Regulation of the biomass and activity of soil microorganisms by microfauna

Microcosm experiments showed that the microbial biomass and the respiration activity in soil were regulated by nematodes. Depending on nematode number and plant residue composition, the trophic activity of nematodes can either stimulate or inhibit microbial growth and respiration as compared to soil containing no nematodes. The stimulating effect was observed when nitrogen-free (starch) or low-nitrogen (wheat straw, C : N = 87) organic substrates were applied. Inhibition occurred when a substrate rich in nitrogen (alfalfa meal, C : N = 28) was decomposed and the nematode population exceeded the naturally occurring level. A conceptual model was developed to describe trophic regulation by microfauna (nematodes) of the microbial productivity and respiration ctivity and decomposition of not readily decomposable organic matter in soil. The stimulating and inhibiting influence of microfauna on soil microorganisms was not a linear function of the rate of microbial consumption by nematodes. These effects are largely associated with the induced change in the physiological state of microorganisms rather than with the mobilization of biogenic elements from the decomposed microbial biomass.     

Regulation of the biomass and activity of soil microorganisms by microfauna

Microcosm experiments showed that the microbial biomass and the respiration activity in soil were regulated by nematodes. Depending on nematode number and plant residue composition, the trophic activity of nematodes can either stimulate or inhibit microbial growth and respiration as compared to soil containing no nematodes. The stimulating effect was observed when nitrogen-free (starch) or low-nitrogen (wheat straw, C:N = 87) organic substrates were applied. Inhibition occurred when a substrate rich in nitrogen (alfalfa meal, C:N = 28) was decomposed and the nematode population exceeded the naturally occurring level. A conceptual model was developed to describe trophic regulation by microfauna (nematodes) of the microbial productivity and respiration activity and decomposition of not readily decomposable organic matter in soil. The stimulating and inhibiting influence of microfauna on soil microorganisms was not a linear function of the rate of microbial consumption by nematodes. These effects are largely associated with the induced change in the physiological state of microorganisms rather than with the mobilization of biogenic elements from the decomposed microbial biomass.     

Rumen ciliates: their metabolism and relationships with bacteria and their hosts

To explore the ruminal ecosystem, this paper is an attempt to illustrate the biochemistry and the metabolism of rumen protozoa. Different culture techniques (gnotobiotic, axenic, continuous culture) of ciliate protozoa are reviewed. The ability of ciliates to invade plant tissues, their association and the degradation of plant cell constituents (cellulose, hemicellulose, pectin, glycolipids), and the use of starch and soluble sugars for polysaccharide storage are determined. The interrelationships between ciliate protozoa and bacteria are discussed. These include the enzymic degradation of the engulfed plant particles, the bacterial nitrogen (amino acids, nucleic acids), and vitamins and trace element supplies as nutrient sources for protozoa. The composition of the rumen ciliate population, controlled by phylogenetic factors, geographical distribution, feeding habits and physiological status of the host, by competition between microorganisms and by the diet (nature of the diet, number of meals), is related. The transmission and establishment of the microfauna and its contribution to the microbial nitrogen available for the host are discussed.     

Measurement of microbial biomass phosphorus in rhizosphere soil

³²P-labelled monocalcium phosphate solution was supplied by point injection to the root system of wheat plants grown in soil cores in a controlled environment. There was no detectable incorporation of³²P into organic P fractions in the soil remaining after roots were removed, confirming field observations. The techniques used to measure organic P (including biomass P) could detect an incorporation of³²P into soil microbial biomass equivalent to 0.3 μgP.g^?1 soil, compared to a total soil biomass P content estimated to be ca. 6.5 μgP.g^?1 soil. The limited incorporation of the added P into microbial biomass in the root-free soil may be due partly to a limited diffusion of³²P into the non-rhizosphere soil and partly to the removal of³²P-labelled microbial biomass adhering to or in very close association with the root surface. it is proposed that in studies of soil nutrient status, total soil biomass P (roots + soil flora + microfauna) should be measured, rather than attempting an estimate of microbial P. A sequential extraction procedure using a single soil sample, where a biocide is added to the extracting solution, is proposed as an alternative to the conventional procedure for measuring soil biomass P where two soil samples, one treated with a biocide, are extracted simultaneously.     

Protozoan and metazoan communities treating a simulated petrochemical industry wastewater in a rotating disc biological reactor

The microfauna of adhered biofilms treating a simulated petrochemical plant wastewater was investigated in relation to the organic loading and the toxicity. Experiments in a six-compartment laboratory rotating biological reactor were performed at organic loadings of 0.99, 1.38 and 1.97g/l.day. The concentration of organic compounds in the artificial wastewater (phenol, acetophenone and styrene), toxicity of the wastewater, number of representative types of microfauna, their biomass and species diversity were monitored along the reactor. During this study 25 species were identified and attributed to seven classes of the three types Sarcomastigophora, Ciliophora and Nemathelminthes. Eight species from 18 ciliates have been reported in the literature as being commonly found inhabitants of aerobic wastewater treatment plants. An inverse relationship between the number of microfauna representatives and the organic loading was found. The presence of the most common species was related to the reactor operating conditions. A correlation between the toxicity of the wastewater measured by the Paramecium express-test and the distribution and abundance of microfauna was established. This express-test made it possible to predict the biological quality of the biofilm of activated sludge. Therefore, it is recommended as one of the control parameters to monitor systems of biological wastewater treatment.     

土壤酶计量揭示了武夷山黄山松林土壤微生物沿海拔梯度的碳磷限制变化

了解土壤胞外酶活性和酶计量的变化对评估山地生态系统土壤养分有效性和微生物的营养限制状况具有重要意义.然而,亚热带山地森林土壤微生物的营养限制状况对海拔梯度变化的响应及其驱动因素尚不清楚.本研究以武夷山不同海拔(1200～2000 m)黄山松林为对象,测定了土壤基本性质、微生物生物量以及与碳(C)、氮(N)、磷(P)循环...     

Microbial mechanisms of carbon priming effects revealed during the interaction of crop residue and nutrient inputs in contrasting soils

Agronomic practices such as crop residue return and additional nutrient supply are recommended to increase soil organic carbon (SOC) in arable farmlands. However, changes in the priming effect (PE) on native SOC mineralization in response to integrated inputs of residue and nutrients are not fully known. This knowledge gap along with a lack of understanding of microbial mechanisms hinders the ability to constrain models and to reduce the uncertainty to predict carbon (C) sequestration potential. Using a ¹³C‐labeled wheat residue, this 126‐day incubation study examined the dominant microbial mechanisms that underpin the PE response to inputs of wheat residue and nutrients (nitrogen, phosphorus and sulfur) in two contrasting soils. The residue input caused positive PE through “co‐metabolism,” supported by increased microbial biomass, C and nitrogen (N) extracellular enzyme activities (EEAs), and gene abundance of certain microbial taxa (Eubacteria, β‐Proteobacteria, Acidobacteria, and Fungi). The residue input could have induced nutrient limitation, causing an increase in the PE via “microbial nutrient mining” of native soil organic matter, as suggested by the low C‐to‐nutrient stoichiometry of EEAs. At the high residue, exogenous nutrient supply (cf. no‐nutrient) initially decreased positive PE by alleviating nutrient mining, which was supported by the low gene abundance of Eubacteria and Fungi. However, after an initial decrease in PE at the high residue with nutrients, the PE increased to the same magnitude as without nutrients over time. This suggests the dominance of “microbial stoichiometry decomposition,” supported by higher microbial biomass and EEAs, while Eubacteria and Fungi increased over time, at the high residue with nutrients cf. no‐nutrient in both soils. Our study provides novel evidence that different microbial mechanisms operate simultaneously depending on organic C and nutrient availability in a residue‐amended soil. Our results have consequences for SOC modeling and integrated nutrient management employed to increase SOC in arable farmlands.     

Trophic interactions in soils as they affect energy and nutrient dynamics. V. Phosphorus transformations

Regeneration of nutrients from relatively nutrient-poor organic residues is essential for overall operation of an ecosystem. Nutrients thus released are, however, inadequate for the needs of the decomposer populations, and a much faster nutrient turnover involving bacterial immobilization and release occurs concurrently. Evidence from aquatic ecosystems indicates that bacteria release little phosphorus, for which they have high demand, whereas bacterial grazers play an important role in regeneration of bacterial phosphorus. Our studies extend these relationships to terrestrial ecosystems. We studied phosphorus immobilization and mineralization in soil incubations, simulating rhizospheres with combinations of bacterial, amoebal, and nematode populations. Bacteria quickly assimilated and retained much of the labile inorganic phosphorus as carbon substrates were metabolized. Most of this bacterial phosphorus was mineralized and returned to the inorganic phosphorus pool by the amoebae. Nematode effects on phosphorus mineralization were small, except for indirect effects on amoebal activity. The observed remineralization may reflect direct excretion by the amoebae, physiological effects on the bacterial populations, or both. These results suggest a major role of microfauna in nutrient cycling.     

Microbial community responses to soil tillage and crop rotation in a corn/soybean agroecosystem

The acreage planted in corn and soybean crops is vast, and these crops contribute substantially to the world economy. The agricultural practices employed for farming these crops have major effects on ecosystem health at a worldwide scale. The microbial communities living in agricultural soils significantly contribute to nutrient uptake and cycling and can have both positive and negative impacts on the crops growing with them. In this study, we examined the impact of the crop planted and soil tillage on nutrient levels, microbial communities, and the biochemical pathways present in the soil. We found that farming practice, that is conventional tillage versus no‐till, had a much greater impact on nearly everything measured compared to the crop planted. No‐till fields tended to have higher nutrient levels and distinct microbial communities. Moreover, no‐till fields had more DNA sequences associated with key nitrogen cycle processes, suggesting that the microbial communities were more active in cycling nitrogen. Our results indicate that tilling of agricultural soil may magnify the degree of nutrient waste and runoff by altering nutrient cycles through changes to microbial communities. Currently, a minority of acreage is maintained without tillage despite clear benefits to soil nutrient levels, and a decrease in nutrient runoff—both of which have ecosystem‐level effects and both direct and indirect effects on humans and other organisms.     

Predicting microbial growth dynamics in response to nutrient availability

Developing mathematical models to accurately predict microbial growth dynamics remains a key challenge in ecology, evolution, biotechnology, and public health. To reproduce and grow, microbes need to take up essential nutrients from the environment, and mathematical models classically assume that the nutrient uptake rate is a saturating function of the nutrient concentration. In nature, microbes experience different levels of nutrient availability at all environmental scales, yet parameters shaping the nutrient uptake function are commonly estimated for a single initial nutrient concentration. This hampers the models from accurately capturing microbial dynamics when the environmental conditions change. To address this problem, we conduct growth experiments for a range of micro-organisms, including human fungal pathogens, baker’s yeast, and common coliform bacteria, and uncover the following patterns. We observed that the maximal nutrient uptake rate and biomass yield were both decreasing functions of initial nutrient concentration. While a functional form for the relationship between biomass yield and initial nutrient concentration has been previously derived from first metabolic principles, here we also derive the form of the relationship between maximal nutrient uptake rate and initial nutrient concentration. Incorporating these two functions into a model of microbial growth allows for variable growth parameters and enables us to substantially improve predictions for microbial dynamics in a range of initial nutrient concentrations, compared to keeping growth parameters fixed.     

Microbiota, fauna, and mesh size interactions in litter decomposition

Plant litter decomposition is a key process in carbon and nutrient cycling. The critical role of soil-faunal community composition in decomposition has been demonstrated using different mesh size litterbags to control exposure of litter to different faunal size classes. However, the faunal community surrounding the litterbags has not been manipulated despite potentially large indirect effects of their activity on biotic and abiotic processes that control litter decomposition at the habitat-scale.
We combined microcosm and litterbag techniques to facilitate a more comprehensive understanding of the role of direct and indirect effects of soil-faunal community composition on litter decomposition. We placed litterbags of three mesh sizes across model grassland miniecosystems manipulated to enable communities containing 1) microfauna; 2) micro- and meso-fauna; 3) micro-, meso- and macro-fauna. All communities contained bacteria and fungi. The approach permitted correction of mesh size artefacts inherent to field studies. Indirect effects have been divided into two separate terms, direct-indirect effects and indirect effects.
Decomposition in micromesh litterbags was significantly decreased by the indirect effects of meso- and macro-fauna. In macrofauna communities, increased mesh size significantly increased decomposition through mesh size per se and faunal effects. Relative effects of manipulated faunal community composition on litter mass loss and C:N ratio were equivalent for green and senesced litter. The presence of meso- and macro-fauna increased litter decomposition rate overall despite inhibiting decomposition by microfauna, bacteria and fungi through indirect effects.     

Unrecognized controls on microbial functioning in Blue Carbon ecosystems: The role of mineral enzyme stabilization and allochthonous substrate supply

Tidal wetlands are effective carbon sinks, mitigating climate change through the long‐term removal of atmospheric CO₂. Studies along surface‐elevation and thus flooding‐frequency gradients in tidal wetlands are often used to understand the effects of accelerated sea‐level rise on carbon sequestration, a process that is primarily determined by the balance of primary production and microbial decomposition. It has often been hypothesized that rates of microbial decomposition would increase with elevation and associated increases in soil oxygen availability; however, previous studies yield a wide range of outcomes and equivocal results. Our mechanistic understanding of the elevation–decomposition relationship is limited because most effort has been devoted to understanding the terminal steps of the decomposition process. A few studies assessed microbial exo‐enzyme activities (EEAs) as initial and rate‐limiting steps that often reveal important insight into microbial energy and nutrient constraints. The present study assessed EEAs and microbial abundance along a coastal ecotone stretching a flooding gradient from tidal flat to high marsh in the European Wadden Sea. We found that stabilization of exo‐enzymes to mineral sediments leads to high specific EEAs at low substrate concentrations in frequently flooded, sediment‐rich zones of the studied ecotone. We argue that the high background activity of a mineral‐associated enzyme pool provides a stable decomposition matrix in highly dynamic, frequently flooded zones. Furthermore, we demonstrate that microbial communities are less nutrient limited in frequently flooded zones, where inputs of nutrient‐rich marine organic matter are higher. This was reflected in both increasing exo‐enzymatic carbon versus nutrient acquisition and decreasing fungal versus bacterial abundance with increasing flooding frequency. Our findings thereby suggest two previously unrecognized mechanisms that may contribute to stimulated microbial activity despite decreasing oxygen availability in response to accelerated sea‐level rise.     

Effect of Inorganic Nutrients on Relative Contributions of Fungi and Bacteria to Carbon Flow from Submerged Decomposing Leaf Litter

The relative contributions of fungi and bacteria to carbon flow from submerged decaying plant litter at different levels of inorganic nutrients (N and P) were studied. We estimated leaf mass loss, fungal and bacterial biomass and production, and microbial respiration and constructed partial carbon budgets for red maple leaf disks precolonized in a stream and then incubated in laboratory microcosms at two levels of nutrients. Patterns of carbon flow for leaf disks colonized with the full microbial assemblage were compared with those colonized by bacteria but in which fungi were greatly reduced by placing leaf disks in colonization chambers sealed with membrane filters to exclude aquatic hyphomycete conidia but not bacterial cells. On leaves colonized by the full microbial assemblage, elevated nutrient concentrations stimulated fungi and bacteria to a similar degree. Peak fungal and bacterial biomass increased by factors of 3.9 and 4.0; cumulative production was 3.9 and 5.1 times higher in the high nutrient in comparison with the low nutrient treatment, respectively. Fungi dominated the total microbial biomass (98.4 to 99.8%) and cumulative production (97.3 and 96.5%), and the fungal yield coefficient exceeded that of bacteria by a factor of 36 and 27 in low- and high-nutrient treatments, respectively. Consequently, the dominant role of fungi in leaf decomposition did not change as a result of nutrient manipulation. Carbon budgets indicated that 8% of leaf carbon loss in the low-nutrient treatment and 17% in the high-nutrient treatment were channeled to microbial (essentially fungal) production. Nutrient enrichment had a positive effect on rate of leaf decomposition only in microcosms with full microbial assemblages. In treatments where fungal colonization was reduced, cumulative bacterial production did not change significantly at either nutrient level and leaf decomposition rate was negatively affected (high nutrients), suggesting that bacterial participation in carbon flow from decaying leaf litter is low regardless of the presence of fungi and nutrient availability. Moreover, 1.5 and 2.3 times higher yield coefficients of bacteria in the reduced fungal treatments at low and high nutrients, respectively (percentage of leaf carbon loss channeled to bacterial production), suggest that bacteria are subjected to strong competition with fungi for resources available in leaf litter.     

The Quantitative Importance of the Benthic Microfauna of an Arctic Tundra Pond

The microfauna (protozoa and micrometazoa) and bacteria and microalgae of the sediment of an arctic tundrapond at Barrow, Alaska were quantified through the summer. Very small protozoans (i.e. zooflagellates) and burrowing micrometazoans were found to be the most important components of the microfauna, whereas ciliates play a smaller role. This composition of microfauna is attributed to the mechanical property of the detrital sediment.Through a combination of laboratory experiments and field observations the grazing rates of protozoa for bacteria and microalgae in the field were estimated; protozoa were found to be important as bacterial grazers, but they consume only a modest fraction of the microalgae. An estimate of the grazing activity of the micrometazoans, based on indirect considerations, is also offered. It is of the same magnitude as that of protozoans but microalgae play a relatively larger role for the former. Based on previous studies on the pond it is estimated that microfaunal grazing constitutes about 30% of that of the detritus feeding macrofauna and that all categories of grazers together do not consume the total microbial production. The reasons for this results and the fate of this surplus production of algae and bacteria are discussed.     

Variability of water temperature may influence food-chain length in temperate streams

Nutrient enrichment may alter population dynamics of species in different ways depending on their life strategies. The aim of this study was to test the effect of different nutrient concentrations on the population development of two bacterivorous freshwater nematodes, Bursilla monhystera and Plectus aquatilis. Microcosms with autoclaved natural sand from a pristine stream (Fuirosos, NE of Spain) were enriched with different levels of phosphate, nitrate and ammonia as inorganic nutrients and glucose as a biodegradable dissolved organic carbon source. Although leaching of carbon and nutrients from the detritus fraction in the sediment initially may have overruled differences between treatments, later samplings revealed bottom-up control, with Bursilla monhystera abundances positively correlated to bacterial abundances at high nutrient concentrations. Nevertheless, there were several indications that nematodes in turn affected microbial abundance, most likely through excretion of ammonia and through grazing. In contrast to B. monhystera, Plectus aquatilis at high nutrient concentrations showed a unimodal abundance curve, while not increasing in abundance at low nutrient concentrations. Glucose enrichment did not have any stimulatory effect on either microbial or nematode abundances, probably as a result of unfavourable C:N:P stoichiometry. P enrichment, by contrast, stimulated microbial and Bursilla abundances. Our results indicate that episodic nutrient enrichment may affect populations of bacterial-feeding nematodes in the short term. Their longer-term dynamics may, however, be more dependent on leaching of carbon and nutrients from the pools of sediment-bound detritus.     

Urbanisation and earthquake disturbance influence microbial nutrient limitation in streams

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When do grazers accelerate or decelerate soil carbon and nitrogen cycling in tundra? A test of theory on grazing effects in fertile and infertile habitats

It is generally predicted that grazers enhance soil microbial activity and nutrient availability and promote soil bacteria in fertile ecosystems, but retard microbial activity and nutrient availability and promote soil fungi in infertile ecosystems. We tested these predictions in tundra by comparing grazing effects between fertile and infertile habitats and with/without nutrient manipulation by fertilization. Grazing decreased soil N content in fertile and in fertilized plots in infertile habitats while increased it in infertile tundra habitats, which directly opposed our prediction. We conclude that this unpredicted outcome probably resulted from nutrient transport between habitats. Also contrasting with our hypothesis, grazing increased fungal rather than bacterial abundance in fertilized plots at both habitats. In support with predictions, grazing increased microbial activity for soil C decomposition in fertile but decreased it in infertile habitats. The effect of grazing on soil C decomposition followed same patterns as grazer‐induced changes in the activity of β‐glucosidase, which is an extracellular enzyme synthesized by soil microorganisms for degrading soil cellulose. We suggest that the theoretical framework on grazer–soil interactions should incorporate microbial potential for extracellular enzyme production (‘microscale’ grazer effects) and nutrient translocation by grazers among habitats (‘macroscale’ grazer effects) as important mechanisms by which grazers influence soil processes and nutrient availability for plants at contrasting levels of habitat fertility.     

肠道菌群功能与影响因素研究进展

人体肠道作为一种营养丰富的天然环境有多达100兆个微生物,其中绝大多数存于结肠内,密度接近1011~1012/m L。人类肠道内的微生物多样性是微生物菌落和宿主共同进化的结果,自然选择和进化使肠道菌群与宿主处于一种动态平衡且稳定的关系。文章综述了肠道菌群对宿主可能产生的影响以及引起肠道菌群发生改变的某些因素,肠道微生物影响宿主的代谢、营养吸收、免疫功能以及神经功能调节,而饮食及其他条件又能引起肠道菌群的改变。深入分析肠道菌群的具体结构、探索不同微生物在宿主体内究竟发挥着怎样的作用以及如何充分利用微生物的不同特性改善人类健康应成为今后研究的重点方向。     

Soil Fertility and the Impact of Exotic Invasion on Microbial Communities in Hawaiian Forests

Exotic plant invasions into Hawaiian montane forests have altered many important nutrient cycling processes and pools. Across different ecosystems, researchers are uncovering the mechanisms involved in how invasive plants impact the soil microbial community-the primary mediator of soil nutrient cycling. We examined whether the invasive plant, Hedychium gardnerianum, altered microbial community composition in forests dominated by a native tree, Metrosideros polymorpha, under varying soil nutrient limitations and soil fertility properties within forest plots of the Hawaii long-term substrate age gradient (LSAG). Microbial community lipid analysis revealed that when nutrient limitation (as determined by aboveground net primary production [ANPP]) and soil fertility were taken into account, plant species differentially altered soil microbial community composition. Microbial community characteristics differed under invasive and native plants primarily when N or P was added to the older, highly weathered, P-limited soils. Long-term fertilization with N or P at the P-limited site led to a significant increase in the relative abundance of the saprophytic fungal indicator (18:2 omega 6c,9c) under the invasive plant. In the younger, N-limited soils, plant species played a minor role in influencing soil microbial community composition. We found that the general rhizosphere microbial community structure was determined more by soil fertility than by plant species. This study indicates that although the aggressive invasion of a nutrient-demanding, rapidly decomposable, and invasive plant into Hawaiian forests had large impacts on soil microbial decomposers, relatively little impact occurred on the overall soil microbial community structure. Instead, soil nutrient conditions were more important determinants of the overall microbial community structure within Hawaii's montane forests.