specific distribution and importance of anammox bacteria and n-damo bacteria were studied in an urban wetland, Xixi Wetland, Zhejiang Province (China). Anammox bacteria related to Candidatus Brocadia, Candidatus Kuenenia and Candidatus Anammoxoglobus, and n-damo bacteria related to “Candidatus Methylomirabilis oxyfera” were present in the collected soil samples. The abundance of anammox bacteria (2.6–8.6 × 10⁶ copies g⁻¹ dry soil) in the shallow soils (0–10 cm and 20–30 cm) was higher than that (2.5–9.8 × 10⁵ copies g⁻¹ dry soil) in the deep soils, whereas the abundance of n-damo bacteria (0.6–1.3 × 10⁷ copies g⁻¹ dry soil) in the deep soils (50–60 cm and 90–100 cm) was higher than that (3.4–4.5 × 10⁶ copies g⁻¹ dry soil) in the shallow soils. Anammox activity was detected at all depths, and higher potential rates (12.1–21.4 nmol N₂ g⁻¹ dry soil d⁻¹) were observed at depths of 0–10 cm and 20–30 cm compared with the rates (3.5–8.7 nmol N₂ g⁻¹ dry soil d⁻¹) measured at depths of 50–60 and 90–100 cm. In contrast, n-damo was mainly occurred at depths of 50–60 cm and 90–100 cm with potential rates of 0.7–5.0 nmol CO₂ g⁻¹ dry soil d⁻¹. This study suggested the niche segregation of the anammox bacteria and n-damo bacteria in wetland soils, with anammox bacteria being active primarily in deep soils and n-damo bacteria being active primarily in shallow soils.     

Lantana camara——an Ecological Bioindicator Plant for Decontamination of Pb-Impaired Soil Under Organic Waste-Supplemented Scenarios

Heavy metal extraction and processing from ores releases elements into the environment. Soil, being an "unfortunate" sink, has its bionomics impaired and affected by metal pollution. Metals sneak into the food chain and pose risk to humans and other edaphicdependent organisms. For decontamination, the use of an ecosystem-friendly approach involving plants is known as phytoremediation.In this study, different lead(Pb) concentrations(80, 40, 20, and 10 mg kg~(-1)) were used to contaminate a well-characterized soil,(un)supplemented with organic waste empty fruit bunch(EFB) or spent mushroom compost(SMC), with non-edible plant—Lantana camara. Lead removal by L. camara ranged from 45.51% to 88.03% for supplemented soil, and from 23.7% to 57.8% for unsupplemented soil(P 0.05). The EFB-supplemented and L. camara-remediated soil showed the highest counts of heavy metal-resistant bacteria(HMRB)(79.67 × 10~6–56.0 × 10~6 colony forming units(CFU) g~(-1) soil), followed by SMC-supplemented and L. camara-remediated soil(63.33 × 10~6–39.0 × 10~6 CFU g~(-1) soil). Aerial metal uptake ranged from 32.08 ± 0.8 to 5.03 ± 0.08 mg kg~(-1) dry weight, and the bioaccumulation factor ranged from 0.401 to 0.643(P 0.05). Half-lives(t_(1/2)) of Pb were 7.24–2.26 d in supplemented soil,18.39–11.83 d in unsupplemented soil, and 123.75–38.72 d in the soil without plants and organic waste. Freundlich isotherms showed that the intensity of metal absorption(n) ranged from 2.44 to 2.51 for supplemented soil, with regression coefficients of determination(R~2) between 0.901 2 and 0.984 0. The computed free-energy change(?G) for Pb absorption ranged from -5.01 to 0.49 kJ mol~(-1) K~(-1) for EFB-supplemented soil and -3.93 to 0.49 k J mol~(-1) K~(-1) for SMC-supplemented soil.     

硫杆菌以及好养异养型硫氧化菌对元素硫的氧化

The prediction of the oxidation rate of elemental sulfur (S⁰) is a critical step in sulfur (S) fertilizer strategy to supply plant-available sulfur. An incubation experiment was conducted to determine the rate and amount of S⁰ oxidation in relation to the contribution of Thiobacillus spp. and aerobic heterotrophic S-oxidizing bacteria. After 84 days, 16.3% and 22.4% of the total S⁰ applied to the soil were oxidized at 20 and 30 ℃, respectively. The oxidation of S⁰ proved to be a two-step process with a rapid oxidation during the first 28 days and a slow oxidation from then on. The highest oxidation rate of 12.8 μg S cm^-2 d^-1 was measured during the first two weeks at 30 ℃. At 20 ℃ the highest oxidation rate of 10.2 μg S cm^-2 d^-1 was obtained from two to four weeks after start of the experiment. On an average the soil pH declined by 3.6 and 4.0 units after two weeks of experiment. At the same time the electric conductivity increased nine times. With the oxidation of S⁰ the population of Thiobacillus spp. and aerobic heterotrophic S-oxidizing bacteria increased. The corresponding values for Thiobacillus spp. and aerobic heterotrophic S-oxidizing bacteria increased from 2.9 × 10⁵ and 1.4 × 10⁵ g^-1 soil at the start of the experiment to 4 × 10⁸ and 5.6 × 10⁸ g^-1 soil 14 days after S⁰ application, respectively. No Thiobacillus spp. was present eight weeks after S⁰ application. The results suggested that oxidation of residual S⁰ completely relied on aerobic heterotrophic S-oxidizing bacteria.     

Energy efficiency of the mycoparasite Sporidesmium sclerotivorum in vitro and in soil

The energy content of the mycoparasite Sporidesmium sclerotivorum mycelium was 18,389 J g^?1 and 16,334 J g^?1 for macroconidia on a dry weight basis. The energy content of Sclerotinia minor sclerotia, the host of the mycoparasite, was 16,485 J g^?1. In liquid culture, the economic coefficient for the conversion of glucose to mycelium (mycelial dry wt ÷ glucose consumed × 100) was 51–60 whereas the mycelial energy coefficient, [mycelial energy (J) ÷ substrate energy (J) × 100] was 65–75. In soil, the conidial energy coefficient [conidial energy (J) ÷ substrate energy (J) × 100] for the conversion of host sclerotial energy to the macroconidia of the mycoparasite was 19.8, which was 2–9 times that for the conversion of glucose in liquid culture. The conidial energy coefficient when grown on a liquid medium on vermiculite was 23.0. S. sclerotivorum, as an obligate parasite of sclerotia in soil, was most efficient in the conversion of energy in a system where there was a high surface: energy ratio. In liquid culture S. sclerotivorum is more efficient than most other fungi.