Number Of Culturable Microorganisms Research Articles

Effect of long-term radish (Raphanus sativus var. sativus) monoculture practice on physiological variability of microorganisms in cultivated soil

Long-term monoculture may affect soil environment biodiversity. An example of such a plant is radish (Raphanus sativus var. sativus), an economically important crop in Poland, a quick-growing vegetable with intensified harvest throughout the season. The aim of this study was to determine changes in biodiversity of soil under radish cultivation and to compare the research methods applied. The monoculture practice affected soil pH, but the organic carbon content remained stable. 16S RNA-seq analysis revealed changes in soil microbial population, with the dominant phyla Proteobacteria (37.3%), Acidobacteria (19%), and Actinobacteria (16%), and the dominant taxa Gaiella (1.59%), Devosia (1.51%) and Nocardioides (1.43%). These changes have not fully expressed in the number of culturable microorganisms, where only fungal abundance changed significantly. However, the physiological state of microbial cells (λ) indicated that oligotrophs and copiotrophs were in a vegetative (λ > 3.0) state at the beginning of the season and fungi at the end of the year. Changes in the biodiversity of soil microorganisms were visualised using Community Level Physiological Profiling, where an oscillation in Average Well Colour Development (OD560 = 0.78–1.48) was observed in successive months of radish culture, with biodiversity indices (Shannon and Substance richness) remaining similar. The greatest variation in the influence of monoculture practice on soil factors was observed for the soil enzymes activities (for dehydrogenase and peroxidase activities – 0.5 μg TPF/h/g DW and 1.5 μmolPYGL/h/g DW respectively). Alkaline phosphatases predominated among this group of enzymes, and the activity of carbon metabolism enzymes decreased over the season, except for invertases, where an increase in activity of up to 50 μg Glc/h/g DW was observed. All the parameters studied indicated changes in the soil environment. Nevertheless the microbial community remains stable during the whole experiment returning to equilibrium in a quite short time after changing conditions.

Enhancing Native Plant Establishment in Mine Tailings under Drought Stress Conditions through the Application of Organo-Mineral Amendments and Microbial Inoculants

The implementation of phytoremediation strategies under arid and semiarid climates requires the use of appropriate plant species capable of withstanding multiple abiotic stresses. In this study, we assessed the combined effects of organo-mineral amendments and microbial inoculants on the chemical and biological properties of mine tailings, as well as on the growth of native plant species under drought stress conditions. Plants were cultivated in pots containing 1 kg of a mixture of mine tailings and topsoil (i.e., pre-mined superficial soil) in a 60:40 ratio, 6% marble sludge, and 10% sheep manure. Moreover, a consortium of four drought-resistant plant growth-promoting rhizobacteria (PGPR) was inoculated. Three irrigation levels were applied: well-watered, moderate water deficit, and severe water deficit, corresponding to 80%, 45%, and 30% of field capacity, respectively. The addition of topsoil and organo-mineral amendments to mine tailings significantly improved their chemical and biological properties, which were further enhanced by bacterial inoculation and plants’ establishment. Water stress negatively impacted enzymatic activities in amended tailings, resulting in a significant decrease in acid and alkaline phosphatases, urease, and dehydrogenase activities. Similar results were obtained for bacteria, fungi, and actinomycete abundance. PGPR inoculation positively influenced the availability of phosphorus, total nitrogen, and organic carbon, while it increased alkaline phosphatase, urease (by about 10%), and dehydrogenase activity (by 50%). The rhizosphere of Peganum harmala showed the highest enzymatic activity and number of culturable microorganisms, especially in inoculated treatments. Severe water deficit negatively affected plant growth, leading to a 40% reduction in the shoot biomass of both Atriplex halimus and Pennisetum setaceum compared to well-watered plants. P. harmala showed greater tolerance to water stress, evidenced by lower decreases observed in root and shoot length and dry weight compared to well-watered plants. The use of bioinoculants mitigated the negative effects of drought on P. harmala shoot biomass, resulting in an increase of up to 75% in the aerial biomass in plants exposed to severe water deficit. In conclusion, the results suggest that the combination of organo-mineral amendments, PGPR inoculation, and P. harmala represents a promising approach to enhance the phytoremediation of metal-polluted soils under semiarid conditions.

Distinct Changes in Abundance of Culturable Microbial Community and Respiration Activities in Response to Mineral–Organic Mixture Application in Contaminated Soil

The availability and affordability of fertilizers are the main risks currently faced by the fertilizer market. Therefore, there is a need to look for other sources of nutrient supply for plants, while taking care of soil properties. The application of fertilizers with the addition of functionalized materials could help in the efficient use of nutrients. The aim of the study was to assess the impact of the application of mixtures with the addition of zeolite–vermiculite composites (NaX–Ver) on the culturable microorganisms and selected soil properties. A two-year pot experiment was conducted on soil with elevated contents of cadmium, zinc, and lead. The test treatments included soil mixed with NPK and additives in two doses of NaX–Ver combined with leonardite (Leo) or lignite (L). The test plant used in the experiment was maize. The soil material was analyzed for the number of bacteria, mold fungi, actinomycetes, and ammonifiers. Furthermore, soil pH, EC, N total, and SOC contents, as well as soil respiration activity, were tested. The applied fertilizer mixtures had a great effect on changes in the N total and SOC contents. The N total increase was 45.5% in NaX–Ver3%L3% and 51% in NaX–Ver9%Leo6%, and the largest SOC increase (24.3%) was recorded in the NaX–Ver3%Leo3% treatment. The highest respiration activity was determined in NaX–Ver3%Leo3% and NaX–Ver9%Leo6%: 2.12 µg C-CO2 g−1 DM h−1 and 2.14 µg C-CO2 g−1 DM h−1, respectively. A significant correlation between pH values and the number of culturable microorganisms was found. The number of soil microorganisms depended on the type of fertilization used. The best stimulation of the number of culturable soil microorganisms was found in treatments with the addition of 3% of L or Leo in combination with NaX–Ver. The percentage increases in the number of the analyzed culturable microorganisms after the application of leonardite-based fertilization in combination with the zeolite–vermiculite composite were, on average: bacteria, 1096%; mold fungi, 1529%; actinomycetes, 1477%; ammonifiers, 910%.

Soil composition and rootstock genotype drive the root associated microbial communities in young grapevines.

Soil microbiota plays a significant role in plant development and health and appears to be a major component of certain forms of grapevine decline. A greenhouse experiment was conducted to study the impact of the microbiological quality of the soil and grapevine rootstock genotype on the root microbial community and development of young plants. Two rootstocks heterografted with the same scion were grown in two vineyard soils differing in microbial composition and activities. After 4 months, culture-dependent approaches and amplicon sequencing of bacterial 16S rRNA gene and fungal ITS were performed on roots, rhizosphere and bulk soil samples. The root mycorrhizal colonization and number of cultivable microorganisms in the rhizosphere compartment of both genotypes were clearly influenced by the soil status. The fungal diversity and richness were dependent on the soil status and the rootstock, whereas bacterial richness was affected by the genotype only. Fungal genera associated with grapevine diseases were more abundant in declining soil and related root samples. The rootstock affected the compartmentalization of microbial communities, underscoring its influence on microorganism selection. Fluorescence in situ hybridization (FISH) confirmed the presence of predominant root-associated bacteria. These results emphasized the importance of rootstock genotype and soil composition in shaping the microbiome of young vines.

Effects of different application methods of Bacillus subtilis agent on soil microbial diversity and growth of muskmelon

Continuous planting of muskmelon and excessive application of chemical fertilizers have caused a series of problems, such as imbalance of the soil micro-ecological environment, serious soil-borne diseases and yield loss. Application of Bacillus subtilis agent is an important way to improve soil micro-ecological environment, prevent soil-borne diseases, and promote plant growth. In this study, B. subtilis was used as experimental agent to analyze the effects of different application methods on the soil microbial diversity and growth of muskmelon in greenhouse. The number of culturable microorganisms in soil was measured by dilution-plate method. The diversity of soil uncultivated microorganisms was determined by Illumina Miseq sequencing technology. The yield of muskmelon was measured by weighing method. The number of culturable bacteria in the root irrigation, hole application and dipping root application groups was higher than that of the control in different muskmelon growth stages, but there was no significant difference among the three different application methods. The number of soil fungi from B. subtilis agent treatment groups in flowering stage was significantly lower in comparison to the control group. However, B. subtilis agent treatment did not cause significant difference on soil fungi number at the fruiting and pulling stage. Diversity analysis of uncultured microorganisms showed that the Shannon index values of bacteria were higher and Simpson index values were lower respectively in the three B. subtilis treatment groups than that in the control. Moreover, the dipping root treatment produced the lowest Shannon index value and the highest Simpson index value of fungi. NMDS and cluster analysis showed that B. subtilis agents dipping root treatment significantly affected the bacterial and fungal flora, both of which were clustered into one independent branch. The application of B. subtilis agents, especially dipping root treatment, significantly decreased the abundance of Bacteroidetes, increased the abundance of Actinobacteria and Acidobacteria. The B. subtilis agent treatment didn't produce significant effect on the diversity of fungal flora except Chytridiomycota. The height, stem diameter and leaf area of muskmelon increased by applying B. subtilis agents, and dipping root treatment produced the most significant effect. As a new type of environmental protection fertilizer, B. subtilis agent can increase the number of soil culturable microorganisms, improve soil microbial diversity, and promote growth and yield. This study would provide a scientific basis for the rational application of B. subtilis.

Alkaline-thermally treated penicillin V mycelial residue amendment improved the soil properties without triggering antibiotic resistance

Penicillin V mycelial residue (PMR) is a byproduct of the pharmaceutical industry and may be disposed through land application after alkaline-thermal treatment. However, the efficacy of alkaline-thermally treated PMR in soil amelioration and the potential contamination risk caused by introduced penicillin V are poorly understood. In this study, soil pH, the contents of organic matter, available phosphorus, available potassium were measured to study the effect of alkaline-thermally treated PMR on soil fertility; the numbers of culturable microorganisms and the activities of enzymes, which not only reflect the decomposing ability of organic matter but also monitor the ecological suppression in soil ecosystem, were also investigated; moreover, the persistence of introduced penicillin V and the variation of antibiotic resistance genes (ARGs) in soil were examined to evaluate the resulting antibiotic resistance risk. The results indicated that the pH and the content of available potassium in amended soil with treated PMR profoundly improved. In addition, the culturable microorganisms and enzymes were not inhibited throughout the incubation of treated PMR in soil. The stability of treated PMR in soil relatively completed after 43 days. More importantly, the penicillin V derived by treated PMR rapidly depleted within 3 days, which suggested a relatively low environmental persistence. The treated PMR did not enrich the ARGs detected in soil, demonstrating that the addition of treated PMR might not trigger the antibiotic resistance risk in the short-term in soil. In conclusion, our results concluded that alkaline-thermally treated PMR is available for soil application.

Effect of Di-(2-Ethylhexyl) Phthalate on the Microbial Community in Vegetables Phyllosphere

A panel count method and a phospholipid fatty acid analysis technique were used to investigate the responses of Di-(2-Ethylhexyl) Phthalate (DEHP) pollutants to the phyllosphere microbial communities of Chinese Cabbage. The results of plate count analysis showed that the number of culturable microorganisms could be lower than that of water spray after treated with a certain amount of DEHP pollutant. The results of phospholipid fatty acid analysis showed that DEHP pollution treatment had certain effects on the biomass and community structure of leaf microorganisms in leaves of Chinese Cabbage. After spraying 1d, the biomass of the total leaf microorganisms, fungi and bacteria in the leaves of vegetables decreased, which was significantly different from that in the control and the blank groups. There was little change in the ratio of the characteristic phospholipid fatty acids between gram positive bacteria and gram negative bacteria.

Relationships between the properties of Spitsbergen soil, number and biodiversity of rhizosphere microorganisms, and heavy metal concentration in selected plant species

AimsThe aim of this study was to cross correlate data on physico-chemical parameters of soil with rhizosphere microorganisms and plant species in order to gain more knowledge about formation of soil and development of plants in the face of the changing climate on Spitsbergen and relations between them.MethodsWe investigated physico-chemical parameters of soil samples and the number and biodiversity of microorganisms, bacteria (oligotrophic and copiotrophic), and fungi. Moreover, heavy metal concentrations in 6 species of vascular plants collected in different areas were analysed.ResultsThe soil samples varied considerably in pH – from acid to alkaline, texture – from sand to loamy sand, and C:N ratio – from very low to high. In the soils, only partial Cd elevation expressed as the geoaccumulation index (Igeo) and the enrichment factor (EF) was detected. In the plants, the most significantly elevated concentrations of heavy metals expressed as Igeo and EF as well as the biological accumulation factor, bioconcentration factor, and translocation factor were detected in Salix polaris, Dryas octopetala, and Draba corymbosa. The high number of bacteria corresponded with an increase in the ecophysiological diversity index and the low colony development index, whereas a reverse relationship was found for fungi.ConclusionsThere was no significant impact of the geochemical properties on the total content of heavy metals in soil. The similar position of Cd and Pb in the order of heavy metal accumulation in the soil and plants was confirmed. TF showed that mainly these two metals were transported efficiently from roots to shoots. In the plants, the metals were distributed depending on the life form and their higher levels were detected in the woody perennials, e.g. S. polaris, D. octopetala, D. corymbosa, than in the herbaceous perennials. Very high numbers of culturable microorganisms were determined, regardless of the soil properties and plant species, which indicated that they were involved in the transformation of compounds containing C, N, and P and in the availability of heavy metals. The microorganisms and plants colonizing Spitsbergen soils showed great plasticity and adaptability to low temperatures and elevated Cd content.

中国东北黑土土壤剖面微生物群落碳源代谢特征

PDF HTML阅读 XML下载 导出引用 引用提醒 中国东北黑土土壤剖面微生物群落碳源代谢特征 DOI: 10.5846/stxb201509281979 作者: 作者单位: 东北农业大学资源与环境学院,中国科学院东北地理与农业生态研究所海伦农田生态系统国家野外科学观测研究站,东北农业大学资源与环境学院;中国科学院东北地理与农业生态研究所海伦农田生态系统国家野外科学观测研究站 作者简介: 通讯作者: 中图分类号: 基金项目: 国家自然基金资助项目（41371296） Metabolic characteristics of the microbial community on the basis of carbon source in black soil profiles in northeastern China Author: Affiliation: College of Resources and Environmental Sciences, Northeast Agricultural University,National Oservation Station of Hailun Agroecology System, Northeast-Institute of Geography and Agroecology, Chinese Academy of Sciences,College of Resources and Environmental Sciences, Northeast Agricultural University;National Oservation Station of Hailun Agroecology System, Northeast-Institute of Geography and Agroecology, Chinese Academy of Sciences Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:利用Biolog Eco微平板培养法，对中国科学院海伦农田生态系统国家野外科学观测研究站农田（CL）、恢复草地（GL）和人工林地（FL）土壤剖面不同深度土壤中微生物群落碳源代谢特征进行研究。理化性质结果显示，有机碳、全氮和碱解氮含量随深度增加逐渐减少，pH则是上层土壤低于底层。可培养微生物数量从表层（0-20 cm）到底层（180-200 cm）逐渐减少，在表层（0-20 cm）3种可培养微生物数量均为草地 > 农田 > 林地。可培养微生物主要生活在近地表0-60 cm土层中，在60-200cm土层中3种利用方式下可培养细菌、真菌和放线菌数量基本相同。Biolog结果显示，在0-40 cm土层中微生物群落活性最大，底层（180-200 cm）土壤微生物群落活性最小。3种利用方式剖面微生物群落Shannon多样性指数和碳源利用数量从表层到底层逐渐减少，并且与SOC和TN呈极显著正相关关系（P < 0.05）。与农田相比恢复草地和人工林地剖面20-40 cm土层中微生物群落对各类碳源的利用强度都较高，说明没有农业机械作业的植被自然生长条件下根系会打破原来农田中的犁底层，促进表层（0-20 cm）以下微生物群落活性。碳源利用率和主成分分析结果表明长期不同植被覆盖已经改变了剖面微生物群落碳源代谢特征，而且根系已经影响到100 cm的微生物群落，但还没有影响到180-200cm中的微生物群落。 Abstract:Using long-term field experiment of different ecosystems established at the Hailun State Key Experimental Station of Agroecology, Chinese Academy of Sciences, soil profiles down to the parent material layer (200 cm) were collected to investigate microbial metabolic characteristics of the carbon source by using the Biolog ECO micro-plate technique. The field treatments included three different ecosystems:Crop Land (CL), Grass Land (GL), and Forest Land (FL). The results showed that soil organic carbon (SOC), total nitrogen (TN), and effective nitrogen (EN) decreased with soil depth; soil pH increased with soil depth, and it was lower in the surface layer (0-20 cm) than in the bottom layer (180-200 cm). The number of cultivable microorganisms (bacteria, fungi, and actinomycetes) gradually decreased with soil depth; the cultivable microorganisms mainly lived in the top 0-60 cm soil layer. The numbers of the three types of cultivable microorganisms decreased in the order of GL > CL > FL at 0-20 cm soil depth, and the numbers were almost the same in the three ecosystems in the 60-200 cm soil layer. Activities of the soil microbial community were the highest at 0-40 cm soil depth and decreased with soil depth; the lowest value was observed in the 200 cm soil layer. Similar to SOC and TN, the Shannon diversity index and carbon source utilization gradually decreased with soil depth and showed a positive correlation with SOC and TN (P < 0.05). Compared to CL, carbon use efficiency of the soil microbial community improved at subsurface soil depth (20-40 cm) in GL and FL. This demonstrated that the roots of the vegetation could break the plow pan in GL and FL soils without any tillage activities and promote the activities of the soil microbial community below the surface soil layers. Principal component analysis of the utilization intensity of six types of carbon sources showed that the different long-term ecosystems with different vegetation types had changed the carbon utilization intensity of the soil microbial community in the soil profiles. The roots of the vegetation or crops had great influence on the soil microbial community to 100 cm depth, but not to 200 cm depth. 参考文献 相似文献 引证文献

Restoration of rare earth mine areas: organic amendments and phytoremediation.

Overexploitation of rare earth mine has caused serious desertification and various environmental issues, and ecological restoration of a mining area is an important concern in China. In this study, experiments involving dry grass landfilling, chicken manure broadcasting, and plant cultivation were carried out to reclaim a rare earth mine area located in Heping County, Guangdong Province, China. The prime focus was to improve soil quality in terms of nutrients, microbial community, enzyme activity, and physicochemical properties so as to reclaim the land. After 2 years of restoration, an increase of organic matter (OM), available potassium (K), available phosphorus (P) levels, and acid phosphatase (ACP) activity and a reduction of the available nitrogen (N) level and urease (URE) activity in soil were achieved compared to the original mined land. The nutrients and enzyme activities in soil with 5 years of restoration were close to or surpass those in the unexploited land as control. The bulk density, total porosity, water holding capacity, pH, and electrical conductivity (EC) of soil were improved, and the number of cultivable microorganisms and the bacterial diversity in soil were greatly increased with time during ecological restoration, especially for surface soil. Furthermore, the artificial vegetation stably grew at the restored mining sites. The results indicated that organic amendments and phytoremediation could ecologically restore the rare earth mining sites and the mined land could finally be planted as farmland.

Effects of rhamnolipid and initial compost particle size on the two-stage composting of green waste.

Composting is a potential alternative to green waste incineration or deposition in landfills. The effects of the biosurfactant rhamnolipid (RL) (at 0.0%, 0.15%, and 0.30%) and initial compost particle size (IPS) (10, 15, and 25 mm) on a new, two-stage method for composting green waste was investigated. A combination of RL addition and IPS adjustment improved the quality of the finished compost in terms of its physical characteristics, pH, C/N ratio, nutrient content, cellulose and hemicellulose contents, water-soluble carbon (WSC) content, xylanase and CMCase activities, numbers of culturable microorganisms (bacteria, actinomycetes, and fungi), and toxicity to germinating seeds. The production of a stable and mature compost required only 24 days with the optimized two-stage composting method described here rather than the 90-270 days required with traditional composting. The best quality compost was obtained with 0.15% RL and an IPS of 15 mm.

Application of Molecular Techniques to the Elucidation of the Microbial Community Structure of Antique Paintings

This paper uses molecular techniques to describe the microstructure and microbiological communities of sixteenth century artwork and their relationships. The microbiological populations, analysed by denaturing gradient gel electrophoresis (DGGE), were highly influenced by the chemical composition of the pictorial layers detected by energy-dispersive X-ray analysis. DGGE revealed that the diversity of microbial communities was lower in pictorial layers composed of pigments with metals, such as Pb, Cu and Hg, than in those found in pictorial layers without such compounds. The number of cultivable microorganisms, mainly fungi and bacteria, was very low in comparison to those found by DGGE, revealing the presence of both cultivable and as-yet-uncultivated (or not viable) species in the samples analysed. Both fungi and bacteria were present in a non-random spatial distribution. Environmental scanning electron microscopy and fluorescent in situ hybridisation analyses revealed that bacterial populations were usually found in close contact with the surface of the pictorial layers, and fungal populations were located on the bacterial biofilm. This work shows, for the first time, the correlation between the diversity of the microbial populations and the chemical composition of the pictorial layers of an artwork.

Long-term effects of inorganic fertilizers on microbial biomass and community functional diversity in a paddy soil derived from quaternary red clay

Long-term effects of inorganic fertilizers on microbial biomass and community functional diversity were investigated in a paddy soil derived from quaternary red clay in the Red Soil Ecological Experimental Station of the Chinese Academy of Sciences. The original soil is extremely eroded, characterized by low pH and deficiencies of available nutrients, particularly phosphorus and nitrogen. After 13 years application of inorganic fertilizers for flooded double rice crops, the number of cultivable microorganisms was significantly larger, and microbial biomass and community functional diversity were significantly higher in the treatments fertilized with P than those in the treatments without P fertilization. The significant effects of P application were mainly due to enhanced growth of rice crops and accumulation of soil organic carbon through increased root turnover and rhizodeposition. The soil was also deficient in N, but stimulation by N application of microbial biomass and community functional diversity as well as rice crop yields could be achieved only after improvement of the P supply. K application had no effect on rice crop yield or on microbial parameters. Most microbial parameters were mainly correlated with soil organic carbon content rather than P and N, indicating that the application of P and N did not directly affect microbial parameters in the soil, but did so indirectly by increasing crop yields, thus promoting the accumulation of soil organic matter.

Microbial pollution of soil around slurry storage lagoons at a pig-farm

Hygienic evaluation of the microbial pollution of the soil in a pig-farm at distances of 1.0 m and 30.0 m around the slurry storage lagoons, based on the number of cultivable microorganisms (NCM—log CFU/g slurry/soil) and the number of Escherichia coli (NEc—log CFU/g slurry/soil) was performed in the present study. The results from the investigation demonstrated: - NCM and NEc varied widely, with clear differences between the various elements of the “fresh slurry–stored slurry–soil at 1.0 m from the lagoons and soil at 30.0 m from the lagoon” chain; - NCM in stored slurry was higher than that in fresh slurry. Further, it significantly decreased in soil at a distance of 1.0 m and further decreased in soil 30.0 m from the lagoons when compared to the NCM of the previous element in the chain; - NCM in stored pig slurry and in soil around lagoons correlated very well with air temperature and rainfalls, which allowed developing of regression equations for estimation of the microbial activity. Temperature was the factor with the higher impact in regulation of microbial contamination compared to rainfalls. - NEc in soil at 30.0 m from lagoons decreased 32.4 times over fresh slurry, 11.7 times over stored slurry and 3.0 times over soil at 1.0 m from lagoons, i.e. increasing of the distance from lagoons, led to reducing the NEc in the soil. - The slurry obtained from clinically healthy pigs and stored in lagoons was a potential source of soil pollution with saprophytic microorganisms and coliform bacteria, subject to sanitary control.

Estimation of microbial respiration rates in groundwater by geochemical modeling constrained with stable isotopes

Changes in geochemistry and stable isotopes along a well-established groundwater flow path were used to estimate in situ microbial respiration rates in the Middendorf aquifer in the southeastern United States. Respiration rates were determined for individual terminal electron acceptors including O 2, MnO 2, Fe 3+, and SO 4 2−. The extent of biotic reactions were constrained by the fractionation of stable isotopes of carbon and sulfur. Sulfur isotopes and the presence of sulfur-oxidizing microorganisms indicated that sulfate is produced through the oxidation of reduced sulfur species in the aquifer and not by the dissolution of gypsum, as previously reported. The respiration rates varied along the flow path as the groundwater transitioned between primarily oxic to anoxic conditions. Iron-reducing microorganisms were the largest contributors to the oxidation of organic matter along the portion of the groundwater flow path investigated in this study. The transition zone between oxic and anoxic groundwater contained a wide range of terminal electron acceptors and showed the greatest diversity and numbers of culturable microorganisms and the highest respiration rates. A comparison of respiration rates measured from core samples and pumped groundwater suggests that variability in respiration rates may often reflect the measurement scales, both in the sample volume and the time-frame over which the respiration measurement is averaged. Chemical heterogeneity may create a wide range of respiration rates when the scale of the observation is below the scale of the heterogeneity.

Microbial life in deep granitic rock

Granitic rock has aquifers that run through faults and single or multiple fracture systems. They can orientate any way, vertically or horizontally and usually, only parts of hard rock fractures are water conducting. The remaining parts are filled by coatings of precipitated minerals, and clay and gouge material. Sampling hard rock is difficult and the risk of contamination due to intrusion of drilling fluids and cuttings in aquifers is obvious. A recent investigation of the potential for contamination of boreholes in granite during drilling operations, using molecular and growth methods, showed that predominating microorganisms in the drilling equipment were absent in groundwater from the drilled boreholes. The total number of bacteria found in subterranean granitic environments ranges from 103 up to 107 cells per ml groundwater, but the number of cultivable microorganisms is usually much lower. We have used culturing techniques with numeric taxonomy for the identification of cultivable microorganisms and the 16S rRNA gene technique to determine bacterial diversity in granitic groundwater. Members of the genera Bacillus, Desulfovibrio, Desulfomicrobium, Eubacterium, Methanomicrobium, Pseudomonas, Serratia and Shewanella have been found. Several biogeochemical processes in granitic rock have been demonstrated where microorganisms seem to be of major importance. One process is the mobilization of solid phase ferric iron oxy-hydroxides to liquid phase ferrous iron by iron reducing bacteria with organic carbon as electron donor. Another biogeochemical process found to be important is the reduction of sulfate to sulfide by sulfate reducing bacteria. They frequently appear in granitic aquifers at depths, and seem to prefer a moderate salinity, approximately 1%. When groundwater rich in ferrous iron, manganese(II) and reduced sulfur compounds reaches an oxygenated atmosphere such as an open tunnel, gradients suitable for chemolithotrophic bacteria develop. A third process is the conversion of carbon dioxide to organic material with hydrogen as the source of energy, possibly formed through radiolysis, mineral reactions or by volcanic activity. Recent results show that autotrophic methanogens, acetogenic bacteria and acetoclastic methanogens all are present and active in deep granitic rock. These observations announce the existence of a hydrogen driven deep biosphere in crystalline bedrock that is independent of photosynthesis. If this hypothesis is true, life may have been present and active deep down in the earth for a very long time, and it cannot be excluded that the place for the origin of life was a deep subterranean igneous rock environment (probably hot with a high pressure) rather than a surface environment.

Microbial life in deep granitic rock

Granitic rock has aquifers that run through faults and single or multiple fracture systems. They can orientate any way, vertically or horizontally and usually, only parts of hard rock fractures are water conducting. The remaining parts are filled by coatings of precipitated minerals, and clay and gouge material. Sampling hard rock is difficult and the risk of contamination due to intrusion of drilling fluids and cuttings in aquifers is obvious. A recent investigation of the potential for contamination of boreholes in granite during drilling operations, using molecular and growth methods, showed that predominating microorganisms in the drilling equipment were absent in groundwater from the drilled boreholes. The total number of bacteria found in subterranean granitic environments ranges from 103 up to 107 cells per ml groundwater, but the number of cultivable microorganisms is usually much lower. We have used culturing techniques with numeric taxonomy for the identification of cultivable microorganisms and the 16S rRNA gene technique to determine bacterial diversity in granitic groundwater. Members of the genera Bacillus, Desulfovibrio, Desulfomicrobium, Eubacterium, Methanomicrobium, Pseudomonas, Serratia and Shewanella have been found. Several biogeochemical processes in granitic rock have been demonstrated where microorganisms seem to be of major importance. One process is the mobilization of solid phase ferric iron oxy-hydroxides to liquid phase ferrous iron by iron reducing bacteria with organic carbon as electron donor. Another biogeochemical process found to be important is the reduction of sulfate to sulfide by sulfate reducing bacteria. They frequently appear in granitic aquifers at depths, and seem to prefer a moderate salinity, approximately 1%. When groundwater rich in ferrous iron, manganese(II) and reduced sulfur compounds reaches an oxygenated atmosphere such as an open tunnel, gradients suitable for chemolithotrophic bacteria develop. A third process is the conversion of carbon dioxide to organic material with hydrogen as the source of energy, possibly formed through radiolysis, mineral reactions or by volcanic activity. Recent results show that autotrophic methanogens, acetogenic bacteria and acetoclastic methanogens all are present and active in deep granitic rock. These observations announce the existence of a hydrogen driven deep biosphere in crystalline bedrock that is independent of photosynthesis. If this hypothesis is true, life may have been present and active deep down in the earth for a very long time, and it cannot be excluded that the place for the origin of life was a deep subterranean igneous rock environment (probably hot with a high pressure) rather than a surface environment.

Short-term community dynamics in the phyllosphere microbiology of field-grown sugar beet

Short-term fluctuations in the number of culturable microorganisms and the composition of the bacterial community colonising the phyllosphere of field grown sugar beet were determined at 6 h intervals over a 42 h period. The number of culturable bacteria and Erwinia were found to fluctuate diurnally, increasing in size overnight and declining during daylight hours. In contrast, the number of Arthrobacter and yeasts were constant throughout the study, even after rainfall. Over most of the study the number of filamentous fungi and pseudomonads decreased. The short-term fluctuations in bacterial numbers were similar in magnitude to those detected over most of the previous season. No significant variation was observed in microbial numbers between samples taken from three locations within the field. Fatty acid analysis of isolated bacteria revealed the community to be similar in composition to that detected during the same period the previous year and indicated no significant short-term temporal or spatial variation. To limit the effects of diurnal fluctuations on the number of culturable bacteria detected, it is recommended that in long-term studies, samples be collected at the same time of day on each occasion.

Short-term community dynamics in the phyllosphere microbiology of field-grown sugar beet

Short-term fluctuations in the number of culturable microorganisms and the composition of the bacterial community colonising the phyllosphere of field grown sugar beet were determined at 6 h intervals over a 42 h period. The number of culturable bacteria and Erwinia were found to fluctuate diurnally, increasing in size overnight and declining during daylight hours. In contrast, the number of Arthrobacter and yeasts were constant throughout the study, even after rainfall. Over most of the study the number of filamentous fungi and pseudomonads decreased. The short-term fluctuations in bacterial numbers were similar in magnitude to those detected over most of the previous season. No significant variation was observed in microbial numbers between samples taken from three locations within the field. Fatty acid analysis of isolated bacteria revealed the community to be similar in composition to that detected during the same period the previous year and indicated no significant short-term temporal or spatial variation. To limit the effects of diurnal fluctuations on the number of culturable bacteria detected, it is recommended that in long-term studies, samples be collected at the same time of day on each occasion.

Microbial abundance and activities in relation to water potential in the vadose zones of arid and semiarid sites

Numbers and activities of microorganisms were measured in the vadose zones of three arid and semiarid areas of the western United States, and the influence of water availability was determined. These low-moisture environments have vadose zones that are commonly hundreds of meters thick. The specific sampling locations chosen were on or near U.S. Department of Energy facilities: the Nevada Test Site (NTS), the Idaho National Engineering Laboratory (INEL), and the Hanford Site (HS) in southcentral Washington State. Most of the sampling locations were uncontaminated, but geologically representative of nearby locations with storage and/or leakage of waste compounds in the vadose zone. Lithologies of samples included volcanic tuff, basalt, glaciofluvial and fluvial sediments, and paleosols (buried soils). Samples were collected aseptically, either by drilling bore-holes (INEL and HS), or by excavation within tunnels (NTS) and outcrop faces (paleosols near the HS). Total numbers of microorganisms were counted using direct microscopy, and numbers of culturable microorganisms were determined using plate-count methods. Desiccation-tolerant microorganisms were quantified by plate counts performed after 24 h desiccation of the samples. Mineralization of (14)C-labeled glucose and acetate was quantified in samples at their ambient moisture contents, in dried samples, and in moistened samples, to test the hypothesis that water limits microbial activities in vadose zones. Total numbers of microorganisms ranged from log 4.5 to 7.1 cells g(-1) dry wt. Culturable counts ranged from log <2 to 6.7 CFU g(-1) dry wt, with the highest densities occurring in paleosol (buried soil) samples. Culturable cells appeared to be desiccation-tolerant in nearly all samples that had detectable viable heterotrophs. Water limited mineralization in some, but not all samples, suggesting that an inorganic nutrient or other factor may limit microbial activities in some vadose zone environments.