A methane-driven microbial food web in a wetland rice soil

Methane oxidation is a key process controlling methane emission from anoxic habitats into the atmosphere. Methanotrophs, responsible for aerobic methane oxidation, do not only oxidize but also assimilate methane. Once assimilated, methane carbon may be utilized by other organisms. Here we report on a microbial food web in a rice field soil driven by methane. A thin layer of water-saturated rice field soil was incubated under opposing gradients of oxygen and (13)C-labelled methane. Bacterial and eukaryotic communities incorporating methane carbon were analysed by RNA-stable isotope probing (SIP). Terminal restriction fragment length polymorphism (T-RFLP) and cloning showed that methanotrophs were the most prominent group of bacteria incorporating methane carbon. In addition, a few Myxobacteria-related sequences were obtained from the 'heavy' rRNA fraction. Denaturing gradient gel electrophoresis (DGGE) targeting 18S rRNA detected various groups of protists in the 'heavy' rRNA fraction including naked amoeba (Lobosea and Heterolobosea), ciliates (Colpodea) and flagellates (Cercozoa). Incubation of soil under different methane concentrations in air resulted in the development of distinct protozoan communities. These results suggest that methane carbon is incorporated into non-methanotrophic pro- and microeukaryotes probably via grazing, and that methane oxidation is a shaping force of the microeukaryotic community depending on methane availability.     

Community convergence in a simple microbial food web

Previous studies of communities implicate many potential mechanisms that can create alternate stable states. These include density-dependent foraging behavior, size refuges reached by early colonists, environmental feedback following disturbance, and different initial densities of intraguild predators. Previous work shows that alternate states of varying stability can occur in food webs containing the intraguild predators Blepharisma americanum and Tetrahymena vorax. Differences in colonization history could create the alternate states, consisting of dominance by either Blepharisma or Tetrahymena, but it was unclear whether results depended on effects of initial density or only on changes in the resource base. We manipulated initial densities of both species to determine if density effects alone could create alternate stable states. Convergence of these communities over time indicated that differences in initial density did not create alternate stable states. By default, other factors influenced by colonization history, such as resource availability, may produce alternate states. Models of alternate stable-state phenomena should incorporate differences in resource availability in addition to direct competitive and predatory interactions to provide a more complete depiction of the causes of differences in community composition in otherwise similar habitats.     

Modeling the microbial food web

Models of the microbial food web have their origin in the debate over the importance of bacteria as an energetic subsidy for higher trophic levels leading to harvestable fisheries. Conceptualization of the microbial food web preceded numerical models by 10–15 years. Pomeroy's work was central to both efforts. Elements necessary for informative and comprehensive models of microbial loops in plankton communities include coupled carbon and nitrogen flows utilizing a size-based approach to structuring and parameterizing the food web. Realistic formulation of nitrogen flows requires recognition that both nitrogenous and nonnitrogenous organic matter are important substrates for bacteria. Nitrogen regeneration driven by simple mass-specific excretion constants seems to overestimate the role of bacteria in the regeneration process. Quantitative assessment of the link-sink question, in which the original loop models are grounded, requires sophisticated analysis of size-based trophic structures. The effects of recycling complicate calculation of the link between bacteria or dissolved organic matter and mesozooplankton, and indirect effects show that the link might be much stronger than simple analyses have suggested. Examples drawn from a series of oceanic mixed layer plankton models are used to illustrate some of these points. Single-size class models related to traditional P-Z-N approaches are incapable of simulating bacterial biomass cycles in some locations (e.g., Bermuda) but appear to be adequate for more strongly seasonal regimes at higher latitudes.     

Accumulation of selenium in a model freshwater microbial food web.

The transfer of selenium between bacteria and the ciliated protozoan, Paramecium putrinum, was examined in laboratory cultures. The population growth of the ciliate was not inhibited in the presence of the highest concentrations of dissolved selenite or selenate tested (10(3) micrograms liter-1). Experiments with radioactive 75selenite or 75selenate indicated that accumulation of selenium by ciliates through time was low when feeding and metabolism were reduced by incubating at 0 degrees C. However, selenium accumulated in ciliate biomass during incubation with dissolved 75Se and bacteria at 24 degrees C and also when bacteria prelabeled with 75Se were offered as food in the absence of dissolved selenium. When 75Se-labeled bacterial food was diluted by the addition of nonradioactive bacteria, the amount of selenite and selenate in ciliates decreased over time, indicating depuration by the ciliates. In longer-term (> 5-day) fed-batch incubations with 75selenite-labeled bacteria, the selenium concentration in ciliates equilibrated at approximately 1.4 micrograms of Se g (dry weight)-1. The selenium content of ciliates was similar to that of their bacterial food on a dry-weight basis. These data indicate that selenium uptake by this ciliate occurred primarily during feeding and that biomagnification of selenium did not occur in this simple food chain.     

Exogenous carbon turnover within the soil food web strengthens soil carbon sequestration through microbial necromass accumulation

Exogenous carbon turnover within soil food web is important in determining the trade-offs between soil organic carbon (SOC) storage and carbon emission. However, it remains largely unknown how soil food web influences carbon sequestration through mediating the dual roles of microbes as decomposers and contributors, hindering our ability to develop policies for soil carbon management. Here, we conducted a ¹³C-labeled straw experiment to demonstrate how soil food web regulated the residing microbes to influence the soil carbon transformation and stabilization process after 11 years of no-tillage. Our work demonstrated that soil fauna, as a “temporary storage container,” indirectly influenced the SOC transformation processes and mediated the SOC sequestration through feeding on soil microbes. Soil biota communities acted as both drivers of and contributors to SOC cycling, with 32.0% of exogenous carbon being stabilizing in the form of microbial necromass as “new” carbon. Additionally, the proportion of mineral-associated organic carbon and particulate organic carbon showed that the “renewal effect” driven by the soil food web promoted the SOC to be more stable. Our study clearly illustrated that soil food web regulated the turnover of exogenous carbon inputs by and mediated soil carbon sequestration through microbial necromass accumulation.     

Experimental manipulations of microbial food web interactions in a humic lake: shifting biological drivers of bacterial community structure

A previous multiyear study observed correlations between bacterioplankton community composition (BCC) and abundance and the dynamics of phytoplankton populations and bacterivorous grazers in a humic lake. These observations generated hypotheses about the importance of trophic interactions (both top-down and bottom-up) for structuring bacterial communities in this lake, which were tested using two multifactorial food web manipulation experiments that separately manipulated the intensity of grazing and the composition of the phytoplankton community. Our results, combined with field observations, suggest that a hierarchy of drivers structures bacterial communities in this lake. While other studies have noted links between aggregate measures of phytoplankton and bacterioplankton communities, we demonstrate here correlations between succession of phytoplankton assemblages and BCC as assessed by automated ribosomal intergenic spacer analysis (ARISA). We used a novel approach linking community ARISA data to phylogenetic assignments from sequence analysis of 16S rRNA gene clone libraries to examine the responses of specific bacterial phylotypes to the experimental manipulations. The synchronous dynamics of these populations suggests that primary producers may mediate BCC and diversity through labile organic matter production, which evolves in quality and quantity during phytoplankton succession. Superimposed on this resource-mediated control of BCC are brief periods of intense bacterivory that impact bacterial abundance and composition.     

The microbial food web along salinity gradients

The microbial food web was studied along a gradient of salinity in two solar salterns used for the commercial production of salt. The different ponds in the salterns provide a wide range of ecosystems with food webs of different complexities. Abundance of prokaryotes, cell volume, prokaryotic heterotrophic production, chlorophyll a, abundance of heterotrophic flagellates, ciliates and phytoplankton were determined in several ponds in each saltern. Increases in salinity resulted in a progressive reduction in the abundance and number of different groups of eukaryotic microorganisms present, but an increase in biomass of prokaryotes. Maximal activity of both phyto- and bacterioplankton was found at a salinity of around 100 per thousand, where there was also a maximum in chlorophyll a concentration. Growth rates of heterotrophic prokaryotes decreased with increasing salinity. Bacterivory disappeared above 250 per thousand salinity, whereas other loss factors such as viral lysis appeared to be of minor importance throughout the gradient [Guixa-Boixereu et al. (1996) Aquat. Microb. Ecol. 11, 215-227].     

Structure of planktonic microbial food web in a brackish stratified Siberian lake

The distribution of primary components of the microbial community (autotrophic pico- and nanoplankton, phototrophic bacteria, heterotrophic bacteria, microscopic fungi, heterotrophic flagellates, ciliates and heliozoa) in the water column of Lake Shira, a steppe brackish-water, stratified lake in Khakasia, Siberia (Russia), were assessed in midsummer. Bacterioplankton was the main component of the planktonic microbial community, accounting for 65.3 to 75.7% of the total microbial biomass. The maximum concentration of heterotrophic bacteria were recorded in the monimolimnion of the lake. Autotrophic microorganisms contributed more significantly to the total microbial biomass in the pelagic zone (20.2–26.5%) than in the littoral zone of the lake (8.7–14.9%). First of all, it is caused by development of phototrophic sulphur bacteria at the oxic-anoxic boundary. The concentrations of most aerobic phototrophic and heterotrophic microorganisms were maximal in the upper mixolimnion. Heterotrophic flagellates dominated the protozoan populations. Ciliates were minor component of the planktonic microbial community of the lake. Heterotrophic flagellates were the most diverse group of planktonic eucaryotes in the lake, which represented by 36 species. Facultative and obligate anaerobic flagellates were revealed in the monimolimnion. There were four species of Heliozoa and only three of ciliates in the lake.     

Rapid evolution buffers ecosystem impacts of viruses in a microbial food web

Predation and parasitism often regulate population dynamics, community interactions, and ecosystem functioning. The strength of these top-down pressures is variable, however, and may be influenced by both ecological and evolutionary processes. We conducted a chemostat experiment to assess the direct and indirect effects of viruses on a marine microbial food web comprised of an autotrophic host (Synechococcus) and non-target heterotrophic bacteria. Viruses dramatically altered the host population dynamics, which in turn influenced phosphorus resource availability and the stoichiometric allocation of nutrients into microbial biomass. These virus effects diminished with time, but could not be attributed to changes in the abundance or composition of heterotrophic bacteria. Instead, attenuation of the virus effects coincided with the detection of resistant host phenotypes, suggesting that rapid evolution buffered the effect of viruses on nutrient cycling. Our results demonstrate that evolutionary processes are important for community dynamics and ecosystem processes on ecologically relevant time scales.     

Effects of temperature variability on community structure in a natural microbial food web

Climate change research has demonstrated that changing temperatures will have an effect on community‐level dynamics by altering species survival rates, shifting species distributions, and ultimately, creating mismatches in community interactions. However, most of this work has focused on increasing temperature, and still little is known about how the variation in temperature extremes will affect community dynamics. We used the model aquatic community held within the leaves of the carnivorous plant, Sarracenia purpurea, to test how food web dynamics will be affected by high temperature variation. We tested the community response of the first (bacterial density), second (protist diversity and composition), and third trophic level (predator mortality), and measured community respiration. We collected early and late successional stage inquiline communities from S. purpurea from two North American and two European sites with similar average July temperature. We then created a common garden experiment in which replicates of these communities underwent either high or normal daily temperature variation, with the average temperature equal among treatments. We found an impact of temperature variation on the first two, but not on the third trophic level. For bacteria in the high‐variation treatment, density experienced an initial boost in growth but then decreased quickly through time. For protists in the high‐variation treatment, alpha‐diversity decreased faster than in the normal‐variation treatment, beta‐diversity increased only in the European sites, and protist community composition tended to diverge more in the late successional stage. The mortality of the predatory mosquito larvae was unaffected by temperature variation. Community respiration was lower in the high‐variation treatment, indicating a lower ecosystem functioning. Our results highlight clear impacts of temperature variation. A more mechanistic understanding of the effects that temperature, and especially temperature variation, will have on community dynamics is still greatly needed.     

Turbulence and the microbial food web: effects on bacterial losses to predation and on community structure

Changes in picoplankton population abundance and growth underturbulence have been suggested to be the consequence of turbulenceaffecting larger trophic levels and hence the grazing pressure.We designed a laboratory set-up to assess the effects of turbulenceon plankton assemblages, and tested the degree of food-web complexityneeded to produce cascading effects on picoplankton and theinteractions with nutrient enrichment. Grazing pressure on bacteriawas relaxed under turbulence and we show that one trophic linkis enough to produce effects at the picoplankton level. Nutrientenrichment increased the effect of turbulence as there was morebiomass to act upon. The organisms responsible for driving thegrazing pressure shifts could not be identified since they seemedto change depending on initial conditions and experimental treatment.A trend of increased heterotrophic biomass under turbulencewas found in all cases, which can have important implicationsin community metabolism dynamics.     

Temporal and spatial variability in soil food web structure

Heterogeneity is a prominent feature of most ecosystems. As a result of environmental heterogeneity the distribution of many soil organisms shows a temporal as well as horizontal and vertical spatial patterning. In spite of this, food webs are usually portrayed as static networks with highly aggregated trophic groups over broader scales of time and space. The variability in food web structure and its consequences have seldom been examined. Using data from a Scots pine forest soil in the Netherlands, we explored (1) the temporal and spatial variability of a detrital food web and its components, (2) the effect of taxonomic resolution on the perception of variability over time and across space, and (3) the importance of organic matter quality as an explanatory factor for variability in food web composition. Compositional variability, expressed using the Bray‐Curtis similarity index, was measured over 2.5 years using a stratified litterbag design with three organic horizons per litterbag set. Variability in community composition and organic matter degradation increased over time in the litter horizon only. Seasonal variation in community composition was larger than variation between samples from the same season in different years. Horizontal spatial variability in community composition and organic matter degradation was relatively low, with no increase in variability with increasing distance between samples. Vertically, communities and organic matter degradation was more different between the non‐adjacent litter and humus horizons than between adjacent layers. These findings imply that soil food webs, at least in temperate forest plantations, are more variable than is currently appreciated in experiments and model studies, and that organic matter turnover might be an important factor explaining variability in community composition. Species composition was more variable than functional group composition, which implies that aggregated food webs will seem less sensitive to local temporal and spatial changes than they in fact are.     

Changes in the pelagic microbial food web due to artificial eutrophication

The effect of nutrient enrichment on the structure and carbon flow in the pelagic microbial food web was studied in mesocosm experiments using seawater from the northern Baltic Sea. The experiments included food webs of at least four trophic levels; (1) phytoplankton–bacteria, (2) flagellates, (3) ciliates and (4) mesozooplankton. In the enriched treatments high autotrophic growth rates were observed, followed by increased heterotrophic production. The largest growth increase was due to heterotrophic bacteria, indicating that the heterotrophic microbial food web was promoted. This was further supported by increased growth of heterotrophic flagellates and ciliates in the high nutrient treatments. The phytoplankton peak in the middle of the experiments was mainly due to an autotrophic nanoflagellate, Pyramimonas sp. At the end of the experiment, the proportion of heterotrophic organisms was higher in the nutrient enriched than in the nutrient-poor treatment, indicating increased predation control of primary producers. The proportion of potentially mixotrophic plankton, prymnesiophyceans, chrysophyceans and dinophyceans, were significantly higher in the nutrient-poor treatment. Furthermore, the results indicated that the food web efficiency, defined as mesozooplankton production per basal production (primary production + bacterial production − sedimentation), decreased with increasing nutrient status, possibly due to increasing loss processes in the food web. This could be explained by promotion of the heterotrophic microbial food web, causing more trophic levels and respiration steps in the food web.     

The carbohydrates of Phaeocystis and their degradation in the microbial food web

The ubiquity and high productivity associated with blooms of colonial Phaeocystis makes it an important contributor to the global carbon cycle. During blooms organic matter that is rich in carbohydrates is produced. We distinguish five different pools of carbohydrates produced by Phaeocystis. Like all plants and algal cells, both solitary and colonial cells produce (1) structural carbohydrates, (hetero) polysaccharides that are mainly part of the cell wall, (2) mono- and oligosaccharides, which are present as intermediates in the synthesis and catabolism of cell components, and (3) intracellular storage glucan. Colonial cells of Phaeocystis excrete (4) mucopolysaccharides, heteropolysaccharides that are the main constituent of the mucous colony matrix and (5) dissolved organic matter (DOM) rich in carbohydrates, which is mainly excreted by colonial cells. In this review the characteristics of these pools are discussed and quantitative data are summarized. During the exponential growth phase, the ratio of carbohydrate-carbon (C) to particulate organic carbon (POC) is approximately 0.1. When nutrients are limited, Phaeocystis blooms reach a stationary growth phase, during which excess energy is stored as carbohydrates. This so-called overflow metabolism increases the ratio of carbohydrate-C to POC to 0.4–0.6 during the stationary phase, leading to an increase in the C/N and C/P ratios of Phaeocystis organic matter. Overflow metabolism can be channeled towards both glucan and mucopolysaccharides. Summarizing the available data reveals that during the stationary phase of a bloom glucan contributes 0–51% to POC, whereas mucopolysaccharides contribute 5–60%. At the end of a bloom, lysis of Phaeocystis cells and deterioration of colonies leads to a massive release of DOM rich in glucan and mucopolysaccharides. Laboratory studies have revealed that this organic matter is potentially readily degradable by heterotrophic bacteria. However, observations in the field of accumulation of DOM and foam indicate that microbial degradation is hampered. The high C/N and C/P ratios of Phaeocystis organic matter may lead to nutrient limitation of microbial degradation, thereby prolonging degradation times. Over time polysaccharides tend to self-assemble into hydrogels. This may have a profound effect on carbon cycling, since hydrogels provide a vehicle to move DOM up the size spectrum to sizes subject to sedimentation. In addition, it changes the physical nature and microscale structure of the organic matter encountered by bacteria which may affect the degradation potential of the Phaeocystis organic matter.     

Direct and indirect food web regulation of microbial decomposers in headwater streams

The direct and indirect regulation of primary productivity has been well established in autotrophic‐based ecosystems; however, less is known about the processes affecting decomposers in detrital‐based ecosystems. Because, small headwater, woodland streams are a dominate feature in most ecosystems and are tightly linked to terrestrial detritus, understanding decomposer‐mediated functions in these systems is critical for understanding carbon processes across the landscape. In this light, we conducted a microcosm and mesocosm experiment to test the direct and indirect food web effects on decomposers in small stream ecosystems. The results from the microcosm experiment supported an existing literature, demonstrating that nutrients directly stimulate decomposers and that microbivores directly reduce decomposers. Based on well‐founded food web theory in autotrophic systems, we predicted that fishes from different trophic‐functional guilds would indirectly stimulate decomposers by enhancing dissolved nutrients and by reducing microbivore densities. Our mesocosm experiment partially supported these predictions. Specifically, we found that fishes that consumed mostly terrestrial foods increased decomposers from the bottom–up by enhancing allochthonous nutrient loading into the stream ecosystems. Contrary to our predictions, however, predatory fishes that consume microbivores did not increase decomposers from the top–down. Rather, in streams with the predatory fish species, microbivores increased (rather than decreased) on leaf litter. This may have resulted from an experimental artifact associated with refuge provided by leaf packs. In conclusion, our data demonstrate that decomposers are regulated by similar direct and indirect processes important in autotrophic‐based ecosystems. This provides further evidence that food web processes can regulate leaf decomposition and flux of detrital carbon through ecosystems.     

Identification of dominant bacterial phylotypes in a cadmium-treated forest soil

The presence of heavy metals in soils can lead to changes in microbial community structure, characterized by the dominance of groups that are able to tolerate contamination. Such groups may provide good microbial indicators of heavy-metal pollution in soil. Through terminal restriction fragment length polymorphism (T-RFLP) profiling, changes in the bacterial community structure of an acidic forest soil that had been incubated with cadmium (Cd) for 30 days were investigated. T-RFLP revealed, in particular, three operational taxonomic units (OTUs) strongly dominating in relative abundance in the contaminated soil. By cloning of the amplified 16S rRNA genes and partial sequencing of 25 clones, these three dominant OTUs were phylogenetically characterized. One dominant OTU in the cadmium-contaminated soil was derived from Betaproteobacteria, genus Burkholderia, and the other two were from uncultured members of the class Actinobacteria, closely related to the genus Streptomyces. To confirm T-RFLP data, four primers were designed on the basis of this study's dominant sequences, targeting the OTUs corresponding to Burkholderia or Actinobacteria. Real-time PCR showed that Burkholderia target sequences were more abundant in cadmium-treated soil (7.8 x 10(7)+/- 3.0 x 10(7) targets g(-1) soil) than in untreated soil (4.0 x 10(6)+/- 8.9 x 10(5) targets g(-1) soil). It was concluded that the genus Burkholderia includes species that may be particularly dominant under cadmium contamination.     

Dynamics of microbial planktonic food web components during a river flash flood in a Mediterranean coastal lagoon

Episodic river flash floods, characteristic of Mediterranean climates, are suspected to greatly affect the functioning of microbial food webs. For the first time, the abundance, biomass and diversities of microbial food web components were studied before and during 4 consecutive days after a flash flood that occurred in November 2008, in the surface waters of five stations along a salinity gradient from 20 to 36 in the Thau lagoon. Eukaryotic pico- and nanophytoplankton were discharged from the river into the lagoon and increased by 30- and 70-fold, respectively. Bacteria increased by only 2-fold in the lagoon, from around 4–8 × 10⁶ cells ml⁻¹, probably benefiting from river nutrient input. Chlorophyll a increased 4-fold, and pigment biomarkers showed that the dinophyceae, prasinophyceae and prymnesiophyceae were sensitive to the flood perturbation, whereas the bacillariophyceae, cryptophyceae and chlorophyceae were resistant and/or transported to the lagoon from the river. Predator responses were more complex as total heterotrophic flagellate abundance decreased slightly, whereas those of specific naked ciliates increased, particularly for Uronema sp. The flood also induced a specific change in diversity, from a community dominated by Strobilidium spiralis to a community dominated by Uronema sp. The tintinnid community was particularly sensitive to the flood event as the abundance of all species decreased greatly. The high increases in biomass, mainly brought by the river during the flood, could have eventually sedimented to the benthic layer and/or been transported further into the lagoon, supporting the pelagic food web, or have even been exported to the Mediterranean Sea.     

农田土壤食物网管理的原理与方法

土壤食物网在维持生态系统生产力和健康等方面起着重要作用,但现代农业中,化肥农药等外部投入已经改变或部分替代了土壤食物网的功能,由此也造成一系列的环境问题。为了协调作物高产与环境保护的利益,需要对土壤食物网进行管理,使土壤食物网符合作物生长的需要,即建立健康土壤食物网。管理土壤食物网有两种方式:(1)直接方式,即通过调节食物网各个功能群的组成来管理土壤食物网;(2)间接方式,即根据农田土壤食物网以自下而上调控方式为主、强调低营养阶层的资源限制的原理,通过调节碎屑的数量和质量来管理食物网。在这两种调控方式中,都需要对被管理的食物网进行监测,监测的方式也分两种,一种是直接测定食物网各功能群的数量和生物量,另外一种方式即以线虫为工具来反应土壤食物网的结构。