Microbial decomposition of coumarin in soil

Microbial decomposition of coumarin was studied in samples of chernozem soil by manometric measurement of oxygen consumption, paper chromatography of aromatic metabolic intermediates in soil extract and measurement of their UV spectra, and by the technique of simultaneous adaptation. Coumarin is decomposed in soil viao-coumaric and melilotic acids and at least one other compound of aromatic character. The metabolic pathway including salicylic acid and catechol was not proved. A total of 39 strains of coumarin-decomposing bacteria were isolated from the soil, out of which 25 belong to the genusPseudomonas, 7 to the genusCellulomonas and 7 to the genusAchromobacter. A comparison of the counts of bacteria utilizing coumarin as a sole carbon source in garden soil, in two chernozem soil samples and in acidic brown soil showed that their occurrence bears no relation to the so-called total number of bacteria (grown on agar medium with yeast and soil extracts and with tryptone) or to the content of carbon and nitrogen in the soil, or to its acidity.     

Microbial community changes during the bioremediation of creosote-contaminated soil

AIMS: To investigate the effects of aeration on the ex situ biodegradation of polycyclic aromatic hydrocarbons (PAHs) in creosote-contaminated soil and its effect on the microbial community present. METHODS AND RESULTS: Aerated and nonaerated microcosms of soil excavated from a former timber treatment yard were maintained and sampled for PAH concentration and microbial community changes by terminal restriction fragment length polymorphism (TRFLP) analysis. After an experimental period of just 13 days, degradation was observed with all the PAHs monitored. Abiotic controls showed no loss of PAH. Results unexpectedly showed greater loss of the higher molecular weight PAHs in the nonaerated control. This may have been due to the soil excavation causing initial decompaction and aeration and the resulting changes caused in the microbial community composition, indicated by TRFLP analysis showing several ribotypes greatly increasing in relative abundance. Similar changes in both microcosms were observed but with several possible key differences. The species of micro-organisms putatively identified included Bacilli, pseudomonad, aeromonad, Vibrio and Clostridia species. CONCLUSIONS: Excavation of the contaminated soil leads to decompaction, aeration and increased nutrient availability, which in turn allow microbial biodegradation of the PAHs and a change in the microbial community structure. SIGNIFICANCE AND IMPACT OF THE STUDY: Understanding the changes occurring in the microbial community during biodegradation of all PAHs is essential for the development of improved site remediation protocols. TRFLP allows useful monitoring of the total microbial community.     

Microbial population changes during bioremediation of an experimental oil spill.

Three crude oil bioremediation techniques were applied in a randomized block field experiment simulating a coastal oil spill. Four treatments (no oil control, oil alone, oil plus nutrients, and oil plus nutrients plus an indigenous inoculum) were applied. In situ microbial community structures were monitored by phospholipid fatty acid (PLFA) analysis and 16S rDNA PCR-denaturing gradient gel electrophoresis (DGGE) to (i) identify the bacterial community members responsible for the decontamination of the site and (ii) define an end point for the removal of the hydrocarbon substrate. The results of PLFA analysis demonstrated a community shift in all plots from primarily eukaryotic biomass to gram-negative bacterial biomass with time. PLFA profiles from the oiled plots suggested increased gram-negative biomass and adaptation to metabolic stress compared to unoiled controls. DGGE analysis of untreated control plots revealed a simple, dynamic dominant population structure throughout the experiment. This banding pattern disappeared in all oiled plots, indicating that the structure and diversity of the dominant bacterial community changed substantially. No consistent differences were detected between nutrient-amended and indigenous inoculum-treated plots, but both differed from the oil-only plots. Prominent bands were excised for sequence analysis and indicated that oil treatment encouraged the growth of gram-negative microorganisms within the alpha-proteobacteria and Flexibacter-Cytophaga-Bacteroides phylum. alpha-Proteobacteria were never detected in unoiled controls. PLFA analysis indicated that by week 14 the microbial community structures of the oiled plots were becoming similar to those of the unoiled controls from the same time point, but DGGE analysis suggested that major differences in the bacterial communities remained.     

Qualitative microbiological changes during decomposition of plant material in a sandy sierozem soil

The successive qualitative microbial changes during the decomposition of bajra stalk in a sandy sierozem soil were studied.Alternaria spp.,Aspergillus spp.,Cladosporium spp.,Fusarium spp.Gliocladium spp.,Mucor spp. andRhizopus spp. were most common fungi. The bacteria observed wereAchromobacter, Arthrobacter, Bacillus, Micrococcus, Pseudomonas andXanthomonas. Cellvibrio andCellulomonas were also observed.     

Microbial decomposition of carboxymethyl cellulose continuously added to the soil

If heterocontinuous flow-cultivation method was used to study the degradation of soluble carboxymethyl cellulose (CMC) in soil, neither the potential CM-cellulase activity of the soil nor the total degree of CMC mineralization significantly differed under aerobic condition and in a nitrogen atmosphere. In contrast, the end products of the enzymatic hydrolysis and their mutual proportions were different: under anaerobic conditions, the formation of reducing sugars was increased at the expense of CO₂ production and organic acids were detectable in the extract. The composition of soil microflora also differed. Addition of ammonium ions affected the maximum CM-cellulase activity in the soil, the degree of substrate mineralization, the proportion of CO₂ and reducing sugars that are formed and the concentration of the present soil microflora.     

Microbial activity during leaf decomposition in an Alaskan subarctic stream

Fungal biomass and growth and microbial respiration were studied for two field seasons in a second-order subarctic stream where water temperature is 0°C for approximately 6 months. Leaf packs (5-g) of alder Alnus tenuifolia , birch Betula papyrifera and willows Salix alaxensis and Salix arbusculoides immersed in autumn of 1979 and 1980 were sampled until June 1980 and January 1981, respectively. Fungal growth and microbial respiration occurred in submerged detritus at 0°C. Total and FDA-active hyphal lengths were measured, the active proportion averaging 25% of the total (all leaf species, both years). Generally, microbial respiration peaked in all leaf species after two weeks in the stream. As water approached 0°C, respiration declined by 20–50% depending on leaf species, but often increased later in decomposition (at 0°C). Seasonal trends in microbial respiration and FDA-active hyphal lengths were not similar although maximal respiration usually occurred as FDA-active hyphae were growing most rapidly. The calculated leaf weight loss due to microbial respiration was small (7–10%) in all leaf species, compared with total weight loss over 98 d. Scanning electron microscopy provided a visual record of leaf surface microorganisms and apparent leaf cuticle dissolution by fungi and bacteria.     

凋落物分解过程中土壤微生物群落的变化

凋落物分解是生态系统碳循环和营养物质循环的关键过程, 受多种因素共同影响。土壤微生物是影响凋落物分解的重要因素, 其群落组成在一定程度上依赖于所处植物群落的特征。因此, 研究分解过程中微生物群落组成的变化及其对植物多样性的响应, 有利于对凋落物分解机制的理解。本文采用分解袋野外原位分解的方法, 对凋落物分解过程中微生物群落的变化及其对所处森林环境中树木的种类和遗传多样性的响应进行了研究。结果表明: (1)凋落物分解183天后, 土壤中微生物群落的多样性降低, 并且森林群落的物种多样性与微生物群落多样性呈负相关关系; (2)凋落物分解前后, 土壤中真菌和细菌群落的磷脂脂肪酸(PLFA)量均有所增加, 说明凋落物分解为微生物生存和繁殖提供了养分; (3)地形因素是影响微生物群落变化最显著的因素, 可解释微生物群落变化的29.55%; 其次是凋落物的基质质量, 可以解释15.39%; 最后是森林群落的多样性, 可以解释8.45%; 这3种因素共同解释率为2.97%。综上所述, 与森林群落的植物多样性相比, 样地的地形因素与凋落物的基质质量对微生物群落的影响更显著。     

Microbial degradation of hydrocarbons in soil during aerobic/anaerobic changes and under purely aerobic conditions

Microbial hydrocarbon degradation in soil was studied during periodical aerobic/anaerobic switching and under purely aerobic conditions by using a pilot-scale plant with diesel-fuel-contaminated sand. The system worked according to the percolation principle with controlled circulation of process water and aeration. Periodical switching between 4 h of aerobic and 2 h of anaerobic conditions was achieved by repeated saturation of the soil with water. Whatever the cultivation mode, less than 50% of the diesel was degraded after 650 h because the hydrocarbons were adsorbed. Contrary to expectations, aerobic/anaerobic changes neither accelerated the rate of degradation nor reduced the residual hydrocarbon content of the soil. Obviously the pollutant degradation rate was determined mainly by transport phenomena and less by the efficiency of microbial metabolism. The total mass of oxygen consumed and carbon dioxide produced was greater under aerobic/anaerobic changing than under aerobic conditions, although the mass of hydrocarbons degraded was nearly the same. As shown by an overall balance of microbial growth and by a carbon balance, the growth yield coefficient was smaller during aerobic/anaerobic changes than under aerobic conditions. Received: 25 November 1997 /  Received revision: 15 January 1998 / Accepted: 18 January 1998     

Microbial changes occurring in soil as a result of storage

Summary Changes in numbers of various microbial groups in the interim between collection and analysis of a tropical soil were determined. Although the number of most organisms decreased as a result of storage, the percentage distribution of several groups increased. The greatest decreases occurred in the top layers of soil. Both the numbers and the relative distribution of actinomycetes increased after storage. The possible significance of this increase in the detection of fungistatic materials in soil is discussed. Numbers of fungi were higher after storage in all soil depths, except in the top layer where essentially no change occurred. The vertical distribution and relative frequency of isolation of fungal species after storage is presented. The percentage distribution of spore-forming and CO₂-tolerant bacteria was higher after storage, but that of CO₂-tolerant fungi was lower.The significance of these results in soil microbiological studies, as well as possible causes of the changes, are discussed.     

Microbial community structure changes during bioremediation of PAHs in an aged coal-tar contaminated soil by in-vessel composting

The microbial community structure changes of an aged-coal-tar soil contaminated with polycyclic aromatic hydrocarbons (PAHs) were investigated during simulated bioremediation at the laboratory-scale using an in-vessel composting approach. The composting reactors were operated using a logistic three-factor factorial design with three temperatures (T=38, 55 or 70 °C), four soil to green-waste amendment ratios (S:GW=0.6:1, 0.7:1, 0.8:1 or 0.9:1 on a dry weight basis) and three moisture contents (MC=40%, 60% or 80%). Relative changes in microbial populations were investigated by following the dynamics of phospholipid fatty acid (PLFA) signatures using a ¹³C-labeled palmitic acid internal standard and sensitive GC/MS analysis during in-vessel composting over 98 days. The results of this investigation indicated that fungal to bacterial PLFA ratios were significantly influenced by temperature (p<0.05), and Gram-positive to Gram-negative bacterial ratios were significantly influenced by temperature (p<0.001) and S:GW ratio (p<0.01) during in-vessel composting. Additionally, the Gram-positive to Gram-negative bacterial ratios were correlated to the extent of PAH losses (p<0.005) at 70 °C.     

Microbial communities acclimate to recurring changes in soil redox potential status

Rapidly fluctuating environmental conditions can significantly stress organisms, particularly when fluctuations cross thresholds of normal physiological tolerance. Redox potential fluctuations are common in humid tropical soils, and microbial community acclimation or avoidance strategies for survival will in turn shape microbial community diversity and biogeochemistry. To assess the extent to which indigenous bacterial and archaeal communities are adapted to changing in redox potential, soils were incubated under static anoxic, static oxic or fluctuating redox potential conditions, and the standing (DNA‐based) and active (RNA‐based) communities and biogeochemistry were determined. Fluctuating redox potential conditions permitted simultaneous CO₂ respiration, methanogenesis, N₂O production and iron reduction. Exposure to static anaerobic conditions significantly changed community composition, while 4‐day redox potential fluctuations did not. Using RNA : DNA ratios as a measure of activity, 285 taxa were more active under fluctuating than static conditions, compared with three taxa that were more active under static compared with fluctuating conditions. These data suggest an indigenous microbial community adapted to fluctuating redox potential.     

Variations in microbial isotopic fractionation during soil organic matter decomposition

The soil microbial biomass (SMB) is known to participate in key soil processes such as the decomposition of soil organic matter (SOM). However, its contribution to the isotopic composition of the SOM is not clear yet. Shifts in the ¹³C and ¹⁵N natural abundances of the SMB and SOM fractions (mineralised, water soluble and non-extractable) were investigated by incubating an unamended arable soil for 6 months. Microbial communities were also studied using Fatty Acid Methyl Ester specific isotope analysis. The SMB was significantly ¹³C and ¹⁵N-enriched relative to other fractions throughout the incubation. However, significant isotopic variations with time were also observed due to the rapid consumption of relatively ¹³C-enriched water soluble compounds. The increase in the difference in SMB and water soluble ¹⁵N compositions as the water soluble C/N ratio decreased, indicated a shift from N assimilation to N dissimilation during the incubation. These changes also induced modifications of the microbial community structure. Once the system reached a steady-state (after 1 month), the isotopic trends appeared to corroborate those obtained in long term experiments in the field in that there was a constant microbial isotopic fractionation leading to a ¹³C and ¹⁵N enrichment of the SOM over the long-term. This work also suggests that caution must be exercised when interpreting short term incubation studies since perturbations associated with experimental set-up can have an important effect on C and N dynamics, microbial fractionation of ¹³C and ¹⁵N and microbial community structure.     

Microbial changes in clover rhizosphere after foliar and soil application of cobalt

Application of cobalt(II) nitrate to the leaves of red clover (Trifolium pratense L.) resulted in a pronounced increase of dry weight and the number of root nodules. Counts of bacteria in the rhizosphere, content of ammonia and production of carbon dioxide m rhizosphere soil were also higher, whereas the content of nitrates decreased Differences m the counts of bacteria, aotmomycetes, Azotobaoter, anaerobic bacteria and cellulose decomposing bacteria m the rhizosphere of control and treated plants were not directly related to the way of application of cobalt. GeneraPenicillium, Fusarium andTrichoderma predominated among fungi. The relative occurrence of pemcillia was higher after the application of cobalt, the incidence of fusaria was lower. The effects of foliar and soil application of cobalt on rhizosphere microflora were not identical.     

Microbial study of farmhouse ewe cheese during storage in olive oil

The effect of storing farmhouse ewe cheese in oil and in vacuo over long periods of time on physicochemical properties (water activity and pH) and the microbiota of the cheese was investigated. The storage conditions were found to scarcely influence the sample pH. Also, the initial water activity (a(w) = 0.961) and its value after 9 months of storage (0.927) were both very similar to those for naturally ripened cheese. The incidence of pathogenic microbial groups was found to decrease with storage time (counts fell below 1 log CFU/g). The flora that effects proteolytic changes in cheese consisted of lactic microorganisms (viz. lactococci and lactobacilli), in addition, after 6 months of storage, of enterococci. The last are responsible for the formation of large amounts of soluble nitrogen (SN), non-protein nitrogen (NPN) and aminoacid nitrogen (NH2-N), which provide this type of cheese with very special sensory features while preventing dehydration and thus lengthening its shelf life.     

Microbial growth and detritus transformations during decomposition of leaf litter in a stream

SUMMARY. 1. Despite the widely accepted importance of bacteria and fungi in degrading detritus in aquatic ecosystems there is still very little quantitative information on the abundance and dynamics of these microorganisms. Using epifluorescent microscopy, we measured the biomass of bacteria and fungi during decomposition of three types of leaf detritus. Bacterial production was determined from the rate of incorporation of ³H-thymidine into DNA.
2. The transformation of leaf carbon into dissolved organic carbon and fine particulate organic carbon was followed in order to compare the amounts of leaf material that were converted into these 'end-products' of decomposition versus the amount converted into microbial biomass.
3. The amount of microbial carbon in the leaf-detritus complex never exceeded 5.2% of the total carbon, and fungal biomass was always much greater than bacterial biomass. Despite the greater standing stock of fungi, the rapid turnover of bacteria (doubling about once per day) implies that their role in degrading leaf litter or as a food source for detritivores might be as great as for fungi.
4. Removal of microbial biomass from leaf litter may occur as release of fungal spores and consumption or shedding of bacterial biomass. Fungal spores can be a significant part of the fine particulate organic carbon released from leaf detritus and potentially represent an important food resource for filter-feeding organisms.     

Short-term changes in soil nutrients during wetland creation

This study examined changes in pH and extractable nutrients in soilsfollowing wetland creation. Sample plots were established in two areas: (1) an old-field with parts that were flooded during wetland creation, and (2) a native wetland in a floodplain of the Ohio River called Green Bottom Swamp. Soils were sampled before inundation and eight months afterwards. Compared to old-field soils in the pre-inundation period, swamp soils exhibited: (1) higher acidity, (2) lower NO3 and higher NH4 concentrations, (3) higher extractable P, Fe, and Mn, and (4) lower Ca, Mg, and Zn concentrations. Eight months after inundation, the old-field soil redox decreased from +210 mV in the old field –290 mV, and extractable NO3 and Ca decreased and extractable NH4 and Fe increased, but pH and extractable P, Mn, Mg, and Zn changed either slightly or not at all. These results suggest that eight months is an insufficient period of time for a complete change. Other results suggest that the response of nitrogen during the wetland creation processes may be extremely rapid.