Psychrophilic Microorganisms from Areas Associated with the Viking Spacecraft

Microorganisms capable of growth at 7 C were enumerated and isolated from soil samples from the manufacture and assembly areas of the Viking spacecraft. Populations ranging from 4.2 X 10(3) to 7.7 X 10(6)/g of soil were isolated from the 15 soil samples examined. Temperature requirements were determined, and those growing at 3 C, but not at 32 C, were designated as obligate psychrophiles in this investigation. Populations of soil bacteria, including aerobic sporeformers, ranging from 1.5 X 10(2) to 9.8 X 10(5)/g were capable of growth at 3 C, but not at 32 C. Bacterial isolates were identified to major generic groups. No psychrophilic sporeformers were isolated from soil from the manufacture area, but psychrophilic sporeformers ranged from 0 to 6.1 X 10(3)/g from soil from the assembly area.     

Effect of soil macroaggregates crushing on C mineralization in a tropical deciduous forest ecosystem

Soil aggregates strongly influence C dynamics by affecting microbial activity. Our study tested the effect of soil crushing on C mineralization by laboratory incubation experiments of soil samples from a tropical deciduous forest ecosystem in Western Mexico. Soil samples were taken in January (dry season) and in October (rainy season). For each sampling date, the incubation experiment had a two factorial design with litter and macroaggregates (>250 μm) crushing as the main factors, both with two levels (with and without). At both sampling dates, the soil samples with intact macroaggregates had significantly higher C mineralization than the soil samples in which macroaggregates were crushed. The pH of leached solution was higher in the crushed soil samples than in uncrushed soil samples. The reduction of C mineralization caused by the disruption of soil aggregates is explained by the disturbance of environmental conditions within macroaggregates. The effect of macroaggregates crushing also reduced the differences of C mineralization between both seasons. We concluded that macroaggregates promote microbial activity by reducing the impact of variations in soil chemical and physical environmental conditions.     

Association of microbial community composition and activity with lead,chromium, and hydrocarbon contamination

Microbial community composition and activity were characterized in soil contaminated with lead (Pb), chromium (Cr), and hydrocarbons. Contaminant levels were very heterogeneous and ranged from 50 to 16,700 mg of total petroleum hydrocarbons (TPH) kg of soil(-1), 3 to 3,300 mg of total Cr kg of soil(-1), and 1 to 17,100 mg of Pb kg of soil(-1). Microbial community compositions were estimated from the patterns of phospholipid fatty acids (PLFA); these were considerably different among the 14 soil samples. Statistical analyses suggested that the variation in PLFA was more correlated with soil hydrocarbons than with the levels of Cr and Pb. The metal sensitivity of the microbial community was determined by extracting bacteria from soil and measuring [(3)H]leucine incorporation as a function of metal concentration. Six soil samples collected in the spring of 1999 had IC(50) values (the heavy metal concentrations giving 50% reduction of microbial activity) of approximately 2.5 mM for CrO(4)2- and 0.01 mM for Pb2+. Much higher levels of Pb were required to inhibit [14C]glucose mineralization directly in soils. In microcosm experiments with these samples, microbial biomass and the ratio of microbial biomass to soil organic C were not correlated with the concentrations of hydrocarbons and heavy metals. However, microbial C respiration in samples with a higher level of hydrocarbons differed from the other soils no matter whether complex organic C (alfalfa) was added or not. The ratios of microbial C respiration to microbial biomass differed significantly among the soil samples (P < 0.05) and were relatively high in soils contaminated with hydrocarbons or heavy metals. Our results suggest that the soil microbial community was predominantly affected by hydrocarbons.     

Influence of soil temperature on niacin and thiamine in honey mesquite

Summary The influence of soil temperature was examined on niacin and thiamine concentration in honey mesquite (Prosopis glandulosa var.glandulosa) seedlings. The seedlings were grown in soil temperature regimes of 21, 27, and 32°C in a controlled environment growth room. Nodulation randomly occurred on the roots of the seedlings, necessitating separate analysis according to the occurrence of nodulation. Roots of nodulated seedlings from the 21°C soil temperature regime contained greater quantities of niacin and thiamine compared to root samples from seedlings grown in either 27 or 32°C regimes. Niacin concentration of non-nodulated seedlings was highest in samples from seedlings grown in the 27°C soil temperature regime and lowest in samples from seedlings grown in the 21°C regime. Thiamine concentration was the greatest from non-nodulated seedlings grown in the 27°C soil temperature regime, while the thiamine concentration of non-nodulated samples from the 32°C regime was the least. Optimal soil temperature for honey mesquite root growth appears to be about 27°C. At sub-optimal soil temperatures niacin might have limited ‘growth’ while at supra-optimal soil temperatures, thiamine might be a limiting factor. College of Agricultural Sciences Contribution No. T-9-164.     

Microbial diversity of soil from two hot springs in Uttaranchal Himalaya

Soil samples collected from two hot springs, Soldhar and Ringigad, both located in the Garhwal region of Uttaranchal Himalaya were analysed for their physical, chemical and microbial components. The alkaline pH, total absence of carbon and nitrogen, and high temperature were features common to soil samples from both sites. The Soldhar samples contained higher amounts of Cu, Fe and Mn. Ringigad soil was devoid of Cu, but had much higher phosphate. While the optimum incubation temperature for isolating the maximum microbial counts from soil samples from the two sites was 50 degrees C, microbial growth in broth was also observed when incubated at 80 degrees C. Microscopic examination revealed three types of microbial populations, i.e., bacteria, yeast and filamentous organisms. The soil samples were found to be dominated by spore forming rods. Out of 58 aerobic isolates, 53 were gram positive bacilli. Gram positive anaerobic oval rods were also observed up to 60 degrees C. Soil dilution plates revealed the presence of antagonistic and phosphate solubilizing populations.     

Control of clubroot by soil partial sterilization with particular reference to the treatment of small natural foci of infection

Experiments were made on field plots with four soil partial sterilants applied at different dose rates or as combination treatments. The effects of treatments on clubroot were assessed by growing cabbages on the field plots or in a glasshouse in soil removed from the plots. In two experiments, no plants grown on plots or seedlings grown in soil samples from plots treated with Dowfume M.C.2 or Telone were infected with clubroot, whilst only one infected seedling was found in soil samples from those plots treated with chloropicrin. Although relatively few infected plants were recovered from Basamid treated plots, many infected seedlings were found in soil samples from those plots. The effectiveness of these treatments as indicated by seedling survival was Dowfume M.C.2 < chloropicrin < Telone < Basamid. At five sites a combination of Dowfume M.C.2 at 98 g/m² with 40 g/m² Basamid resulted in all cabbage seedlings grown in soil samples being disease free.     

Common Mesophilic Anaerobes, Including Clostridium botulinum and Clostridium tetani, in 21 Soil Specimens

A relatively rich medium was markedly superior to a dilute medium for the isolation of anaerobic bacteria from soil. The obligate anaerobes isolated from 21 soil samples were all clostridia and the counts ranged from 2.7 X 10-2 to 3.3 X 10-6 per g. The organisms most frequently isolated were Clostridium subterminate, C. sordelii, C. sporogenes, C. indolis, C. bifermentans, C. mangenoti, and C. perfringens. Seventeen other species were also recognized but almost one-third of the isolates could not be identified with any known species of Clostridium. C. botulinum type A was demonstrated in six soil samples, and type B in one. These soils were neutral to alkaline in reaction (average pH 7.9) and low in organic matter content (1.4%). The association of C. botulinum types A and B with neutral to alkaline soils was statistically significant (P = 0.001) as was their association with soils low in organic matter (P = 0.005). C. botulinum types E and F were found in one soil sample, pH 4.5, with organic matter 13.7%. C. tetani was isolated from two soil samples, both of intermediate pH value and higher than average organic matter content.     

Soil Water Content and Organic Carbon Availability Are Major Determinants of Soil Microbial Community Composition

Exploration of environmental factors governing soil microbial community composition is long overdue and now possible with improved methods for characterizing microbial communities. Previously, we observed that rice soil microbial communities were distinctly different from tomato soil microbial communities, despite management and seasonal variations within soil type. Potential contributing factors included types and amounts of organic inputs, organic carbon content, and timing and amounts of water inputs. Of these, both soil water content and organic carbon availability were highly correlated with observed differences in composition. We examined how organic carbon amendment (compost, vetch, or no amendment) and water additions (from air dry to flooded) affect microbial community composition. Using canonical correspondence analysis of phospholipid fatty acid data, we determined flooded, carbon-amended (+C) microcosm samples were distinctly different from other +C samples and unamended (–C) samples. Although flooding without organic carbon addition influenced composition some, organic carbon addition was necessary to substantially alter community composition. Organic carbon availability had the same general effects on microbial communities regardless of whether it was compost or vetch in origin. In addition, flooded samples, regardless of organic carbon inputs, had significantly lower ratios of fungal to bacterial biomarkers, whereas under drier conditions and increased organic carbon availability the microbial communities had higher proportions of fungal biomass. When comparing field and microcosm soil, flooded +C microcosm samples were most similar to field-collected rice soil, whereas all other treatments were more similar to field-collected tomato soil. Overall, manipulating water and carbon content selected for microbial communities similar to those observed when the same factors were manipulated at the field scale.     

Keratinolytic fungi in Egyptian soils

The frequency of occurrence of keratinolytic fungi in seventy soil samples collected from different sites in Upper Egypt and in the coastal area of the Mediterranean and baited with human and animal hair and pigeon feathers was determined.Twenty-one species in addition to an unidentified species, which belong to sixteen genera were collected.Chrysosporium indicum, C. tropicum, C. keratinophilum andMicrosporum gypseum were the most frequent fungal species recovered from baited soils.The eight soil samples collected from the salt marshes of the coastal Mediterranean area were completely free from any keratinolytic fungi, whereas the sixty-two soil samples collected from cultivated soils contributed a species ranging from one to four species.     

Functional diversity and community structure of micro-organisms in three arctic soils as determined by sole-carbon-source-utilization

Functional diversities of micro-organisms in arctic soils at three incubation temperatures were assessed using sole-carbon-source-utilization (SCSU). Soil samples were collected from an area of anthropogenic fertilization (mixed Dorset/Thule/Historic site), an area of animal enrichment (bird rock perches), and unaltered tundra (raised beach; control soil site). The micro-organisms were extracted from the soil samples and inoculated into Gram-negative (GN) Biolog plates incubated at 30°C, 10°C, and 4°C. Calculations of the Shannon index, substrate utilization richness, Shannon evenness, and the Jaccard coefficient of similarity were based upon substrate utilization on the Biolog plates. Principal component analysis distinguished microbial communities in enriched soils from unenriched soils. At 10°C and 4°C, Shannon indices of enriched soil microbial communities (10°C: soils influenced by wild animals=4.28, soils influenced by human activities=4.20; 4°C: soils influenced by wild animals=4.15, soils influenced by human activities=4.03) were significantly higher than unenriched soil microbial communities (10°C: 3.66; 4°C: 3.38). Substrate utilization richness and evenness displayed similar trends. Although Jaccard coefficients showed uniformity across the different soil samples, cluster analysis supported patterns demonstrated by PCA. Lower temperatures (4°C and 10°C) yielded greater resolution between soil microbial communities than 30°C based on Biolog colour development patterns.     

Ecology of pathogenic yeasts in Amazonian soil

In an investigation of Amazonian soil as a natural reservoir for pathogenic fungi, 1,949 soil samples collected from diverse geographical and ecological settings of the Brazilian Amazon Basin were analyzed for the presence of non-keratinophilic fungi by the indirect mouse inoculation procedure and for the presence of keratinophilic fungi by the hair bait technique. All soil samples were acidic with low pH values. From 12% of the soil samples, 241 yeast and yeastlike isolates pertaining to six genera and 82 species were recovered, of which 63% were Torulopsis and 26% were Candida species. Nine fungi with known pathogenic potentials were encountered among 43% (104) of the isolates: T. glabrata, C. guilliermondii, C. albicans, C. pseudotropicalis, C. stellatoidea, C. tropicalis, Rhodotorula rubra, and Wangiella dermatitidis. The yeast flora was marked by species diversity, low frequency of each species, random geographical distribution, and an apparent lack of species clustering. The composition and distribution of the yeast flora in soil differed from those of the yeast flora harbored by bats, suggesting that the Amazonian external environment and internal bat organs act as independent natural habitats for yeasts.     

Ecology of pathogenic yeasts in Amazonian soil.

In an investigation of Amazonian soil as a natural reservoir for pathogenic fungi, 1,949 soil samples collected from diverse geographical and ecological settings of the Brazilian Amazon Basin were analyzed for the presence of non-keratinophilic fungi by the indirect mouse inoculation procedure and for the presence of keratinophilic fungi by the hair bait technique. All soil samples were acidic with low pH values. From 12% of the soil samples, 241 yeast and yeastlike isolates pertaining to six genera and 82 species were recovered, of which 63% were Torulopsis and 26% were Candida species. Nine fungi with known pathogenic potentials were encountered among 43% (104) of the isolates: T. glabrata, C. guilliermondii, C. albicans, C. pseudotropicalis, C. stellatoidea, C. tropicalis, Rhodotorula rubra, and Wangiella dermatitidis. The yeast flora was marked by species diversity, low frequency of each species, random geographical distribution, and an apparent lack of species clustering. The composition and distribution of the yeast flora in soil differed from those of the yeast flora harbored by bats, suggesting that the Amazonian external environment and internal bat organs act as independent natural habitats for yeasts.     

Keratinolytic Fungi in Egyptian Soils

The frequency of occurrence of keratinolytic fungi in seventy soil samples, collected from different sites in Upper Egypt and in the coastal area of the Mediterranean, was determined by baiting with human and animal hairs and pigeon feathers. Twenty-one species, in addition to an unidentified species, which belong to sixteen genera were collected. Chrysosporium indicum, C. tropicum, C. keratinophilum, and Microsporum gypseum were the most frequent fungal species recovered from the baited soils. The soil samples collected from the salt marshes of the coastal Mediterranean area were completely free from any keratinolytic fungi, whereas the soil samples collected from cultivated soils contributed species, ranging from one to four species.     

Effects of open-top chambers and substrate type on biogeochemical processes at disturbed boreal forest sites in northwestern Quebec

In the context of land use change, the dynamics of the water extractable organic carbon (WEOC) pool and CO₂ production were studied in soil from a native oak-beech forest and a Douglas fir plantation during a 98-day incubation at a range of temperatures from 8°C to 28°C. The soil organic carbon, water contents and mineralisation rates of soil samples from the 0–5 cm layer were higher in the native forest than in the Douglas fir plantation. During incubation, a temperature-dependent shift in the δ¹³C of respired CO₂ was observed, suggesting that different carbon compounds were mineralised at different temperatures. The initial size of the WEOC pool was not affected by forest type. The WEOC pool size of samples from the native forest did not change consistently over time whereas it decreased significantly in samples from the Douglas plantation, irrespective of soil temperature. No clear changes in the δ¹³C values of the WEOC were observed, irrespective of soil origin. The fate of the WEOC, independent of soil organic carbon content or mineralisation rates, appeared to relate to forest types. Replacement of native oak-beech forest with Douglas fir plantation impacts carbon input to the soil, mineralisation rates and production of dissolved organic carbon.     

Prevalence of Clostridium botulinum type E and coexistence of C. botulinum nonproteolytic type B in the river soil of Japan.

Soil samples from 98 sites in the whole systems of four rivers in Japan were examined for the presence of Clostridium botulinum. Type E organism was prevalently shown throughout the whole river systems including upper part; detection rates of type E toxin in soil culture ranged from 33 to 82%. This type was also detected in soil of adjacent mountainous district. Type B and C toxins were detected at 7% and 9% of the sites examined, respectively. C. botulinum type E and nonproteolytic type B strains were isolated from enrichment cultures of soil samples. These results suggest that the terrestrial origin of type E organism would be considered as one of the reasons for the high incidence of this organism in the sea areas, and prove that C. botulinum nonproteolytic type B exists in the soil of Japan.     

Selective isolation and distribution of Actinobispora strains in soil

A simplified enrichment method for selective isolation of Actinobispora strains from soil is described. Actinobispora spores were tolerant to dry-heat treatment at 110 degrees C for 15 min. Actinobispora was more resistant to 1 microgram/mL leucomycin, 1 microgram/mL novobiocin, and 0.5 microgram/mL tunicamycin than Streptomyces dominant in soil, which prevents selective isolation of Actinobispora. Percentages of Actinobispora colonies on the isolation plate were increased by addition of antibiotics and dry-heat treatment of the soil samples. By combining the techniques described above, this genus was isolated from 105 out of 574 soil samples (18% of the samples tested). It was recovered from the soil samples with pH values ranging 5.0 to 8.9, and 78% of strains were isolated from neutral soil (pH 6.0-8.0). A number of Actinobispora strains were isolated from various soils around the world. Actinobispora strains are widely distributed in the world at relatively high frequency.     

Properties of Soil Pore Space Regulate Pathways of Plant Residue Decomposition and Community Structure of Associated Bacteria

Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO₂ emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis of amplified 16S–18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75–80% of the added plant residue was decomposed, cumulative CO₂ emission constituted 1,200 µm C g^-1 soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO₂ emission constituted 2,000 µm C g^-1 soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO₂ emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C decomposition processes.     

天然灌木林改造成板栗林对土壤碳库和氮库的影响

在浙江省安吉县采集了相邻的天然灌木林和板栗林土壤,分析土壤水溶性碳(WSOC)、微生物生物量碳(MBC)、易氧化碳(ROC)、水溶性有机氮(WSON)和微生物生物量氮(MBN),并利用核磁共振方法分析土壤总有机碳的波谱特征,研究天然灌木林改造成板栗林对土壤碳库和氮库的影响.结果表明： 天然灌木林改造成板栗林后,土壤中的碱解氮、有效磷和速效钾显著增加,而WSOC、MBC、ROC、WSON和MBN显著下降.天然灌木林和板栗林土壤有机碳以烷基碳和烷氧碳为主.天然灌木林改造成板栗林后,土壤有机碳中的烷氧碳和羰基碳比例显著下降,而烷基碳和芳香碳比例以及A/O-A值和芳香度均显著增加.天然灌木林改造成板栗林并长期集约经营后,土壤活性碳库和氮库含量均显著下降,而土壤碳库的稳定性显著增加.     

Clostridium botulinum in the soil of Paraguay

Seventeen soil samples of Paraguay were examined for the presence of Clostridium botulinum. Botulinum type A, C1 and F toxins were detected in soil cultures. Type E toxin was not detected in any of soil cultures including those from river and lake shores.     

Transport of a genetically engineered Pseudomonas fluorescens strain through a soil microcosm.

Vertical soil microcosms flushed with groundwater were used to study the influence of water movement on survival and transport of a genetically engineered Pseudomonas fluorescens C5t strain through a loamy sand and a loam soil. Transport of cells introduced into the top 1 cm of the vertical soil microcosms was dependent on the flow rate of water and the number of times microcosms were flushed with groundwater. The presence of wheat roots growing downward in the microcosms contributed only slightly to the movement of P. fluorescens C5t cells to lower soil regions of the loamy sand microcosms, but enhanced downward transport in the loam microcosms. Furthermore, the introduced P. fluorescens C5t cells were detected in the effluent water samples even after three flushes of groundwater and 10 days of incubation. As evidenced by a comparison of counts from immunofluorescence and selective plating, nonculturable C5t cells occurred in day 10 soil and percolated water samples, primarily of the loamy sand microcosms. Vertical soil microcosms that use water movement may be useful in studying the survival and transport of genetically engineered bacteria in soil under a variety of conditions prior to field testing.