Divergence of feeding channels within the soil food web determined by ecosystem type

Understanding trophic linkages within the soil food web (SFW) is hampered by its opacity, diversity, and limited niche adaptation. We need to expand our insight between the feeding guilds of fauna and not just count biodiversity. The soil fauna drive nutrient cycling and play a pivotal, but little understood role within both the carbon (C) and nitrogen (N) cycles that may be ecosystem dependent. Here, we define the structure of the SFW in two habitats (grassland and woodland) on the same soil type and test the hypothesis that land management would alter the SFW in these habitats. To do this, we census the community structure and use stable isotope analysis to establish the pathway of C and N through each trophic level within the ecosystems. Stable isotope ratios of C and N from all invertebrates were used as a proxy for trophic niche, and community‐wide metrics were obtained. Our empirically derived C/N ratios differed from those previously reported, diverging from model predictions of global C and N cycling, which was unexpected. An assessment of the relative response of the different functional groups to the change from agricultural grassland to woodland was performed. This showed that abundance of herbivores, microbivores, and micropredators were stimulated, while omnivores and macropredators were inhibited in the grassland. Differences between stable isotope ratios and community‐wide metrics, highlighted habitats with similar taxa had different SFWs, using different basal resources, either driven by root or litter derived resources. Overall, we conclude that plant type can act as a top‐down driver of community functioning and that differing land management can impact on the whole SFW.     

Quantitative patterns of development of community of <Emphasis Type="Italic">Pseudomonas aeruginosa</Emphasis> dissociants

The stationary phase of batch culture of Pseudomonas aeruginosa dissociants has been described by a variational model of consumption and growth. The generalized entropy functional was used as the objective function. The model parameters include the requirements of the dissociants for the main nutrients: carbon, nitrogen, and phosphorus. The variational model was used to calculate the limiting regions and microbial community composition during stationary growth for different initial combinations of the resources as a function of the limiting resources. A correspondence between the experimental data and model calculations has been demonstrated. A possibility to control the community structure is discussed.     

Testing the limits of 454 pyrotag sequencing: reproducibility, quantitative assessment and comparison to T-RFLP fingerprinting of aquifer microbes

The characterization of microbial community structure via 16S rRNA gene profiling has been greatly advanced in recent years by the introduction of amplicon pyrosequencing. The possibility of barcoding gives the opportunity to massively screen multiple samples from environmental or clinical sources for community details. However, an on-going debate questions the reproducibility and semi-quantitative rigour of pyrotag sequencing, similar to the early days of community fingerprinting. In this study we demonstrate the reproducibility of bacterial 454 pyrotag sequencing over biological and technical replicates of aquifer sediment bacterial communities. Moreover, we explore the potential of recovering specific template ratios via quantitatively defined template spiking to environmental DNA. We sequenced pyrotag libraries of triplicate sediment samples taken in annual sampling campaigns at a tar oil contaminated aquifer in Düsseldorf, Germany. The abundance of dominating lineages was highly reproducible with a maximal standard deviation of ~4% read abundance across biological, and ~2% across technical replicates. Our workflow also allows for the linking of read abundances within defined assembled pyrotag contigs to that of specific 'in vivo' fingerprinting signatures. Thus we demonstrate that both terminal restriction fragment length polymorphism (T-RFLP) analysis and pyrotag sequencing are capable of recovering highly comparable community structure. Overall diversity was roughly double in amplicon sequencing. Pyrotag libraries were also capable of linearly recovering increasing ratios (up to 20%) of 16S rRNA gene amendments from a pure culture of Aliivibrio fisheri spiked to sediment DNA. Our study demonstrates that 454 pyrotag sequencing is a robust and reproducible method, capable of reliably recovering template abundances and overall community structure within natural microbial communities.     

A Method of Profiling Microbial Communities Based on a Most-Probable-Number Assay That Uses BIOLOG Plates and Multiple Sole Carbon Sources

A new approach to the community-level BIOLOG assay was proposed. This assay, which we call the BIOLOG-MPN assay, is a most-probable-number (MPN) assay that uses BIOLOG plates and multiple sole carbon sources, and the profiles obtained by this assay consist of MPNs estimated for the substrates in the BIOLOG plates. In order to demonstrate the performance of the BIOLOG-MPN assay, it was applied to pure cultures, model bacterial communities that contain two strains in different ratios, and microbial community samples. MPN estimation using BIOLOG plates worked well for the substrates on which utilizers can grow at a sufficiently high rate for color development under the conditions of the assay procedure. Furthermore, the results obtained using model communities showed that the MPNs obtained reflected the mixing ratios of pure cultures in the model communities. The profiles obtained using model communities and community samples were differentiated properly by statistical analyses. The results suggest that the BIOLOG-MPN assay is a promising procedure for obtaining a quantitative picture of the community structure.     

A method of profiling microbial communities based on a most-probable-number assay that uses BIOLOG plates and multiple sole carbon sources.

A new approach to the community-level BIOLOG assay was proposed. This assay, which we call the BIOLOG-MPN assay, is a most-probable-number (MPN) assay that uses BIOLOG plates and multiple sole carbon sources, and the profiles obtained by this assay consist of MPNs estimated for the substrates in the BIOLOG plates. In order to demonstrate the performance of the BIOLOG-MPN assay, it was applied to pure cultures, model bacterial communities that contain two strains in different ratios, and microbial community samples. MPN estimation using BIOLOG plates worked well for the substrates on which utilizers can grow at a sufficiently high rate for color development under the conditions of the assay procedure. Furthermore, the results obtained using model communities showed that the MPNs obtained reflected the mixing ratios of pure cultures in the model communities. The profiles obtained using model communities and community samples were differentiated properly by statistical analyses. The results suggest that the BIOLOG-MPN assay is a promising procedure for obtaining a quantitative picture of the community structure.     

Community composition and size structure of murid rodents in relation to the biogeography of the Japanese archipelago

We investigated the geographical patterns of community composition and size structure of murid rodent assemblages in Japan. Rodent faunal composition showed three biogeograpbic zones in the studied area (Hokkaido, northern Honshu and southern Honshu), which are characterized by endemic species or genera. There was a large discrepancy between distribution patterns of murine species, which are generalist and widespread in Japan, and arvicoline species, which are more specialized and locally restricted. We also found a strong degree of nestedness of the murid rodent fauna, i.e. smaller faunas were subsets of larger ones, which is typical of relict fauna. The structure of murid rodent assemblages was studied using the size and shape of the lower incisor, in order to test for the effect of interspecific competition on community-wide patterns. We used two different approaches: one tests for regularity in the size structure of the community (Barton and David test), and the other one tests for minimum mean overlap size in the community between species (randomization procedure). There was no congruence between the results of the two tests: we did not find any case of regular size structure, whereas mean size overlaps were minimum or even zero in about half of the cases studied. Thus, the evolution of rodent communities on islands seems to be characterized by minimization of size overlaps, perhaps as a result of interspecific competition. Also, the reduction of island area, which is correlated with a decrease in species richness, is accompanied by an increase in Hutchinsonian size ratios and a decrease in the total size range of the community. These patterns may be linked to the reduced diversity of environmental resources on islands.     

Uncoupling the effects of shade and food resources of vegetation on Mediterranean ants: an experimental approach at the community level

Vegetation is one of the main factors affecting the composition and structure of ant communities. The effect of vegetation is both by offering food resources and by modifying the proportion of ground cover exposed to shade conditions. However, it is difficult in field studies to uncouple the effects of food resources and shade on animal communities. The goal of this study was to analyze experimentally the effects of vegetation through food and shade supply on the structure and composition of a Mediterranean ant community. We have crossed these two factors in a factorial design where we have eliminated vegetation in experimental treatments and we have simulated the effects of vegetation by manipulating separately the supply of food resources and shade. The expected decrease in ant abundance and richness in plots without food resources but with shade was only partially confirmed by the results, because there was a decrease in the number of ant species but not a significant decrease in overall ant abundance in plots without food resources. We did not confirm the second hypothesis that the decrease in shade while maintaining food resources resulted in an increase of heat-tolerant, subordinate species and, consequently, ant richness. Species composition differed in the different experimental treatments. Stress-tolerant species were abundant in areas without shade and without food resources. Heat-tolerant species were mainly present in plots without shade but with food resources. Finally, species with high requirements of shade and/or food resources were associated to control plots with both shade and food resources from vegetation. Overall, this study provides an experiment that uncouples experimentally shade and food resources and dissects their effects on the whole ant community, and shows that the effects of the two factors are independent and affect different components of ant community structure and composition.     

The effects of wildfire on Spheciformes wasp community structure: the importance of local habitat conditions

Changes of the structure of a community of Spheciformes wasps (Hymenoptera: Apoidea) along a 15 year recovery gradient after wildfires in a Mediterranean agroecosystem are reported and analysed. The species that contribute to determining the structure, change in dominance amongst the most abundant species, and variation in guild structure of the community with the passage of time since fire, as well as the environmental variables contributing to the structure of the community are also analyzed. Mediterranean Spheciformes communities are highly resistant to fire. The sampling year, representative of different climate conditions, and the time since the fire, were the main variables which affected community variation local conditions of the habitat was more important than time since fire in determining community. Local conditions; presence of trophic resources, nesting sites, and presence of prey for feeding the larvae, depended on climatological conditions and the time since fire. Variations were detected in the dominance values of the most abundant species, together with displacements among species within the same genus, as a function of the local conditions, the existing resources, and the time since the wildfire. Therefore, change in community structure cannot be attributed solely to the effect of the fire, as both climatic and environmental conditions contribute to community structure.     

Links between resources, C metabolism and the major components of bacterioplankton community structure across a range of freshwater ecosystems

We explored the patterns in bacterioplankton community metabolism (BCM) and four components of community structure [composition (BCC), metabolic capacities (MC), physiological structure (PS) and single-cell characteristics (SCC)], between lakes, rivers and marshes within a watershed in Québec, to assess the connections that exist between them and with the main resources (organic matter, nutrients). Habitat types were well segregated by both resources and BCM and their corresponding dissimilarity matrices were significantly correlated, suggesting that BCM tracks resource conditions in a consistent manner across ecosystem types. MC also segregated the various habitats and was correlated to BCM but less so to resources, whereas BCC at times resulted in a clear separation of habitats, but was rarely correlated to resources and never to BCM, suggesting a higher degree of ecosystem specificity at this particular level. Finally, there was no clear separation of habitats in terms of PS and SCC, and none covaried with resources or BCM. The habitat patterns based on these different components of structure were rarely correlated to each other, indicating weak deterministic connections between them. MC appears to mediate the link between resources and BCM more directly and consistently across systems; BCC appears to be more influenced by ecosystem-specific factors that weaken its overall connection to both resources and BCM, whereas PS and SCC show no discernible patterns. Our results thus suggest that the bottom-up regulation of BCM by resources is mediated by complex shifts within components of community structure that can be directional, ecosystem-specific or apparently random, which combined nevertheless result in a systematic overall response to resources in terms of C metabolism.     

A taxonomic wish-list for community ecology

Community ecology seeks to explain the number and relative abundance of coexisting species. Four research frontiers in community ecology are closely tied to research in systematics and taxonomy: the statistics of species richness estimators, global patterns of biodiversity, the influence of global climate change on community structure, and phylogenetic influences on community structure. The most pressing needs for taxonomic information in community ecology research are usable taxonomic keys, current nomenclature, species occurrence records and resolved phylogenies. These products can best be obtained from Internet-based phylogenetic and taxonomic resources, but the lack of trained professional systematists and taxonomists threatens this effort. Community ecologists will benefit most directly from research in systematics and taxonomy by making better use of resources in museums and herbaria, and by actively seeking training, information and collaborations with taxonomic specialists.     

Characterization of the sediment bacterial community in groundwater discharge zones of an alkaline fen: a seasonal study.

The cell density, activity, and community structure of the bacterial community in wetland sediments were monitored over a 13-month period. The study was performed at Cedar Bog, an alkaline fen. The objective was to characterize the relationship between the sediment bacterial community in groundwater upwelling zones and the physical and chemical factors which might influence the community structure and activity. DNA, protein, and lipid synthesis were measured at three different upwelling zones by using [3H]thymidine, [14C]leucine, and [14C]glucose incorporation, respectively. The physiological status (apparent stress) of the consortium was assessed by comparing [14C]glucose incorporation into membrane and that into storage lipids. Bacterial cell density was determined by acridine orange direct counts, and gross bacterial community structure was determined by bisbenzimidazole-cesium chloride gradient analysis of total bacterial community DNA. Both seasonal and site-related covariation were observed in all estimates of bacterial biomass and activity. Growth rate estimates and cell density peaked in late July at 2.5 x 10(8) cells/g/day and 2.7 x 10(9) cells/g, respectively, and decreased in December to 2.0 x 10(7) cells/g/day and 1.5 x 10(9) cells/g, respectively. Across sites, membrane-to-storage-lipid ratios were generally highest in late spring and peaked in September for one site. Overall, the data indicate dynamic seasonal differences in sediment bacterial community activity and physiology, possibly in response to changing physical and chemical environmental factors which included the C/N/P ratios of the perfusing groundwater. By contrast, total cell numbers were rather constant, and community structure analysis indicated that the overall community structure was similar throughout the study.     

新疆乌尔禾地区盐渍土壤耐盐细菌多样性与群落结构研究

研究新疆北部乌尔禾地区盐渍土壤中微生物群落结构及多样性,以期发现新的高盐环境耐盐性微生物资源菌株。采用传统分离培养法获得可培养耐盐菌株并对菌株形态学、16S rRNA基因测序、耐盐特性进行研究,同时结合高通量测序技术分析新疆乌尔禾地区盐渍土壤耐盐细菌的多样性与群落结构。共分离得到耐盐细菌11株,分属6个属,均为中度耐盐菌,以芽胞杆菌属(Bacillus)为优势菌。对盐渍土壤微生物16S rRNA(V3～V4)基因测序,共获得细菌序列290 952条,分属24个门410个属,变形菌门(Proteobacteria, 60.31%)、厚壁菌门(Firmicutes, 21.52%)、拟杆菌门(Bacteroidetes, 6.9%)和放线菌门(Actinobacteria, 6%)相对丰度较高。优势属为克吕沃尔菌属(Kluyvera,21%)、Hafnia-Obesumbacterium(19.6%)和假单胞菌属(Pseudomonas,7.5%)。结果表明,新疆乌尔禾地区盐渍土壤耐盐细菌优势菌群以芽胞杆菌属(Bacillus)居多,细菌群落结构较复杂,潜在可利用微生物资源较为丰富,对高盐极端环境耐盐微生物新资源有进一步研究的意义。     

Relationships between the human sex ratio and the woman’s microenvironment

Independent samples of women were surveyed to test Trivers and Willard’s hypothesis that the mother’s condition and her ability to invest in her offspring affect the (secondary) sex ratio of her offspring. Patterns of sex ratios (number of males per 100 females) were analyzed in conjunction with four attributes of a mother’s microenvironment: level of health in her community, family structure, relative access to resources, and her birthing history. The results inferentially support the hypothesis that the microenvironment of the woman would act to bias the sex ratio of her offspring. These specific data lend support to Trivers and Willard’s general hypothesis.     

Links between soil microbial communities and plant traits in a species‐rich grassland under long‐term climate change

Climate change can influence soil microorganisms directly by altering their growth and activity but also indirectly via effects on the vegetation, which modifies the availability of resources. Direct impacts of climate change on soil microorganisms can occur rapidly, whereas indirect effects mediated by shifts in plant community composition are not immediately apparent and likely to increase over time. We used molecular fingerprinting of bacterial and fungal communities in the soil to investigate the effects of 17 years of temperature and rainfall manipulations in a species‐rich grassland near Buxton, UK. We compared shifts in microbial community structure to changes in plant species composition and key plant traits across 78 microsites within plots subjected to winter heating, rainfall supplementation, or summer drought. We observed marked shifts in soil fungal and bacterial community structure in response to chronic summer drought. Importantly, although dominant microbial taxa were largely unaffected by drought, there were substantial changes in the abundances of subordinate fungal and bacterial taxa. In contrast to short‐term studies that report high resistance of soil fungi to drought, we observed substantial losses of fungal taxa in the summer drought treatments. There was moderate concordance between soil microbial communities and plant species composition within microsites. Vector fitting of community‐weighted mean plant traits to ordinations of soil bacterial and fungal communities showed that shifts in soil microbial community structure were related to plant traits representing the quality of resources available to soil microorganisms: the construction cost of leaf material, foliar carbon‐to‐nitrogen ratios, and leaf dry matter content. Thus, our study provides evidence that climate change could affect soil microbial communities indirectly via changes in plant inputs and highlights the importance of considering long‐term climate change effects, especially in nutrient‐poor systems with slow‐growing vegetation.     

Altitudinal patterns of diversity and functional traits of metabolically active microorganisms in stream biofilms

Resources structure ecological communities and potentially link biodiversity to energy flow. It is commonly believed that functional traits (generalists versus specialists) involved in the exploitation of resources depend on resource availability and environmental fluctuations. The longitudinal nature of stream ecosystems provides changing resources to stream biota with yet unknown effects on microbial functional traits and community structure. We investigated the impact of autochthonous (algal extract) and allochthonous (spruce extract) resources, as they change along alpine streams from above to below the treeline, on microbial diversity, community composition and functions of benthic biofilms. Combining bromodeoxyuridine labelling and 454 pyrosequencing, we showed that diversity was lower upstream than downstream of the treeline and that community composition changed along the altitudinal gradient. We also found that, especially for allochthonous resources, specialisation by biofilm bacteria increased along that same gradient. Our results suggest that in streams below the treeline biofilm diversity, specialisation and functioning are associated with increasing niche differentiation as potentially modulated by divers allochthonous and autochthonous constituents contributing to resources. These findings expand our current understanding on biofilm structure and function in alpine streams.     

Seasonal changes in a cactus‐hoverfly (Diptera: Syrphidae) network

1. We analysed a cacti‐syrphid community focusing on the exploitation of decaying cacti resources by the flies, i.e. if exploitation exhibited a nested topology as a structural pattern, or whether it was temporally random. If availability of cactus resources was predictable during the rainy season, it would then be exploited by a more structured community, or as resource availability would be unpredictable during the dry season, we should expect it to be exploited by a random community. 2. We registered 12 Copestylum species (9 in dry and 11 in rainy season). Four cactus species were recorded per season, three were shared between seasons. 3. The community of Copestylum larvae in the rainy season was not randomly assembled but highly nested, revealing a highly structured pattern of resource use. It exhibited a random organization for the dry season. The high nestedness value obtained for the rainy season suggests that factors along with competition must play a major role in determining community structure. 4. Succession in the cacti‐syrphid community mediated by microorganisms involved in necrosis is an important factor structuring nested subsets. The studied networks were small, which may limit the power of the analysis, and strong conclusions could also be limited.     

Performance and Microbial Diversity of a Trickle‐Bed Air Biofilter under Interchanging Contaminants

A trickle‐bed air biofilter (TBAB) was evaluated under conditions of interchanging the feed volatile organic compounds (VOCs) in the sequence methyl ethyl ketone (MEK), toluene, methyl isobutyl ketone (MIBK), styrene, and then back to MEK. The obtained performance results revealed that the biofilter provided high removal efficiency within the critical loading of each VOC, which was previously defined in the non‐interchanging VOC fed biofilter. The biofilter easily acclimated to the oxygenated compounds (MEK and MIBK), but re‐acclimation was delayed for the aromatic compounds (toluene and styrene). Ratios of the molar mass of CO₂ produced per molar mass of VOC removed were investigated. It has been found that the ratios for the aromatic compounds closely resembled the theoretical complete chemical oxidation based ratios while larger differences were encountered with the oxygenated compounds. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA genes was used to assess the impact of interchanging VOCs on the bacterial community structure in the biofilter. The results from denaturing gradient gel electrophoresis (DGGE) showed that the structure of the microbial community in the biofilter was different after each interchange of VOCs.     

宁夏荒漠草原植物群落结构和物种多样性研究

采用样方法对宁夏荒漠草原植物群落进行了调查,对群落结构、功能群物种组成和物种多样性以及群落生产力的关系进行探讨。结果表明,群落生产力除受物种多样性的影响外,也受物种本身特征和环境资源的影响。在荒漠草原中功能群盖度与群落初级生产力无显著的相关关系。功能群内物种多样性、物种数和个体数量上呈现一定的互为消长关系。     

Population size and areas of stratification in the variational model of ecosystem

The formulations of the variational task for finding the relative population size of species in community at a stationary stage of growth and of the theorem of stratification are given. Algorithms of finding the relative size of populations for communities consisting of two and three species consuming two or three resources were obtained. The borders of areas of stratification were described in which one, two, or three resources are limiting. For two species and two resources, the formulae of the dependence of relative size on the ratio of resources were derived, and the shape of this dependence for real requirements of species was demonstrated.     

元江锥群落垂直结构的构建机制初探

基于功能性状探讨物种共存机制,已成为近年来群落生态学研究的热点内容。为探讨群落垂直结构构建的成因,该研究以昆明筇竹寺地区的半湿润常绿阔叶林为对象,调查乔木层、灌木层及草本层不同层次间植物叶片的功能性状。结果表明:(1)植物各功能性状均存在不同程度的随层次变化的趋势。(2)按照植物的生活型将元江锥群落分为乔木、灌木以及草本3层,与功能性状的聚类结果基本一致。(3)乔木、灌木和草本3个层次的S.E.S PW值均小于0,可知群落内物种的功能性状结构均呈现显著的发散。综上结果认为,植物群落不同物种的叶片功能特征对群落垂直方向上不同光照和水分条件组合的适应是群落垂直结构构成的主要影响因素,支持生境过滤是群落垂直结构构建的主要生态过程; 在不同层次内的物种具有不同的功能性状,同一层次内通过竞争排斥加大物种多样性; 群落垂直结构的形成是群落内垂直方向上环境因子发生变化的结果,对资源有不同需求的物种分布在不同空间高度上,群落垂直结构则是对资源的有效利用,增加了群落内物种多样性。