The rate of change of a soil bacterial community after liming as a function of temperature

The response of a bacterial community to liming of a forest humus soil (pH 4.9 increased to pH 7.5) was studied in the laboratory at three temperatures (5, 20, and 30°C). As a comparison an unlimed soil (pH 4.9) and a soil limed in the field 15 years ago (pH around 6) were also included. The bacterial community tolerance of pH was measured using TdR incorporation. The pH of the bacterial suspensions (bacteria directly extracted from soil) was altered to 3.6 and 8.3 using different buffers before measuring TdR incorporation. The logarithmic ratio between TdR incorporation at 8.3 and 3.6 was then used as an indicator of the community pH tolerance. The rate of changes in the community tolerance to pH after liming was fastest for the soil incubated at 30°C, but only minor differences in rate of change could be seen between samples incubated at 5 and 20°C. Changes in phospholipid fatty acid (PLFA) pattern after increasing the pH were most rapid for the bacterial community in the soil incubated at 30°C followed by the soil incubated at 20°C, whereas no changes could be seen in the PLFA pattern of the soil incubated at 5°C, even after 82 days’ incubation. Thus, the changes in the PLFA pattern were considerably slower than the changes in bacterial community tolerance to pH measured using TdR incorporation.     

一株产环糊精葡萄糖基转移酶的地衣芽孢杆菌的选育、产酶条件及酶学特性

从土壤分离物中筛选到一株环糊精葡萄糖基转移酶 (CGTase)产生菌 4 0 3,96h发酵酶活为 0 95U mL。经紫外辐射和硫酸二乙酯复合诱变而获得突变株CLS4 0 3,96h发酵酶活达 1 36U mL ,提高 4 3%。该突变菌株被鉴定为地衣芽孢杆菌 (Bacilluslicheniformis) ,产CGTase的最佳碳源为可溶性淀粉 ,最佳氮源为硝酸铵 ,最适初始pH为 6 5 ,最适培养温度为 35℃ ,发酵期间CGTase的产生高峰 (第 96h)滞后于菌体生物量高峰 (第 4 8h) 2d。菌株所产CGTase的最适反应pH为 6 0 ,最适温度为 5 5℃ ,在pH 6 0～ 7 5间和 5 0℃下保持 1h后的剩余酶活均达 90 %以上 ;酶液中适量添加Ca2 能大幅提高CGTase在 5 5℃下的稳定性。经高效液相色谱分析 ,CGTase作用于淀粉后的产物以α 环糊精为主 ,β 环糊精为次 ,二者比例为 2 4 7∶1,环糊精总产率达 2 9 8% ,但产物中不含γ 环糊精     

Proteolytic activity of Trichoderma viride in mixed culture with Sclerotium rolfsii in soil.

Cultures of Sclerotium rolfsii and Trichoderma viride together in autoclaved soil were assayed at intervals during 8 days of incubation for proteolytic activity (PA) of T. viride. Significant proteolytic activity was detected only in soil containing T. viride (i.e., T. viride alone or S. rolfsii + T. viride); greatest activity occurred between 3 and 4 days after infestation and declined rapidly thereafter. Maximal PA in the mixed-culture soil was accompanied by an increase in soil pH. optimal pH values for PA was 5.5-6.5 with a maximum at 6.0.     

Evaluation of measures intended to increase the fertilizer-N recovery by lowland rice

Red clover root material confined in mesh bags was buried in three different limed and unlimed soils and incubated for 196 days at room temperature. Remaining amounts of organic matter, as well as concentrations of C and N of the decomposing material were determined three times during the incubation and finally the concentration of soil mineral N and pH of remaining roots was also assessed. Liming only temporarily affected the decomposition rate of organic matter and N release, and at the end of the incubation no effects could be observed due to liming. A possible explanation is that the decomposing root residues provide a well buffered micro-environment for the decomposing microflora. Liming did not change the pH of the root residues even when 97–98% of dry mass had disappeared from the mesh bags. Concentrations of mineral N were higher in limed than in unlimed soils.     

Factors influencing biohydrogenation and conjugated linoleic acid production by mixed rumen fungi

The objective of this study was to evaluate the effect of soluble carbohydrates (glucose, cellobiose), pH (6.0, 6.5, 7.0), and rumen microbial growth factors (VFA, vitamins) on biohydrogenation of linoleic acid (LA) by mixed rumen fungi. Addition of glucose or cellobiose to culture media slowed the rate of biohydrogenation;only 35-40% of LA was converted to conjugated linoleic acid (CLA) or vaccenic acid (VA) within 24 h of incubation, whereas in the control treatment, 100% of LA was converted within 24 h. Addition of VFA or vitamins did not affect biohydrogenation activity or CLA production. Culturing rumen fungi at pH 6.0 slowed biohydrogenation compared with pH 6.5 or 7.0. CLA production was reduced by pH 6.0 compared with control (pH 6.5), but was higher with pH 7.0. Biohydrogenation of LA to VA was complete within 72 h at pH 6.0, 24 h at pH 6.5, and 48 h at pH 7.0. It is concluded that optimum conditions for biohydrogenation of LA and for CLA production by rumen fungi were provided without addition of soluble carbohydrates, VFA or vitamins to the culture medium; optimum pH was 6.5 for biohydrogenation and 7.0 for CLA production.     

Alfalfa,Medicago sativa L., in highly weathered,acid soils

Summary Seedlings of a broad based population of alfalfa, (Medicago sativa L.), were visually selected for 2 generations (cycles) in an acid Cecil soil (pH=4.8). Simultaneously, 2 generations of selections were made in a limed Cecil soil (pH=6.2) amended with phosphorus. When tested in acid soil (pH=4.8) with added P, the cycle 2 acid selections yielded significantly more top yield than either the limed selections or the original seed. When grown in the limed soil (pH=6.2) without added P, the acid selections yielded significantly less. There were no significant differences among selections in other soil conditions (pH=4.8, no P added and pH=6.2, P added). Root weight and length and nodule fresh weight correlated well with top yield in all treatments. The yield of the 10 parent varieties and polycrossed seed of their cycle 1 acid and cycle 1 limed selections were compared under two soil conditions (acid and limed). The results of this test indicate that some varieties were more responsive to acid soil selection than other. Overall, none of the 10 varieties showed any decreases in total top yield due to one cycle of selection in either the acid or limed soil conditions.     

Importance of Inoculum Properties on the Structure and Growth of Bacterial Communities during Recolonisation of Humus Soil with Different pH

The relationship between community structure and growth and pH tolerance of a soil bacterial community was studied after liming in a reciprocal inoculum study. An unlimed (UL) humus soil with a pH of 4.0 was fumigated with chloroform for 4 h, after which ?<?1 % of the initial bacterial activity remained. Half of the fumigated soil was experimentally limed (EL) to a pH of 7.6. Both the UL and the EL soil were then reciprocally inoculated with UL soil or field limed (FL) soil with a pH of 6.2. The FL soil was from a 15-year-old experiment. The structural changes were measured on both bacteria in soil and on bacteria able to grow on agar plates using phospholipids fatty acid (PLFA) and denaturing gradient gel electrophoresis (DGGE) analysis. The developing community pH tolerance and bacterial growth were also monitored over time using thymidine incorporation. The inoculum source had a significant impact on both growth and pH tolerance of the bacterial community in the EL soil. These differences between the EL soil inoculated with UL soil and FL soil were correlated to structural changes, as evidenced by both PLFA and DGGE analyses on the soil. Similar correlations were seen to the fraction of the community growing on agar plates. There were, however, no differences between the soil bacterial communities in the unlimed soils with different inocula. This study showed the connection between the development of function (growth), community properties (pH tolerance) and the structure of the bacterial community. It also highlighted the importance of both the initial properties of the community and the selection pressure after environmental changes in shaping the resulting microbial community.     

Effects of soil acidity on nodulation ofAlnus glutinosa and viability ofFrankia

Summary Black alder seedlings were grown from seed for 7 weeks in six soils limed to various pH levels and inoculated withFrankia in two inoculation-seeding time combinations (inoculated and seeded concurrently; inoculated then seeded 5 weeks after inoculation). Three mine soils and three non-mine soils were used. Soil pHs in the study ranged from 3.6 to 7.6. In the second inoculation-seeding time combination, a series of soil samples at each of the pH levels below 7.0 were relimed to pH 7.0 immediately prior to seeding. The purpose of the study was to examine the effects of soil acidity on the nodulation of black alder byFrankia and the viability ofFrankia in acid soils. Based on the average number of nodules established per seedling, soil pH was determined to be a significant factor affecting nodulation in the mine soils. The highest levels of nodulation occurred between soil pH 5.5 and 7.2. Below pH 5.5, nodulation was reduced. There was also evidence of decreased viability of the endophyte below pH 4.5.     

Effect of Acidity on the Composition of an Indigenous Soil Population of Rhizobium trifolii Found in Nodules of Trifolium subterraneum L.

Acidity affected which members of an indigenous soil population of Rhizobium trifolii nodulated Trifolium subterraneum L. cv. Mt. Barker. In three experiments involving plants grown either in mineral salts agar adjusted to pH 4.8 or 6.8 and inoculated with a soil suspension or grown directly in samples of unamended soil (pH 4.8) or soil amended with CaCO₃ (pH 6.4), 121 of 151 isolates of R. trifolii were placed into four serogroups. Seventy-nine of these isolates were placed into two serogroups (6 and 36) whose nodulating ability was affected by the pH of the plant root environment. Representatives of serogroup 6 occupied the greatest percentage of the nodules at the low pH in both mineral salts agar (77%) and in unlimed soil (47 and 57%). The same serogroup was a minor nodule occupant at the higher pH in mineral salts agar (0%) and in limed soil (0 and 10%). In contrast, serogroup 36 was virtually absent in nodules formed at the low pH, whereas it was the dominant serogroup at the higher pH in both mineral salts agar (32%) and in limed soil (35 and 49%). Despite the isolates from within each serogroup being antigenically identical, separation of cellular proteins by sodium dodecyl sulfate-polyacrylamide gradient gel electrophoresis revealed four and six different gel types within serogroups 6 and 36, respectively. Isolates represented by one or two gel types dominated the contribution of each serogroup to the nodule population. Further evidence for differences between isolates within each gel type were revealed from measurements of symbiotic effectiveness.     

Effect of soil ammonium concentration on N2O release and on the community structure of ammonia oxidizers and denitrifiers

The effect of ammonium addition (6.5, 58, and 395 microg of NH4+-N g [dry weight] of soil(-1)) on soil microbial communities was explored. For medium and high ammonium concentrations, increased N2O release rates and a shift toward a higher contribution of nitrification to N2O release occurred after incubation for 5 days at 4 degrees C. Communities of ammonia oxidizers were assayed after 4 weeks of incubation by denaturant gradient gel electrophoresis (DGGE) of the amoA gene coding for the small subunit of ammonia monooxygenase. The DGGE fingerprints were invariably the same whether the soil was untreated or incubated with low, medium, or high ammonium concentrations. Phylogenetic analysis of cloned PCR products from excised DGGE bands detected amoA sequences which probably belonged to Nitrosospira 16S rRNA clusters 3 and 4. Additional clones clustered with Nitrosospira sp. strains Ka3 and Ka4 and within an amoA cluster from unknown species. A Nitrosomonas-like amoA gene was detected in only one clone. In agreement with the amoA results, community profiles of total bacteria analyzed by terminal restriction fragment length polymorphism (T-RFLP) showed only minor differences. However, a community shift occurred for denitrifier populations based on T-RFLP analysis of nirK genes encoding copper-containing nitrite reductase with incubation at medium and high ammonia concentrations. Major terminal restriction fragments observed in environmental samples were further described by correspondence to cloned nirK genes from the same soil. Phylogenetic analysis grouped these clones into clusters of soil nirK genes. However, some clones were also closely related to genes from known denitrifiers. The shift in the denitrifier community was probably the consequence of the increased supply of oxidized nitrogen through nitrification. Nitrification activity increased upon addition of ammonium, but the community structure of ammonium oxidizers did not change.     

Effect of Acidity on the Composition of an Indigenous Soil Population of Rhizobium trifolii Found in Nodules of Trifolium subterraneum L

Acidity affected which members of an indigenous soil population of Rhizobium trifolii nodulated Trifolium subterraneum L. cv. Mt. Barker. In three experiments involving plants grown either in mineral salts agar adjusted to pH 4.8 or 6.8 and inoculated with a soil suspension or grown directly in samples of unamended soil (pH 4.8) or soil amended with CaCO(3) (pH 6.4), 121 of 151 isolates of R. trifolii were placed into four serogroups. Seventy-nine of these isolates were placed into two serogroups (6 and 36) whose nodulating ability was affected by the pH of the plant root environment. Representatives of serogroup 6 occupied the greatest percentage of the nodules at the low pH in both mineral salts agar (77%) and in unlimed soil (47 and 57%). The same serogroup was a minor nodule occupant at the higher pH in mineral salts agar (0%) and in limed soil (0 and 10%). In contrast, serogroup 36 was virtually absent in nodules formed at the low pH, whereas it was the dominant serogroup at the higher pH in both mineral salts agar (32%) and in limed soil (35 and 49%). Despite the isolates from within each serogroup being antigenically identical, separation of cellular proteins by sodium dodecyl sulfate-polyacrylamide gradient gel electrophoresis revealed four and six different gel types within serogroups 6 and 36, respectively. Isolates represented by one or two gel types dominated the contribution of each serogroup to the nodule population. Further evidence for differences between isolates within each gel type were revealed from measurements of symbiotic effectiveness.     

Nitrification in some tropical soils

Summary Nitrification of soil N in 8 mineral and 2 histosols having a wide range in pH (3.4 to 8.6), organic C (1.22 to 22.70%) and total N (0.09 to 1.20%) was studied by measuring nitrate fromation under aerobic incubation of the soil samples at 30°C for 4 weeks. The amounts of NO₃-N produced in the soils varied from 0 to 123 μg/g of soil. Soil N in the two acid sulfate soils and one other acid soil did not nitrify under conditions that stimulate nitrification. Soils having pH more than 6.0 nitrified at a rapid rate and released NO₃-N ranging from 98 to 123 μg/g. The two organic soils differed considerably in their capacity to nitrify though the total amounts of mineral N released were similar in these soils. The amounts of NO₃-N formed in the soils was highly positively correlated with the soil pH but was not significantly correlated with the organic C of total N content of the soils. Statistical analysis also showed that nitrate formation was not significantly correlated with soil pH in soils having pH higher than 6.0.     

Rates of production and utilization of lactate by microbial communities from the human colon

Lactate metabolism was studied in mixed bacterial communities using single-stage continuous flow fermentors inoculated with faecal slurries from four different volunteers and run for 6 days at pH 5.5 and 6.0, using carbohydrates, mainly starch, as substrates. A continuous infusion of [U-(13) C]starch and l-[3-(13) C]lactate was performed on day 5 and a bolus injection of l-[3-(13) C]lactate plus dl-lactate on day 6. Short-chain fatty acids and lactate concentrations plus enrichments and numbers of lactate-producing and -utilizing bacteria on day 5 were measured. Faecal samples were also collected weekly over a 3-month period to inoculate 24-h batch culture incubation at pH 5.9 and 6.5 with carbohydrates alone or with 35 mmol L(-1) lactate. In the fermentors, the potential lactate disposal rates were more than double the formation rates, and lactate concentrations usually remained below detection. Lactate formation was greater (P<0.05) at the lower pH, with a similar tendency for utilization. Up to 20% of butyrate production was derived from lactate. In batch cultures, lactate was also efficiently used at both pH values, especially at 6.5, although volunteer and temporal variability existed. Under healthy gut environmental conditions, bacterial lactate disposal seems to exceed production markedly.     

Survival of Rhizobium in Acid Soils

A Rhizobium strain nodulating cowpeas did not decline in abundance after it was added to sterile soils at pH 6.9 and 4.4, and the numbers fell slowly in nonsterile soils at pH 5.5 and 4.1. A strain of R. phaseoli grew when added to sterile soils at pH 6.7 and 6.9; it maintained large, stable populations in soils of pH 4.4, 5.5, and 6.0, but the numbers fell markedly and then reached a stable population size in sterile soils at pH 4.3 and 4.4. The abundance of R. phaseoli added to nonsterile soils with pH values of 4.3 to 6.7 decreased similarly with time regardless of soil acidity, and the final numbers were less than in the comparable sterile soils. The minimum pH values for the growth of strains of R. meliloti in liquid media ranged from 5.3 to 5.9. Two R. meliloti strains, which differed in acid tolerance for growth in culture, did not differ in numbers or decline when added to sterile soils at pH 4.8, 5.2, and 6.3. The population size of these two strains was reduced after they were introduced into nonsterile soils at pH 4.8, 5.4, and 6.4, and the number of survivors was related to the soil pH. The R. meliloti strain that was more acid sensitive in culture declined more readily in sterile soil at pH 4.6 than did the less sensitive strain, and only the former strain was eliminated from nonsterile soil at pH 4.8; however, the less sensitive strain also survived better in limed soil. The cell density of the two R. meliloti strains was increased in pH 6.4 soil in the presence of growing alfalfa. The decline and elimination of the tolerant, but not the sensitive, strain was delayed in soil at pH 4.6 by roots of growing alfalfa.     

The relationship between soil pH and population level of Pratylenchus loosi in tea plantations of Iran

Tea root lesion nematode, Pratylenchus loosi, is one of the most important crop pests in Iran, which causes loss in quantity and quality of tea. This study was carried out to identify the relationship between soil pH and population level of P. loosi. One hundred and eighty-three soil and root samples were taken randomly from all of the tea plantations in Iran. The nematodes were extracted from root samples with Coolen and d’Herd methods and from soil samples by sieving and centrifugation. Soil pH was measured by two methods: 1:1 dilution of soil:deionised water and 1:1 dilution of soil:dilute calcium chloride 0.01?M (Cacl₂) solution. Range of mean population of P. loosi per gram of root was 0.66–884 and per 100?g of soil was 1–186 in all samples. The highest population of P. loosi was observed at pH 3.5–4.5 as if 71.33% of infested samples were observed at soil pH 3.5–4.5. The results of regression analyses showed that at pH ranges between 3.5 and 4.5, there is a correlation (P???0.05) between soil pH and mean population of nematode per gram of feeder roots. This study demonstrated that the population density and damage potential of this nematode likely increases at pH?<?4.5.     

Nitrification and mineralization potentials in a limed Ultisol in the humid tropics

Summary We studied the effect of liming on the rates of mineralization and nitrification in a coarse-textured kaolinitic Ultisol. Soil samples were taken from field plots which received lime rates from 0 to 4mt/ha three years prior to the study. The pH of the soil samples varied from 4.2 to 6.1. Ammonification of soil organic N and added urea source proceeded readily and was not affected by lime rate. Nitrification occurred in both limed and unlimed soils but the rate of nitrification depended upon the rate of lime application. Soil pH, exchangeable Ca and exchangeable A1 were significantly correlated with the amount of NO₃-N accumulated at the end of the 65 days incubation period. Nitrification of NH₄-N from ammonium sulfate was absent in soils receiving lower rates of lime which gave pH values ranging from 4.2 to 4.8. Added ammonium source was nitrified readily after a 3-week delay period in the soil (pH 6.1) which received a higher rate of lime (4 mt/ha).     

Effect of varying static and changing moisture levels during incubation on extractability of soil phosphate

Summary A sandy loam (pH 6.5) was incubated at 28°C at static moisture levels, ranging from 10 per cent saturation to 133 per cent saturation (waterlogging), for 6 and 12 weeks; other samples covering the same moisture range were first incubated for 6 weeks, and after changing all moisture levels to 50 per cent saturation were incubated for a further 6 weeks.With increasing static soil moisture level during incubation there was a slight reduction in Morgan-extractable phosphate up to 70 per cent saturation, but thereafter, due to anaerobic effects, there were considerable increases in extractable phosphate with increasing moisture level.With changing moisture level during incubation the effects of anaerobiosis became apparent where original moisture level was greater than 50 per cent saturation; extractable phosphate was reduced to levels lower than those occurring where the soil was maintained continuously at 50 per cent saturation. The extent of reduction in extractable phosphate increased with original soil saturation level.     

Effect of pre-incubation pH on the growth characteristics of Aeromonas hydrophila at 5°C, as assessed by two methods

Two strains of Aeromonas hydrophila (the type strain ATCC 7966 and a food-derived strain JAH4) were pre-incubated at 5°C in Brain Heart Infusion (BHI) broth with pH adjusted to 6.0 or 7.0, and then incubated at the same temperature in BHI broth with pH adjusted to 6.0, 6.5, 7.0 and 7.5. Growth kinetics during incubation were determined by two methods: viable count (VC) and measurement of optical density (O.D.). Pre-incubation at different pH values did not significantly affect the maximum specific growth rates of the strains during incubation, but the lag phases were shorter after pre-incubation at pH 6.0 than at pH 7.0. The VC method was more sensitive than O.D. measurements for assessing lag phase.     

Inhibitory effect of water-soluble chitosan on growth of Streptococcus mutans

The present study was undertaken to evaluate the effects of pH and the degree of polymerization of chitosan on the inhibition of growth of Streptococcus mutans. Three types of chitosan, polymer, oligomer and monomer, were used at 4% (W/V) and three different levels of pH: 6.0, 6.5 and 7.4. Bactericidal activity was calculated by the growth ratio. Chitosan oligomer significantly inhibited bacterial growth at a pH value of 6.5. All three types of chitosan strongly inhibited bacterial growth at pH 6.0. Furthermore, nearly complete inhibition was obtained with 2%(W/V) chitosan solution at constant pH 6.5. This study is the first to report that water-soluble chitosan directly suppresses the growth of the typical cariogenic bacterium S. mutans even at pH 6.5, without causing demineralization of the tooth surface.     

Molecular assessment on impact of uranium ore contamination in soil bacterial diversity

Impact of uranium (U) ore and soluble uranium (at pH 4.0) contamination on agricultural soil bacterial diversity was assessed by using laboratory microcosms for one year. Diversity and abundance of metabolically active bacterial populations in periodically collected microcosm’s samples were analyzed by extracting total RNA and preparation of cDNA followed by analysis of 16S rRNA gene by DGGE and real time PCR. DGGE analysis revealed prominent shift of soil bacterial population due to uranium ore contamination within 12 months while uranium ore along with soluble U completely destroyed the soil bacterial diversity within first six months. Real time PCR based analysis indicated 100–200 folds increase in 16S rRNA gene copies of total as well as individual bacterial taxa in both U ore amended and unamended soils in first six months while increase in incubation period upto 12 months showed reduction of the same only in U ore amended soil. Antagonistic effect of U ore contamination on soil bacterial diversity indicated the severe impact of U mining likely to have on nearby ecosystems. Role of U at acidic pH in destroying the diversity completely is noteworthy as it corroborated the disastrous consequence of acid mine drainage generated from U mine sites.