Trophic interactions in soils as they affect energy and nutrient dynamics. I. Introduction

The dynamics of nutrient transformations at the soil-root interface are complex but amenable to controlled experimental study. Using a conceptual model we introduce a series of papers which ascertain the role of microfloral-faunal trophic interactions in carbon, nitrogen, and phosphorus transformations in soil microcosms.     

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.     

Trophic interactions in soils as they affect energy and nutrient dynamics. III. Biotic interactions of bacteria,amoebae, and nematodes

Bacteria (Pseudomonas), amoebae (Acanthamoeba), and nematodes (Mesodiplogaster) were raised in soil microcosms with and without glucose additions. Nematode and amoebal grazing on bacteria significantly reduced bacterial populations by the end of a 24-day incubation period. Amoebal numbers decreased in the presence of nematodes with a corresponding increase in nematode numbers which reached a maximum of 230 nematodes/g of soil in the treatment with amoebae and glucose additions. After 24 days the nematode populations in the treatments without carbon additions were dominated by resistant dauer larvae indicating the unavailability of food. Although larval numbers were high in the treatments with glucose additions, the adult component of the population was still increasing at the end of the 24-day experiment. The effect of the presence of amoebae on nematode abundance was of the same magnitude as addition of 600g glucose-C.     

Trophic interactions in soils as they affect energy and nutrient dynamics. IV. Flows of metabolic and biomass carbon

Flows of biomass and respiratory carbon were studied in a series of propylene-oxide sterilized soil microcosms. One-half of the microcosms received three pulsed additions of 200 ppm glucose-carbon to mimic rhizosphere carbon inputs. Biotic variables were: bacteria (Pseudomonas) alone, or amoebae (Acanthamoeba) and nematodes (Mesodiplogaster) singly, or both combined in the presence of bacteria.Over the 24-day experiment, respiration was significantly higher in the microcosms containing the bacterial grazers. Biomass accumulation by amoebae was significantly higher than that by nematodes. The nematodes respired up to 30-fold more CO₂ per unit biomass than did amoebae. Similar amounts of carbon flowed into both respiratory and biomass carbon in microcosms with fauna, compared with the bacteria-alone microcosms. However, partitioning of available carbon by the microfauna varied considerably, with little biomass production and relatively more CO₂-C produced in the nematode-containing microcosms. The amoebae, in contrast, allocated more carbon to tissue production (about 40% assimilation efficiency) and correspondingly less to CO₂.     

Iron dynamics in the rhizosphere as a case study for analyzing interactions between soils,plants and microbes

Plant and Soil - Iron is an essential element for plants and microbes. However, in most cultivated soils, the concentration of iron available for these living organisms is very low because its...     

Trophic interactions affect the population dynamics and risk of extinction of basal species in food webs

This paper addresses effects of trophic complexity on basal species, in a Lotka–Volterra model with stochasticity. We use simple food web modules, with three trophic levels, and expose every species to random environmental stochasticity and analyze (1) the effect of the position of strong trophic interactions on temporal fluctuations in basal species’ abundances and (2) the relationship between fluctuation patterns and extinction risk. First, the numerical simulations showed that basal species do not simply track the environment, i.e. species dynamics do not simply mirror the characteristics of the applied environmental stochasticity. Second, the extinction risk of species was related to the fluctuation patterns of the species.More specifically, we show (i) that despite being forced by random stochasticity without temporal autocorrelation (i.e. white noise), there is significant temporal autocorrelation in the time series of all basal species’ abundances (i.e. the spectra of basal species are red-shifted), (ii) the degree of temporal autocorrelation in basal species time series is affected by food web structure and (iii) the degree of temporal autocorrelation tend to be correlated to the extinction risks of basal species.Our results emphasize the role of food web structure and species interactions in modifying the response of species to environmental variability. To shed some light on the mechanisms we compare the observed pattern in abundances of basal species with analytically predicted patterns and show that the change in the predicted pattern due to the addition of strong trophic interactions is correlated to the extinction risk of the basal species. We conclude that much remain to be understood about the mechanisms behind the interaction among environmental variability, species interactions, population dynamics and vulnerability before we quantitatively can predict, for example, effects of climate change on species and ecological communities. Here, however, we point out a new possible approach for identifying species that are vulnerable to environmental stochasticity by checking the degree of temporal autocorrelation in the time series of species. Increased autocorrelation in population fluctuations can be an indication of increased extinction risk.     

Trophic interactions between viruses, bacteria and nanoflagellates under various nutrient conditions and simulated climate change

Population dynamics in the microbial food web are influenced by resource availability and predator/parasitism activities. Climatic changes, such as an increase in temperature and/or UV radiation, can also modify ecological systems in many ways. A series of enclosure experiments was conducted using natural microbial communities from a Mediterranean lagoon to assess the response of microbial communities to top-down control [grazing by heterotrophic nanoflagellates (HNF), viral lysis] and bottom-up control (nutrients) under various simulated climatic conditions (temperature and UV-B radiations). Different biological assemblages were obtained by separating bacteria and viruses from HNF by size fractionation which were then incubated in whirl-Pak bags exposed to an increase of 3°C and 20% UV-B above the control conditions for 96 h. The assemblages were also provided with an inorganic and organic nutrient supply. The data show (i) a clear nutrient limitation of bacterial growth under all simulated climatic conditions in the absence of HNF, (ii) a great impact of HNF grazing on bacteria irrespective of the nutrient conditions and the simulated climatic conditions, (iii) a significant decrease in burst size (BS) (number of intracellular lytic viruses per bacterium) and a significant increase of VBR (virus to bacterium ratio) in the presence of HNF, and (iv) a much larger temperature effect than UV-B radiation effect on the bacterial dynamics. These results show that top-down factors, essentially HNF grazing, control the dynamics of the lagoon bacterioplankton assemblage and that short-term simulated climate changes are only a secondary effect controlling microbial processes.     

Population dynamics of type I and II methanotrophic bacteria in rice soils

Methane-oxidizing bacteria (methanotrophs) consume a significant but variable fraction of greenhouse-active methane gas produced in wetlands and rice paddies before it can be emitted to the atmosphere. Temporal and spatial dynamics of methanotroph populations in California rice paddies were quantified using phospholipid biomarker analyses in order to evaluate the relative importance of type I and type II methanotrophs with depth and in relation to rice roots. Methanotroph population fluctuations occurred primarily within the top 0-2 cm of soil, where methanotroph cells increased by a factor of 3-5 over the flooded rice-growing season. The results indicate that rice roots and rhizospheres were less important than the soil-water interface in supporting methanotroph growth. Both type I and type II methanotrophs were abundant throughout the year. However, only type II populations were strongly correlated with soil porewater methane concentrations and rice growth.     

Physiological responses of bacteria in biofilms to disinfection.

In situ enumeration methods using fluorescent probes and a radioisotope labelling technique were applied to evaluate physiological changes of Klebsiella pneumoniae within biofilms after disinfection treatment. Chlorine (0.25 mg of free chlorine per liter [pH 7.2]) and monochloramine (1 mg/liter [pH 9.0]) were employed as disinfectants in the study. Two fluorgenic compounds, 5-cyano-2,3-ditolyl tetrazolium chloride and rhodamine 123, and tritiated uridine incorporation were chosen for assessment of physiological activities. Results obtained by these methods were compared with those from the plate count and direct viable count methods. 5-Cyano-2,3-ditolyl tetrazolium chloride is an indicator of bacterial respiratory activity, rhodamine 123 is incorporated into bacteria in response to transmembrane potential, and the incorporation of uridine represents the global RNA turnover rate. The results acquired by these methods following disinfection exposure showed a range of responses and suggested different physiological reactions in biofilms exposed to chlorine and monochloramine. The direct viable count response and respiratory activity were affected more by disinfection than were the transmembrane potential and RNA turnover rate on the basis of comparable efficiency as evaluated by plate count enumeration. Information revealed by these approaches can provide different physiological insights that may be used in evaluating the efficacy of biofilm disinfection.     

Physiological and genetic responses of bacteria to osmotic stress.

The capacity of organisms to respond to fluctuations in their osmotic environments is an important physiological process that determines their abilities to thrive in a variety of habitats. The primary response of bacteria to exposure to a high osmotic environment is the accumulation of certain solutes, K+, glutamate, trehalose, proline, and glycinebetaine, at concentrations that are proportional to the osmolarity of the medium. The supposed function of these solutes is to maintain the osmolarity of the cytoplasm at a value greater than the osmolarity of the medium and thus provide turgor pressure within the cells. Accumulation of these metabolites is accomplished by de novo synthesis or by uptake from the medium. Production of proteins that mediate accumulation or uptake of these metabolites is under osmotic control. This review is an account of the processes that mediate adaptation of bacteria to changes in their osmotic environment.     

Trophic interactions in changing landscapes: responses of soil food webs

Soil communities in landscapes that are rapidly changing due to a range of anthropogenic processes can be regarded as highly transient systems where interactions between competing species or trophic levels may be seriously disrupted. In disturbed communities dispersal in space and time has a role in ensuring continuity of community function. Stable communities, in undisturbed systems, are more dependent on competition and other biotic interactions between species. We predicted how food web components would respond to disturbance, based on their dispersal and colonizing abilities. During decomposition, flows of energy and nutrients generally follow either a bacterial-based path, with bacteria as the primary decomposer and bacterial-feeding fauna and their predators forming the associated food web, or a fungal-based channel. Trophic links that were generally resistant to change were the organisms of the bacterial pathway that have high abilities to disperse in time and passively disperse in space. Organisms in the fungal pathway were less resistant to disturbance. Resource inputs to the soil system are derived from plants, either through root exudation and root turnover during active growth or from dead plant material following senescence or agricultural tillage. Disturbances to the soil system can arise as a direct action on the soil, or indirectly from effects on the above-ground plant community. Disturbance-induced changes in plant community composition will change the soil food web composition. Organisms involved in direct interactions with plants (e.g. AM-mycorrhizal fungi) were also predicted to be vulnerable to disturbance.

Zusammenfassung

Bodengemeinschaften in Landschaften, die sich aufgrund einer Reihe von anthropogenen Prozessen schnellstens verändern, können als sehr kurzlebige Systeme angesehen werden, in denen Interaktionen zwischen konkurrierenden Arten oder trophischen Leveln nachhaltig unterbrochen sind. In gestörten Gemeinschaften hat die Ausbreitung in Raum und Zeit eine Rolle bei der Wahrung der Kontinuität von Gemeinschaftsfunktionen. Stabile Gemeinschaften, in ungestörten Systemen, sind stärker von Konkurrenz und anderen biotischen Interaktionen zwischen den Arten abhängig. Wir sagten voraus, wie Nahrungsnetzkomponenten auf Störung antworten würden, basierend auf ihrer Ausbreitungs- und Kolonisationsfähigkeit. Während der Zersetzung folgen die Flüsse von Energie und Nährstoffen im Allgemeinen entweder einem Weg, der auf Bakterien basiert, mit Bakterien als den primären Zersetzern und bacterienfressender Fauna und ihre Predatoren, die das assoziierte Nahrungsnetz bilden, oder sie folgen einem Kanal, der auf Pilzen basiert. Trophische Verknüpfungen, die im Allgemeinen resistent gegen Veränderungen waren, waren die Organismen des bakteriellen Weges, die große Möglichkeiten haben sich in Zeit und passiv im Raum auszubreiten. Organismen des pilzbasierten Weges waren weniger widerstandsfähig gegenüber Störungen. Die Ressourcenzufuhr in das Bodensystem stammte von Pflanzen, entweder über Wurzelausscheidungen und/oder Wurzelturnover während des aktiven Wachstums oder von totem Pflanzenmaterial aufgrund von Seneszenz oder landwirtschatlicher Bodenbearbeitung. Störungen des Bodensystems können durch direkte Einwirkungen auf den Boden oder indirekt durch Effekte der oberirdischen Pflanzemeinschaft entstehen. Störungsinduzierte Veränderungen in der Zusammensetzung der Pflanzengemeinschaft werden die Zusammensetzung des Bodennahrungsnetzes verändern. Für Organismen, die an direkten Interaktionen mit Pflanzen beteiligt sind (beispielsweise AM-Mykorrhizapilze), wurde ebenfalls vorhergesagt, dass sie anfällig für Störungen sind.     

Physiological responses to salinity in selected lines of wheat

Two selections of bread wheat, Triticum aestivum L., differing in their relative salt resistance, were grown in salinized solution culture, and relative growth rates, osmotic adjustment, ion accumulation, and photosynthesis were monitored to study the responses of the plants to salinity.

Differences in water relations were minimal and were only apparent for 3 days following salinization. The lines differed substantially in their relative growth rates and photosynthetic responses for several weeks following salinization, despite full osmotic adjustment. Concentrations of major cations and Cl⁻ in the plant organs were remarkably similar in both lines, indicative of minimal differences in gross ion absorption and translocation.

The authors interpret these results to suggest that the major difference between these two lines of wheat was their response to specific ion effects, at the level of the organ, tissue, cell, and subcellular entities. Superior compartmentation of toxic ions by the more salt-tolerant line, presumably in the vacuole, might have enabled it to maintain its cytoplasmic metabolic apparatus in a stabler and more nearly normal state than the sensitive line was able to do; a measure of true cytoplasmic toleration of salt may also be a factor.

     

Trophic interactions among heterotrophic microplankton,nanoplankton, and bacteria in Lake Constance

A considerable portion of the pelagic energy flow in Lake Constance (FRG) is channelled through a highly dynamic microbial food web. In-situ experiments using the lake water dilution technique according to Landry & Hasset (1982) revealed that grazing by heterotrophic nanoflagellates (HNF) smaller than 10 µm is the major loss factor of bacterial production. An average flagellate ingests 10 to 100 bacteria per hour. Nano- and micro-ciliates have been identified as the main predators of HNF. If no other food is used between 3 and 40 HNF are consumed per ciliate and hour. Other protozoans and small metazoans such as rotifers are of minor importance in controlling HNF population dynamics.Clearance rates varied between 0.2 and 122.8 nl HNF^–1 h^–1 and between 0.2 and 53.6 µl ciliate^–1 h^–1, respectively.Ingestion and clearance rates measured for HNF and ciliates are in good agreement with results obtained by other investigators from different aquatic environments and from laboratory cultures. Both the abundance of all three major microheterotrophic categories — bacteria, HNF, and ciliates — and the grazing pressure within the microbial loop show pronounced seasonal variations.     

海南生态区植物根际解磷细菌的筛选及分子鉴定

【目的】了解海南酸性土壤解磷细菌溶解Ca3(PO4)2和FePO4特性;筛选高效稳定的解磷菌株,为应用研究提供菌源。【方法】采集海南21种植物的根际土样品,用营养琼脂、结晶紫-营养琼脂、酵母粉-甘露醇琼脂,稀释涂布法分离土壤细菌,选取平板上菌落形态有明显区别的代表性菌落,用最低营养琼脂进行纯化;Ⅰ筛用Ca3(PO4)2固体培养基培养5 d,挑取有溶磷圈的菌落;Ⅱ筛用Ca3(PO4)2培养液在32℃、200 r/min条件培养6 d,挑取解磷量大于200 mg/L的菌株;Ⅲ筛是在4次继代培养及每次15 d的4℃保藏后,用Ca3(PO4)2培养液培养6 d,挑取解磷量大于200 mg /L的菌株。称Ⅲ筛的选出菌株为高效稳定的解磷细菌(PSBHS),用FePO4培养液对PSBHS培养6 d,并测定解磷量;用简并引物扩增PSBHS 16S rDNA基因一个长度约1460 bp的片段,测序后,通过Blast检索同源序列,鉴定解磷细菌分类。【结果】共分离到363个代表性菌株,通过Ⅰ筛、Ⅱ筛、Ⅲ筛的代表性菌株分别是126个、45个、14个;14个PSBHS在Ca3(PO4)2培养液中经6 d培养,解磷量达201.0 mg/L ~623.3 mg/L,培养结束时pH值(3.82~4.34)与解磷量呈极显著负相关（r = -0.8155)。14个PSBHS在FePO4培养液中经6 d培养,解磷量只有1.6 mg/L ~34.2 mg/L,培养结束时pH值(2.87~5.67)与解磷量也呈极显著负相关(r = -0.6836)。16S rDNA序列分析,确定了6个PSBHS为Acinetobacter, 3个为Pseudomonas, 3个为Serratia, 2个为Enterobacter。     

Trophic dynamics in a whole lake experiment: size-structured interactions and recruitment variation

Horizontal and vertical heterogeneity as a result of size‐structured processes are important factors influencing indirect effects in food webs. In a whole‐lake experiment covering 5 years, we added the intermediate consumer roach (Rutilus rutilus) to two out of four lakes previously inhabited by the omnivorous top predator perch (Perca fluviatilis). We focused our study on the direct consumption effect of roach presence on zooplankton (and indirectly phytoplankton) versus the indirect effect of roach on zooplankton (and phytoplankton) mediated via effects on perch reproductive performance. The patterns in zooplankton and phytoplankton abundances were examined in relation to population density of roach and perch including young‐of‐the‐year (YOY) perch in the light of non‐equilibrium dynamics. The presence of roach resulted in changed seasonal dynamics of zooplankton with generally lower biomasses in May–June and higher biomasses in July–August in roach lakes compared to control lakes. Roach presence affected perch recruitment negatively and densities of YOY perch were on average higher in control lakes than in treatment lakes. In years when perch recruitment did not differ between lakes as a result of experimental addition of perch eggs, total zooplankton biomass was lower in treatment lakes than in control lakes. Phytoplankton biomass showed a tendency to increase in roach lakes compared to control lakes. Within treatment variation in response variables was related to differences in lake morphometry in treatment lakes. Analyses of the trophic dynamics of each lake separately showed strong cascading effects of both roach and YOY perch abundance on zooplankton and phytoplankton dynamics. Consideration of the long transients in the dynamics of top predators (fish) in aquatic systems that are related to their long life span involving ontogenetic niche shifts is essential for making relevant interpretations of experimental perturbations. This conclusion is further reinforced by the circumstance that the intrinsic dynamics of fish populations may in many cases involve high amplitude dynamics with long time lags.     

Physiological and regulatory convergence between osmotic and nutrient stress responses in microbes

Bacterial cells are regularly confronted with simultaneous changes in environmental nutrient supply and osmolarity. Despite the importance of osmolarity and osmoregulation in bacterial physiology, the relationship between the cellular response to osmotic perturbations and other stresses has remained largely unexplored. Bacteria cultured in hyperosmotic conditions and bacteria experiencing nutrient stress exhibit similar physiological changes, including metabolic shutdown, increased protein instability, dehydration, and condensation of chromosomal DNA. In this review, we highlight overlapping molecular players between osmotic and nutrient stresses. These connections between two seemingly disparate stress response pathways reinforce the importance of central carbon metabolism as a control point for diverse aspects of homeostatic regulation. We identify important open questions for future research, emphasizing the pressing need to develop and exploit new methods for probing how osmolarity affects phylogenetically diverse species.     

几种农田土壤中古菌、泉古菌和细菌的数量分布特征

真核生物、细菌和古菌三者共同构成了生命的三域系统.古菌作为第3种生命形式,不仅能在高温、强酸和高盐等极端环境下生存,而且在海洋、湖泊和土壤等生境中也广泛分布,预示其在整个生态系统中有着不可估量的作用.本文以2个农田剖面土壤和2个长期施肥试验站祁阳(QY)和封丘(FQ)的土壤为对象,以实时定量PCR方法为主要研究手段,对土壤中古菌(包括泉古菌)和细菌的16S rRNA基因拷贝数丰度变化进行了研究.结果表明:土壤泉古菌16S rRNA基因拷贝数要低于古菌l～2个数量级,两者与细菌相比,16S rRNA基因拷贝数大小顺序为土壤泉古菌＜古茵＜细菌,而古菌和泉古菌16S rRNA基因拷贝数与细菌的比值均随土壤深度加深而增大.不同施肥处理对土壤古菌和泉古茵的数量有显著影响.QY试验站土壤古菌和细菌的数量与土壤pH值显著相关(分别为r=0.850,P＜0.01和r=0.676,P＜0.05).FQ古菌、泉古菌和细菌与土壤pH值相关性不显著,与土壤有机质含量相关性均达显著水平(分别为r=0.783,P＜0.05;r=0.827,P＜0.05;r=0.767,P＜0.05).了解古菌包括泉古菌在农田土壤中的分布,可为评价其在生态系统和物质循环中的作用提供重要的理论依据.     

Molecular dynamics simulations of protein-tyrosine phosphatase 1B. II. substrate-enzyme interactions and dynamics

Molecular dynamics simulations of protein tyrosine phosphatase 1B (PTP1B) complexed with the phosphorylated peptide substrate DADEpYL and the free substrate have been conducted to investigate 1) the physical forces involved in substrate-protein interactions, 2) the importance of enzyme and substrate flexibility for binding, 3) the electrostatic properties of the enzyme, and 4) the contribution from solvation. The simulations were performed for 1 ns, using explicit water molecules. The last 700 ps of the trajectories was used for analysis determining enthalpic and entropic contributions to substrate binding. Based on essential dynamics analysis of the PTP1B/DADEpYL trajectory, it is shown that internal motions in the binding pocket occur in a subspace of only a few degrees of freedom. In particular, relatively large flexibilities are observed along several eigenvectors in the segments: Arg(24)-Ser(28), Pro(38)-Arg(47), and Glu(115)-Gly(117). These motions are correlated to the C- and N-terminal motions of the substrate. Relatively small fluctuations are observed in the region of the consensus active site motif (H/V)CX(5)R(S/T) and in the region of the WPD loop, which contains the general acid for catalysis. Analysis of the individual enzyme-substrate interaction energies revealed that mainly electrostatic forces contribute to binding. Indeed, calculation of the electrostatic field of the enzyme reveals that only the field surrounding the binding pocket is positive, while the remaining protein surface is characterized by a predominantly negative electrostatic field. This positive electrostatic field attracts negatively charged substrates and could explain the experimentally observed preference of PTP1B for negatively charged substrates like the DADEpYL peptide.     

The theory of population dynamics—II. Physiological delays

Traditional population models describe changes in population size as a function of changes in the resources. Such first-order models cannot describe certain properties of population dynamics. General models with delays can account for all the observed dynamic complexities but are judged overgeneralized. It is proposed that the simplest model of intermediate complexity that explains such dynamic properties is a second-order model, which describes population dynamics as a function of a physiological variable, the dynamics of which in turn depends on resources. Data on accelerated decline of populations in the absence of food from experiments with brown and green hydra as well as literature data support the arguments.