Growth of saprotrophic fungi and bacteria in soil

Bacterial and fungal growth rate measurements are sensitive variables to detect changes in environmental conditions. However, while considerable progress has been made in methods to assess the species composition and biomass of fungi and bacteria, information about growth rates remains surprisingly rudimentary. We review the recent history of approaches to assess bacterial and fungal growth rates, leading up to current methods, especially focusing on leucine/thymidine incorporation to estimate bacterial growth and acetate incorporation into ergosterol to estimate fungal growth. We present the underlying assumptions for these methods, compare estimates of turnover times for fungi and bacteria based on them, and discuss issues, including for example elusive conversion factors. We review what the application of fungal and bacterial growth rate methods has revealed regarding the influence of the environmental factors of temperature, moisture (including drying/rewetting), pH, as well as the influence of substrate additions, the presence of plants and toxins. We highlight experiments exploring the competitive and facilitative interaction between bacteria and fungi enabled using growth rate methods. Finally, we predict that growth methods will be an important complement to molecular approaches to elucidate fungal and bacterial ecology, and we identify methodological concerns and how they should be addressed.     

Root structure and cellular chloride,sodium and potassium distribution in salinized grapevines

X-ray microanalysis was used to study the patterns of K+, Na+ and Cl- accumulation in salinized (25 mm NaCl) and non-salinized grapevine (Vitis) roots. The aim was to determine whether NaCl affects patterns of Cl- accumulation differentially in the roots of a Cl--excluding genotype and a non-excluding genotype. Two regions of fibrous roots were analysed: (1) a region 2-3 mm basipetal to the root tip; and (2) a region of the root 10-12 mm basipetal to the root tip where the outermost layer is the hypodermis. The ion contents of the hypodermis, cortex, endodermis and pericycle vacuoles were analysed. Data were also collected from the cytoplasm of the endodermal and pericycle cells. The analyses showed that the ion profiles of the hypodermis and the endodermis were significantly different from those of the cortex and pericycle. The hypodermis and endodermis had higher K+ and lower Na+ and Cl- than surrounding cells. Some changes due to salinity such as increased K+ concentrations in the hypodermis were also noted. Chloride concentrations did not differ between the genotypes in the hypodermis, across the cortex or in the endodermis, but were higher in the pericycle of the excluder in comparison with the non-excluding genotype. However, K+/Na+ ratios of the cortex and endodermis were higher in the excluder. The pericycle cells exhibited the greatest ability to sequester Na+ and Cl- in vacuoles. Overall the data show cell-type-specific ion accumulation patterns and small but significant differences were found between genotypes. The possibility that these accumulation patterns arise from differences in uptake properties of cell types and/or result from the spatial distribution of the cell types along the competing symplastic and apoplastic ion transport pathways across the root is discussed.     

盐渍化土壤根际微生物群落及土壤因子对AM真菌的影响

为探明盐渍化土壤影响下AM真菌与根际土壤间的关系,试验选取宁夏碱化龟裂土、草甸盐土、盐化灌淤土3种类型4个样地上典型植被群落,测定了植物根际土壤养分含量、微生物群落结构、AM真菌侵染率以及孢子密度。结果显示:盐渍化土壤根际微生物碳源利用类型显著不同,对芳香类化合物的代谢能力整体较弱;红寺堡草甸盐土上微生物优势群落为氨基酸代谢类群,惠农盐化灌淤土为多聚化合物代谢群,西大滩碱化龟裂土为碳水化合物代谢群。AM真菌孢子密度与微生物碳源代谢群间的关系比较复杂。其中,惠农样点根际土壤孢子密度与多聚化合物微生物代谢群呈显著正相关,西大滩地区孢子密度与碳水化合物微生物代谢群呈显著正相关。土壤有机质、全盐、全氮、碱解氮等土壤肥力因子及土壤中的HCO-3、Na+、Cl-等盐基离子含量能解释AM真菌孢子密度与土壤环境因子之间相互关系的大部分信息。较高的HCO-3浓度促进了AM真菌侵染率的提高,但高盐浓度下Na+和Cl-降低了菌根侵染率。土壤对AM真菌孢子密度、侵染率的影响因土壤盐分组成类型的不同而异。研究结果为深入了解AM真菌多样性,促进宁夏盐碱地的合理开发与利用提供了理论依据。     

Microbodies and glyoxylate-cycle enzyme activities in filamentous fungi

Summary From compartmental analysis of radioisotope elution measurements, concentrations and fluxes of K⁺, Na⁺ and Cl^- were estimated for cortical cells in root segments of onion, Allium cepa L., relative to a complete nutrient solution. The transported fraction of the total efflux was estimated separately. With the Ussing-Teorell flux ratio equation as the criterion, it was concluded that all three ions were actively accumulated from the outside medium into the cytoplasm and that only Na⁺ was actively accumulated into the vacuole. K⁺ and Cl^- moved passively, in both directions across the tonoplast. Failure to account for leakage from the stele via the segment cut ends resulted in an over-estimate of exchange across the tonoplast but did not alter the conclusions qualitatively. The consequences of changing the assumed value of the tonoplast electrical potential (from 0 to+10- mV), and the effects of different experimental procedures, were also assessed, and found not to affect the main conclusions significantly. Separate measurement of ions leaking from the segment ends revealed that Na⁺ was transported almost exclusively in an acropetal direction in the stele. Cl^- appeared at both ends of the segments in similar amounts and K⁺ was transported mainly in the basipetal direction. The implications of these findings for the mechanism and site of ion selectivity are discussed.     

The effect of sodium chloride on enzyme activities from four halophyte species of chenopodiaceae

The in vitro effect of sodium chloride on the enzyme activity of four halophytes, Beta vulgaris ssp. maritima (L.) Thell., Halimione portulacoides (L.) Aell., Salicornia ramosissima Woods and Suaeda maritima (L.) Dum. was investigated. The activity was, in general, affected by sodium chloride in a similar manner to that reported for salt sensitive species. The most notable exceptions were the sodium chloride stimulated ATPases of Beta and Salicornia.     

石油污染土壤的生物修复与土壤酶活性关系

研究了不同油浓度污染土壤经过两个为期125d的生物修复后的土壤中过氧化氢酶、多酚氧化酶和脂肪酶的酶活变化,分析了土壤中3种酶活性的变化特征与规律。结果表明,随着油浓度的增加,土壤中过氧化氢酶和多酚氧化酶的活性下降,脂肪酶活性增加;经过生物修复后,土壤中的过氧化氢酶和多酚氧化酶的活性在第二周期要比第一周期提高,而脂肪酶活性下降;这3种土壤酶活性变化受污染物浓度影响不显著,但不同浓度油污染土壤的修复对过氧化氢酶的影响要大于对多酚氧化酶和脂肪酶的影响。     

荒漠油蒿（Artemisia ordosica）根围AM真菌分布与土壤酶活性

于2007年10月在油蒿(Artemisia ordosica)集中分布区选取4个典型样地,分别从0～10cm、10～20cm、20～30cm、30～40cm和40～50cm土层采集根围土样,分离其丛枝菌根(arbuscular mycorrhiza,AM)真菌并测定了3种土壤酶活性.结果表明,在各样地0～50cm土层中油蒿根系AM真菌菌丝定殖率均很高,有典型的泡囊与丛枝结构.菌丝定殖率与泡囊定殖率呈显著正相关,但菌丝、泡囊和丛枝定殖率与AM真菌孢子密度和土壤酶活性之间都无相关性;孢子密度在不同样地及采样深度间差异明显,与土壤有机质、速效磷和速效氮含量都呈一定正相关关系.孢子密度与脲酶和酸性磷酸酶活性有显著或极显著相关关系,与碱性磷酸酶活性之间的相关性受到土壤pH的显著影响.孢子密度的峰值出现在0～10cm表层土,并随土壤剖面深度增加而降低.土壤酶活性在土壤垂直剖面显示与孢子密度同样的规律.不同样地间AM真菌分布及油蒿根系定殖率的差异表明,油蒿与AM真菌之间有良好共生性,对维护荒漠生态环境系统结构的完整性具有重要意义.     

土霉素暴露对小麦根际抗生素抗性细菌及土壤酶活性的影响

通过培养的方法研究了土霉素暴露和小麦根际抗性细菌的数量、种类、分布特征及土壤酶活性之间的剂量效应关系。结果表明,土霉素暴露下小麦根际单一抗生素抗性细菌数量和抗土霉素—链霉素双重抗性细菌数都明显增加,且与暴露剂量呈正效应关系;同时,土壤磷酸酶、脱氢酶活性下降,但与土霉素的剂量效应关系不明显。从土霉素暴露的土壤中分离到50株抗性细菌,经形态观察、RFLP分组和16S rDNA序列测定与分析,将它们聚集在Actinobacteria、Bacilli、Alphaproteobacteria、Gammaproteobacteria 和Sphingobacteria类群。其中放线菌最多（15株）,占抗性菌总数的30 %;其次是Bacillus属细菌（9株）和Pseudomonas属细菌（8株）,分别占18 %和16 %。同时,具有抗性的人类机会致病菌Pseudomonas、Sphingomonas和Stenotrophomonas属细菌在土霉素暴露的样品中均被分离到,分别占抗性菌株总数的16 %、8 %和4 %。值得注意的是,随着土霉素暴露剂量的增加,小麦根际优势促生菌Bacillus属细菌的抗性检出率逐步降低;但具有抗生素抗性的人类机会致病菌Pseudomonas、Sphingomonas和Stenotrophomonas属细菌的检出率却明显增加,提示可能会进一步增大其机会致病性。     

Effect of coculture of anaerobic fungi isolated from ruminants and non-ruminants with methanogenic bacteria on cellulolytic and xylanolytic enzyme activities

Neocallimastix strain N1, an isolate from a ruminant (sheep), was cocultured with three Methanobacterium formicicum strains, Methanosarcina barkeri, and Methanobrevibacter smithii. The coculture with Methanobacterium formicicum strains resulted in the highest production of cellulolytic and xylanolytic enzymes. Subsequently four anaerobic fungi, two Neocallimastix strains (N1 and N2) from a ruminant and two Piromyces species from non-ruminants (E2 and R1), were grown in coculture with Methanobacterium formicicum DSM 3637 on filter paper cellulose and monitored over a 7-day period for substrate utilisation, fermentation products, and secretion of cellulolytic and xylanolytic enzymes. Methanogens caused a shift in fermentation products to more acetate and less ethanol, lactate and succinate. Furthermore the cellulose digestion rate increased by coculture. For cocultures of Neoallimastix strains with Methanobacterium formicicum strains the cellulolytic and xylanolytic enzyme production increased. Avicelase, CMCase and xylanase were almost completely secreted into the medium, while 40–60% of the -glucosidase was found to be cell bound. Coculture had no significant effect on the location of cellulolytic and xylanolytic enzymes.     

森林母土异地迁播后的土壤真菌和细菌变化

【背景】森林土壤中携带了大量种子和微生物,已经被广泛用于各种退化生态系统的植被恢复。但是,关于土壤迁播到退化生态系统后的真菌和细菌群落变化研究较少。【目的】研究土壤迁播后真菌和细菌的组成和多样性,比对其与森林母土和受体土壤之间的物种组成与群落差异。【方法】通过Illumina HiSeq高通量测序,获取迁播15个月的土壤、森林母土及受体土壤中真菌和细菌特征值,比对其多样性和丰富度。【结果】3类样地真菌优势菌门为担子菌门和子囊菌门,细菌优势菌门为酸杆菌门、变形菌门、放线菌门和绿弯菌门,土壤迁播后显著改变了真菌和细菌优势菌门的相对丰度。主成分分析表明3类样地真菌和细菌群落组成存在显著差异。聚类分析表明迁播土壤与受体土壤聚类距离更近,物种组成更相似,真菌和细菌优势属与受体土壤无显著差异。迁播土壤的真菌和细菌丰富度和多样性与森林母土差异显著(P0.05)。【结论】森林土壤迁播15月后,其细菌和真菌物种组成逐步趋同于受体土壤。该结果为进一步研究石漠化微生物生态系统、改善和提升土壤迁播技术提供支撑。     

Oxidation of elemental sulfur by bacteria and fungi in soil

Laboratory experiments were used to determine the effects of antibiotics, organic C and CaCO3 amendments of sterile reinoculated soil on S0 oxidation by bacteria and fungi. The rate of S0 oxidation in soil with nystatin added was higher than in soil amended with penicillin + streptomycin. This tells us that bacteria were more efficient than fungi in the S0 oxidation process. It was demonstrated that neutrophilic chemolithotrophs were more efficient in this process than heterotrophs. Glucose introduced to the soil had a negative effect and CaCO3 had a positive effect on S0 oxidation. In soil enriched with glucose the number of chemolithotrophs was very low in comparison with extremely numerous heterotrophic bacteria and fungi. It suggests that the role of heterotrophs in S0 oxidation could be important in habitats rich in organic C, e.g. rhizosphere. In soil containing S0, qualitative changes of fungal communities to genera with higher S0 oxidation ability was also noted. In the presented paper, after comparison of the own results with the data of others concerning the natural soils, the role of various microbial groups in S0 oxidation process in soils is discussed.     

Interactions between arbuscular mycorrhizal fungi and soil bacteria

The soil environment is interesting and complicated. There are so many interactions taking place in the soil, which determine the properties of soil as a medium for the growth and activities of plants and soil microorganisms. The soil fungi, arbuscular mycorrhiza (AM), are in mutual and beneficial symbiosis with most of the terrestrial plants. AM fungi are continuously interactive with a wide range of soil microorganisms including nonbacterial soil microorganisms, plant growth promoting rhizobacteria, mycorrhiza helper bacteria and deleterious bacteria. Their interactions can have important implications in agriculture. There are some interesting interactions between the AM fungi and soil bacteria including the binding of soil bacteria to the fungal spore, the injection of molecules by bacteria into the fungal spore, the production of volatiles by bacteria and the degradation of fungal cellular wall. Such mechanisms can affect the expression of genes in AM fungi and hence their performance and ecosystem productivity. Hence, consideration of such interactive behavior is of significance. In this review, some of the most important findings regarding the interactions between AM fungi and soil bacteria with some new insights for future research are presented.     

Growth of fungi and bacteria in the reciprocating jet bioreactor

In a comprehensive study the properties of the reciprocating-jet-bioreactor have been investigated. Fermentations have been carried out with two fungi and one bacterium. The fungi were Cyathus striatus for the production of antibiotics and Aspergillus niger for the production of citric acid. The bacterium Zymomonas mobilis was used in an anaerobic fermentation for the production of ethanol. The reciprocating-jet-bioreactor showed excellent properties as fermenter, especially when the biosuspension is highly viscous and non-Newtonian by nature.Lecture held on the occasion of the Third Joint Schlesinger Seminar at the Institute of Technology of the Technion-Haifa, May, 8–9th, 1990     

Ectohydrolytic enzyme activities of bacteria associated with Orbicella annularis coral

Ectohydrolytic enzyme activity (EEA) potential of 37 bacterial isolates derived from Orbicella annularis coral and 2 coral pathogens (Vibrio shilonii and V. coralliilyticus) was measured as model to infer the role of bacteria in organic matter processing within coral reef ecosystems. Bacterial cell-specific activities of eight enzyme types were measured after incubation in organic matter enriched and unenriched filtered seawater. Max value of activities of alkaline phosphatase, oleate-lipase, stearate-lipase and proteinase were 769.3, 327.6, 82.9 and 36.7 amol cell⁻¹ h⁻¹, respectively. Chitinase, α-mannosidase, α-glucosidase and β-glucosidase were generally lower by comparison (max 4.7–20.7 amol cell⁻¹ h⁻¹). No “super” isolates (bacteria expressing high levels of all ectohydrolases) were found suggesting a “specialization” among individual bacterial strains. Cumulatively, the 39 isolates tested displayed a broad range of cell-specific enzyme activities in both organic matter conditions. Culture-independent measurement of coral mucus layer EEA in O. annularis off a Panama reef showed comparable EEA patterns and diversity as the isolates. Volume-specific EEAs of all enzymes except alkaline phosphatase were 8–48 times higher in mucus than in surrounding seawater (SSW) samples. However, cell-specific EEAs in mucus were generally lower than in the SSW partly due to more abundant cells in the mucus than in SSW. For field samples, ≥ 85% of proteinase was cell-bound, while lipase was preferentially dissolved (40–96%). In general, the production of dissolved EEAs varied among measurements depending on sample source and enzyme types, suggesting a potential role of ectoenzyme size distribution in linking the whole reef ecosystem. Our findings support that the cumulative ectoenzyme expression (“ectoenzymome”) of the coral microbiome has the potential to maintain the functional resilience of the coral holobiont and response to stress through its contribution to organic matter processing within coral reef ecosystems.

     

施加内生真菌对花生连作土壤微生物和酶活性的影响

通过盆栽试验,研究了在土壤中施加植物内生真菌拟茎点霉NJ4.1菌株、B3菌株和角担子菌B6菌株在花生不同生育时期对土壤微生物学特性及酶活力的影响.结果表明:B3处理显著提高花生荚果产量,为对照的1.2倍;施加内生菌NJ4.1、B3和B6能显著增加花生根瘤数量,分别为对照的1.2、1.3和1.3倍.3个加菌处理全生育期平均细菌和放线菌数量高于对照,萌发期和苗期土壤微生物生物量碳(SMBC)显著高于对照,微生物生物量氮(SMBN)在花生萌发期升高,开花期降低.花生开花期土壤DGGE图谱表明,B3处理土壤细菌和真菌条带数量以及多样性最高.从萌发期到成熟期,与对照相比,3个加菌处理的土壤蔗糖酶和过氧化氢酶活性提高,脲酶活性无显著变化.表明施加内生菌对连作花生土壤环境有一定的改善作用,其中施用B3效果最好.     

当归不同生长时期根际丛枝真菌分布及土壤养分和酶活性的动态变化

【目的】探讨当归不同生长时期丛枝菌根真菌(Arbuscular mycorrhizal fungi,AMF)的分布及土壤养分和土壤酶活的变化,以期了解当归不同生长时期AMF与土壤养分和土壤酶活的关系,为AMF在当归种植的应用提供理论依据。【方法】在当归不同生长时期分别采集根际土壤样品,测定其土壤养分、土壤酶活、AMF孢子密度和球囊霉素等因子,分析当归不同生长时期根际土壤AMF孢子密度、土壤养分和土壤酶活等指标的动态变化和相关性。【结果】随着当归生育期的完成,根际土壤AMF孢子密度先降低后持续升高;易提取球囊霉素(Easily extractable glomalin,EEG)和总球囊霉素(Total glomalin,TG)平稳增加,而且EET与TG和脲酶活性呈显著正相关(P0.01),EET和TG与根际土壤有机质和全氮含量以及酸性和中性磷酸酶活性均显著正相关(P0.05);根际土壤有机质和全氮表现为增加的总趋势;有效磷含量呈现为生长前期保持不变、中期显著降低、后期逐渐升高的趋势,而有效钾含量先逐渐增加,生长中后期显著降低的趋势;根际土壤酸性和中性磷酸酶活性均呈现逐渐增加趋势,而脲酶活性表现为生长前期逐渐增加,中后期显著降低;p H值在当归不同生长时期有所波动。相关性分析结果表明,AMF孢子密度与土壤酸性磷酸酶酶活性呈显著正相关,而酸性磷酸酶酶活性与根际土壤全氮、有机质、易提取球囊霉素和总球囊霉素呈显著正相关,与有效磷和有效钾含量呈显著负相关,表明AMF对根际土壤养分和酶活性具有一定的调节作用;主成分分析结果表明,不同生长时期是影响当归根际土壤理化指标的主要因素。【结论】AMF孢子密度在当归根际的动态变化一定程度上反映出了AMF分泌球囊霉素的能力,以及球囊霉素对增加根际土壤碳氮储存的贡献,同时表明球囊霉素影响了当归根际土壤酶活性和其它养分的代谢循环,对改良土壤和促进当归生长发挥重要的作用。     

Evaluation of pyrimidine- and hydantoin-degrading enzyme activities in aerobic bacteria

Abstract The enzyme activities responsible for the reductive pyrimidine base degradation by aerobic bacteria, which produce hydantoin-degrading enzymes, were investigated. Pseudomonas putida IFO 12996, which is a d-stereospecific hydantoinase producer, has dihydropyrimidinase activity, and Comamonas sp. E222c and Blastobacter sp. A17p-4, which are N-carbamoyl-D-amino acid amidohydrolase producers, have β-ureidopropionase activity. Blastobacter sp. also possesses both d-stereospecific hydantoinase and dihydropyrimidinase activities. Thus, two amide ring-opening activities and/or two N -carbamoyl amino acid-hydrolyzing activities coexist in these bacteria. However, the differences of the induction levels of each enzyme activities for the several pyrimidine- and hydantoin-related compounds suggest that these corresponding amide ring-opening or N -carbamoyl amino acid-hydrolyzing activities are not always catalyzed by the same enzymes.     

Variations of soil enzyme activities in a temperate forest soil

Soil enzyme activities (dehydrogenase, urease, phosphatase, and arylsulfatase) in a temperate forest soil were determined in relation to landscape position and seasons. Overstory of the area is dominated by Quercus mongolica, Kalopanax pictus, Carpicus cordata, and Acer pseudo-sieboldianum. The activities were measured in three patches, namely a north-facing backslope, a ridge, and a south-facing backslope in autumn and spring over 2 years. In addition, spatially more detailed analysis for phosphatase was conducted before and after litterfall production in six patches. Dehydrogenase, urease, phosphatase, and arylsulfatase activities varied 1.8–18.5 μg INT-formazan g⁻¹ h⁻¹, 45.4–347.0 μg NH₄ ⁺ g⁻¹ h⁻¹, 0.9–4.5 mmol pNP g⁻¹ h⁻¹, and 0.7–2.6 mmol pNP g⁻¹ h⁻¹, respectively. In general, higher enzyme activities were found in the northern aspect than in the southern aspect. This variation appears to be related to differences in chemical properties (e.g., Fe, Al, and Mg) of soil as well as distribution of leaf litter. Two patterns were discernible in relation to seasonal variations. Dehydrogenase and urease exhibited a positive correlation with mean air temperature, suggesting that temperature would be a major controlling variable for those enzymes. In contrast, higher activities were detected in autumn for phosphatase and arylsulfatase activities, which appeared to be closely related to litter production and distribution. Overall results of this study indicate that soil enzyme activities in a forest floor are influenced by several variables such as temperature, nutrient availability, and input of leaf litter, which are closely related to landscape position.     

Growth of nodule bacteria in soil]

As was found with the aid of capillary microscopy, the nodule bacteria of pea and lupine in soil are encountered as rods, bacteroids, and cocci. The rod-like cells form bacteroids not only in the nodules but also outside, in soil. The bacteroids are viable and later reproduce the coccoid cells (arthrospores). The rods and bacteroids prevail in soil during flowering of the legumes, and the cocci are predominant at the end of vegetation.