Metabolic and Demographic Feedbacks Shape the Emergent Spatial Structure and Function of Microbial Communities

Microbes are predominantly found in surface-attached and spatially structured polymicrobial communities. Within these communities, microbial cells excrete a wide range of metabolites, setting the stage for interspecific metabolic interactions. The links, however, between metabolic and ecological interactions (functional relationships), and species spatial organization (structural relationships) are still poorly understood. Here, we use an individual-based modelling framework to simulate the growth of a two-species surface-attached community where food (resource) is traded for detoxification (service) and investigate how metabolic constraints of individual species shape the emergent structural and functional relationships of the community. We show that strong metabolic interdependence drives the emergence of mutualism, robust interspecific mixing, and increased community productivity. Specifically, we observed a striking and highly stable emergent lineage branching pattern, generating a persistent lineage mixing that was absent when the metabolic exchange was removed. These emergent community properties are driven by demographic feedbacks, such that aid from neighbouring cells directly enhances focal cell growth, which in turn feeds back to neighbour fecundity. In contrast, weak metabolic interdependence drives conflict (exploitation or competition), and in turn greater interspecific segregation. Together, these results support the idea that species structural and functional relationships represent the net balance of metabolic interdependencies.     

Spatial and temporal habitat use patterns for salt marsh nekton: implications for ecological functions

We synthesized information on temporal and spatial patterns of salt marsh habitat use by nekton in order to infer the importance of five main types of marsh function: reproduction, foraging, refuge from predation, refuge from stressful environmental conditions and environmental enhancement of physiology. We then extended the concept that intertidal gradients regulate habitat use patterns of nekton to a more universal concept that applies to all salt marsh habitats. We contend that all marsh habitats are linked to each other and to adjacent estuarine habitats along a depth gradient that mediates gradients in abiotic and biotic conditions. Tidal, diel and seasonal shifts in the magnitude and direction of these gradients result in gradients in tidal, diel and seasonal variation in biotic and abiotic conditions within the salt marsh. Collectively these gradients form the `marsh gradient'. We propose that patterns of marsh use and ecological function for nekton result primarily from physiological and behavioral responses to this marsh gradient. A comparison of habitat use patterns in the context of the marsh gradient is an important – and underutilized – method to study marsh function and essential fish habitat. We note that our limited insight into the function of the marsh habitat results from a significant lack of information on the occurrence and causes of tidal, diel and ontogenetic marsh use patterns by nekton; this is particularly relevant with respect to data on the variation in environmental conditions along marsh gradients over tidal, diel and seasonal cycles and on how environmental variation on these scales influences nekton behavior, growth and survival.     

Oxygen modulates the growth of skin fibroblasts

Elevated oxygen tensions are inhibitory to the growth of skin fibroblasts. Skin fibroblasts grow better at oxygen tensions below 137 mm Hg regardless of seeding density. A wide range of oxygen tensions, including those in the physiological range, strongly modulate the growth of human skin fibroblasts. There were no significant differences between the responses of fetal and postnatal cell lines to changes in ambient oxygen tension. In all cases, higher oxygen tensions significantly impeded cell growth. Seeding cells at 10(4) cells/cm(2) afforded some protection from the deleterious effects of hyperoxia. Oxygen tensions exceeding the amount present in ambient room air also impeded cell growth at this higher seeding density, but the effect did not become significant until the oxygen partial pressure reached 241 mm Hg. At lower oxygen tensions, cells seeded at 10(3) cells/cm(2) grew more rapidly than did cells seeded at 10(4) cells/cm(2). These findings may have implications for the treatment of poorly healing wounds with hyperbaric oxygen.     

The Structure of Microbial Communities in Soil and the Lasting Impact of Cultivation

The structure of microbial communities was examined as a function of community composition and the relative abundance of specific microbial groups to examine the effects that plant community composition and land-use history have on microbial communities in the soil. The sites sampled were part of the Long Term Ecological Research (LTER) project in agricultural ecology at the W.K. Kellogg Biological Station of Michigan State University (Hickory Corners, MI) and included both active and abandoned agricultural fields as well as nearby fields that had never been cultivated. Microbial community structure was assessed by extracting total RNA from soil samples and using 16S rRNA-targeted oligonucleotide probes to quantify the abundance of rRNA from the alpha, beta, and gamma Proteobacteria, the Actinobacteria (Gram positive bacteria with a high mol % G+C genome), the Bacteria, and the Eukarya. In addition, soil microbial communities were characterized by examining fluorescently tagged terminal restriction fragment length polymorphisms (T-RFLP) in PCR amplified 16S rDNA. Microbial community structure was observed to be remarkably similar among plots that shared a long-term history of agricultural management despite differences in plant community composition and land management that have been maintained on the plots in recent years. In contrast, microbial community structure differed significantly between fields that had never been cultivated and those having a long-term history of cultivation.     

Spatial and Temporal Biogeography of Soil Microbial Communities in Arid and Semiarid Regions

Microbial communities in soils may change in accordance with distance, season, climate, soil texture and other environmental parameters. Microbial diversity patterns have been extensively surveyed in temperate regions, but few such studies attempted to address them with respect to spatial and temporal scales and their correlations to environmental factors, especially in arid ecosystems. In order to fill this gap on a regional scale, the molecular fingerprints and abundance of three taxonomic groups – Bacteria, α-Proteobacteria and Actinobacteria – were sampled from soils 0.5–100 km apart in arid, semi-arid, dry Mediterranean and shoreline Mediterranean regions in Israel. Additionally, on a local scale, the molecular fingerprints of three taxonomic groups – Bacteria, Archaea and Fungi – were sampled from soils 1 cm–500 m apart in the semi-arid region, in both summer and winter. Fingerprints of the Bacteria differentiated between all regions (P<0.02), while those of the α-Proteobacteria differentiated between some of the regions (0.01<P<0.09), and actinobacterial fingerprints were similar among all regions (P>0.05). Locally, fingerprints of archaea and fungi did not display distance-decay relationships (P>0.13), that is, the dissimilarity between communities did not increase with geographic distance. Neither was this phenomenon evident in bacterial samples in summer (P>0.24); in winter, however, differences between bacterial communities significantly increased as the geographic distances between them grew (P<0.01). Microbial community structures, as well as microbial abundance, were both significantly correlated to precipitation and soil characteristics: texture, organic matter and water content (R²>0.60, P<0.01). We conclude that on the whole, microbial biogeography in arid and semi-arid soils in Israel is determined more by specific environmental factors than geographic distances and spatial distribution patterns.     

Microbial Communities on the Monuments of Moscow and St. Petersburg: Biodiversity and Trophic Relations

Stone monuments situated in the Alexander Nevsky Abbey, the Summer Garden, and the Smolenskoe Cemetery, St. Petersburg, and marble and limestone sculptures and tombstones situated in the Novodevichy Convent and the Donskoy Monastery, Moscow, were investigated for their microbial contamination. The architectural objects studied date back to the 12th century. The monuments in the Alexander Nevsky Abbey were found to be severely contaminated with micromycetes belonging to 24 genera (primarily of the class Deuteromycetes). The analysis of the samples taken from the monuments of the Donskoy Monastery by the serial dilution technique showed that they were contaminated with bacteria at a density of (1–1.7) × 10⁵ cells/g. This value, however, turned out to be 1 to 2 orders greater when the bacterial population was evaluated by the luciferin–luciferase method. We succeeded in identifying 12 bacterial genera; however, this number may be increased in the course of further studies. Some preventive measures to control the biodeterioration of stone heritage are discussed.     

活性氧对大豆下胚轴线粒体结构与功能的损伤

采用百草枯、H_2O_2和Fenton反应作为外源活性氧,探讨了活性氧对大豆下胚轴离体线粒体的部分功能与结构的伤害。结果表明,活性氧O_2~-,H_2O_2和·OH都能引起线粒体结构的迅速膨胀,呼吸控制比率和氧化磷酸化效率降低,以及细胞色素氧化酶活力下降。通过对线粒体膜脂氢过氧化物和脂质共轭二烯的吸收光谱分析,阐明了活性氧对线粒体的损伤是与膜脂过氧化作用密切相关的。     

Oxygen Uptake In Cysts and Trophozoites of Giardia Lamblia

ABSTRACT. Oxygen uptake in cysts and trophozoites of the parasitic protozoan Giardia lamblia was examined. Both showed oxygen uptake activity, but that of cysts was only 10% to 20% that of trophozoites. Oxygen dependence of oxygen uptake in cysts and trophozoites showed oxygen maxima above which oxygen uptake decreased. the oxygen concentration at which the oxygen uptake rate was greatest was higher for trophozoites than for cysts. the effect of various inhibitors on cyst and trophozoithe oxygen uptake suggested that flavoproteins and quinones play some role in oxygen uptake. the substrate specificities and the effect of inhibitors on G. lamblia trophozoites were similar to those observed for G. muris. Metronidazole, the drug most commonly used in treatment of giardiasis, inhibited oxygen uptake and motility in trophozoites; however, it had no obvious effect on either oxygen uptake or excystation in cysts. Menadione, a redox cycling naphthaquinone, first stimulated, then completely inhibited, oxygen uptake in cysts and trophozoites; a complete loss of cyst viability and trophozoite motility was also observed. the effect of menadione on G. Iamblia may indicate that redox cycling compounds have potential as chemotherapeutic agents for the treatment of giardiasis.     

Association of Host and Microbial Species Diversity across Spatial Scales in Desert Rodent Communities

Relationships between host and microbial diversity have important ecological and applied implications. Theory predicts that these relationships will depend on the spatio-temporal scale of the analysis and the niche breadth of the organisms in question, but representative data on host-microbial community assemblage in nature is lacking. We employed a natural gradient of rodent species richness and quantified bacterial communities in rodent blood at several hierarchical spatial scales to test the hypothesis that associations between host and microbial species diversity will be positive in communities dominated by organisms with broad niches sampled at large scales. Following pyrosequencing of rodent blood samples, bacterial communities were found to be comprised primarily of broad niche lineages. These communities exhibited positive correlations between host diversity, microbial diversity and the likelihood for rare pathogens at the regional scale but not at finer scales. These findings demonstrate how microbial diversity is affected by host diversity at different spatial scales and suggest that the relationships between host diversity and overall disease risk are not always negative, as the dilution hypothesis predicts.     

Methanogenic and Sulphate-Reducing Microbial Communities in Deep Groundwater of Crystalline Rock Fractures in Olkiluoto,Finland

The long-term safety of final disposal of spent nuclear fuel in the deep geosphere is dependent on stability of biogeochemical conditions at the disposal site. Microbial processes, such as sulphate reduction and methanogenesis, may have profound effects on site biogeochemistry. In this study, sulphate-reducing bacteria and methane-producing archaea were investigated at depths ranging from 68 to 545 m in crystalline rock fractures at an intended spent nuclear fuel disposal site in Olkiluoto, Finland. Denaturing gradient gel electrophoresis detected diverse sulphate-reducing bacterial communities in all samples. Although the number of dsrB gene copies was below 10³ copies ml^?1 in all analyzed samples according to real-time quantitative PCR, their abundance was highest in samples that had the highest sulphate concentrations. Several distinct mcrA gene fragments were also recovered from most of the analyzed samples by cloning, although the number of methanogens was lower than that of sulphate-reducing bacteria when measured by mcrA-targeted quantitative PCR. The detected gene fragments were most closely related to sequences obtained from aquatic and deep subsurface environments. Results imply that sulphate reduction, methanogenesis, and anaerobic methane oxidation may all take place in the Olkiluoto deep geobiosphere.     

中国喀斯特地区微生物群落结构和功能的研究进展

频繁的人类生产活动使植被遭到破坏,造成基岩裸露的石漠化现象,严重制约了喀斯特地区自然和社会经济的发展,随着生态修复工程的大力开展,微生物群落的结构和功能在生态修复中逐渐受到重视,因为微生物作为喀斯特生态系统的重要组成部分,不仅在物质循环过程中起着重要作用,也在喀斯特生态系统修复中占有十分重要的地位。所以微生物群落结构和功能的研究可以作为衡量生态系统稳定性的重要指标。就中国喀斯特地区的典型植被恢复的不同阶段、成土过程、不同的土地利用方式、矿山修复过程以及不同水域中的微生物群落结构及功能等方面的研究状况进行系统梳理,结合实例综合论述喀斯特地区生态修复过程中微生物作用的研究进展,以期为喀斯特地区生态修复提供参考。     

Meiobenthos and the oxygen budget of an intertidal sand beach

Field and laboratory experiments are used to construct a partial oxygen budget for a typical fine sand area just above mean tide level in Strangford Lough, Northern Ireland. Oxygen consumption was determined mainly from batch respiration using a YSI electrode. Experiments with different batch sizes indicate that oxygen uptake rate per individual decreased as the number in the test chamber increased. Experiments conducted monthly at ambient environmental temperature with batches of 40 individuals show minimum oxygen consumption occurred at 12 °C in the nematode, copepod and turbellarian populations tested.Modelling the situation for 1 m² of beach in November 1979 gives a meiofaunal demand from 295,250 individuals of a total 40 ml O₂ . h^–1 compared with an estimated 2760 for macrofauna and 1172 for sediment with attached microorganisms. Microfloral production was calculated as 324 ml O₂ . h^–1 in light. The individual meiofaunal respiration values are much higher than those previously reported. The reasons for this and the confidence which can be attached to these and other workers results are discussed. Information from laboratory and field results is used to construct a partial oxygen budget for a typical fine sand area just above mid-tide level in Strangford Lough, Northern Ireland. Oxygen consumption by meiofaunal taxa and Hydrobia was determined from batch respiration experiments using a YSI oxygen electrode, as was consumption and production by sediment with attached microflora. Experiments conducted monthly at ambient temperature indicate minimum oxygen consumption at 12 ° C in the nematode, copepod and turbellarian (Monocelopsis sp.) population tested. Batch size affected consumption; with nematodes, copepods and gastrotrichs (Turbanella varians) uptake per individual decreased as number in the test chamber increased. Later experiments were therefore conducted with a standard batch size of 40 individuals.Inspection of biological and physical data showed conditions in November 1979 were close to the annual mean. Using these and the appropriate laboratory data the calculated values give a meiofaunal oxygen demand per m² of beach of 40 ml h^–1 compared with an estimated 2760 for the macrofauna and 1172 for the sediment with attached micro-organisms. Microfloral oxygen production was 324 ml h^–1 in light. The meiofaunal figures are based on a population of 295,250 individuals per m² with a percentage composition of Nematoda 58.2, Copepoda 22.7, Gastrotricha 14.4, Turbellaria 5.3 and Gnasthostomulida 1.3. These figures give a relative population oxygen uptake of 50.1 : 32.3 : 5.1 : 9.9 : 2.7% respectively. The confidence which can be attached to these and other workers results is discussed.     

Structure of Microbial Communities of the Sediments of Alkaline Transbaikalia Lakes with Different Salinity

The goal of the work was to reveal the differences in the structure of microbial communities of Transbaikalia alkaline lakes stemming from the differences in their salinity and hydrochemical parameters. The lakes studied were Verkhnee Beloe (Buryat Republic, Russia), as well as Khilganta, Gorbunka, and Borzinskoe (Transbaikal krai, Russia) with salinity from 12.3 to 430 g/L, which differed in the mineral composition of the sediments and hydrochemical parameters. Lake sediments were found to contain 47 prokaryotic phyla (42 bacterial and 5 archaeal ones). The phyla Proteobacteria, Euryarchaeota, Bacteroides, Chloroflexi, Actinobacteria, and Firmicutes were predominant, comprising over 95% of the classified sequences. Comparative abundance of archaea increased with salinity from below 1% in Lake Verkhnee Beloe to 35% in Lake Borzinskoe. The most numerous bacterial OTUs belonged to gammaproteobacteria of the genus Halomonas (up to 15% of the number of classified sequences). The most numerous archaeal OTUs were identified at the genus level as members of the genera Halorubrum and Halohasta belonging to the family Halorubraceae, which comprises extremely halophilic Euryarchaeota.     

Electronic Structure Engineering of LiCoO2 toward Enhanced Oxygen Electrocatalysis

Developing low‐cost and efficient electrocatalysts for the oxygen evolution reaction and oxygen reduction reaction is of critical significance to the practical application of some emerging energy storage and conversion devices (e.g., metal–air batteries, water electrolyzers, and fuel cells). Lithium cobalt oxide is a promising nonprecious metal‐based electrocatalyst for oxygen electrocatalysis; its activity, however, is still far from the requirements of practical applications. Here, a new LiCoO₂‐based electrocatalyst with nanosheet morphology is developed by a combination of Mg doping and shear force‐assisted exfoliation strategies toward enhanced oxygen reduction and evolution reaction kinetics. It is demonstrated that the coupling effect of Mg doping and the exfoliation can effectively modulate the electronic structure of LiCoO₂, in which Co³⁺ can be partially oxidized to Co⁴⁺ and the Co–O covalency can be enhanced, which is closely associated with the improvement of intrinsic activity. Meanwhile, the unique nanosheet morphology also helps to expose more active Co species. This work offers new insights into deploying the electronic structure engineering strategy for the development of efficient and durable catalysts for energy applications.     

基于空间结构指数的不同森林群落稳定性研究

以长白山杨桦次生林、云冷杉针阔混交林、云冷杉近原始林为研究对象,基于微观经济学中的柯布—道格拉斯生产函数相关理论,以3个常用的空间结构指标(混交度、大小比数、角尺度)为"投入",林分整体空间结构为"产出",构建林分空间结构生产函数,定义了林分空间结构指数(FSSI)并计算了林分空间结构距离(FSSD)。利用这5个指标分析比较不同演替阶段森林群落的空间结构特点,从而评价各演替阶段的稳定性。结果表明:不同演替阶段森林群落的混交度值均不相同,云冷杉近原始林平均混交度最大,云冷杉针阔混交林次之,杨桦次生林最小;大小比数对不同森林群落空间结构影响较小,其值基本为0.49~0.52;3种森林群落水平分布状态为云冷杉针阔混交林和云冷杉近原始林随机分布,杨桦次生林聚集分布;其空间结构指数大小及与理想结构接近程度排序为:云冷杉近原始林云冷杉针阔混交林杨桦次生林。因此,云冷杉近原始林空间结构较好,稳定性最佳。     

The Influence of the Spatial Structure of Hydromacrophytes and Differentiating Habitat on the Structure of Rotifer and Cladoceran Communities

Research on the similarity of zooplankton in various stands of water vegetation, including rushes (Typha angustifolia), nymphaeids (Nymphaea alba) and submerged macrophytes (Charahispida, C. tomentosa, Myriophyllumverticillatum and Utricularia vulgaris) was carried out on the shallow Wielkowiejskie lake (Poland). The analysis of the similarity of the Rotifera community revealed the strongest relationship between the Myriophyllum and Chara tomentosa beds, with C. hispida attaching them. A second pair of habitats was represented by Typha and Nymphaea stands. Cladocerans revealed the greatest similarity between both zones of Chara. Additionally, two more pairs of habitats were distinguished – Typha and Nymphaea and also Utricularia and Myriophyllum. In most cases, the Shannon-Weaver values were high among macrophyte stations. Forward stepwise regression revealed that the length of Nymphaea stems was a single negative predictor determining the Cladocera densities. The water lily stand possessed the richest pelagic community of zooplankton and had the highest cladoceran diversity index. In accordance with CCA-ordination, out of the environmental variables, the macrophyte stem length and the concentration of P_tot were the strongest predictors in determining the distribution of particular species of the zooplankton community. Mainly pelagic species displayed preferences towards physical parameters of habitat, which is manifested in their greater affinity to a denser spatial structure of macrophyte substratum. The similarity of zooplankton communities in Wielkowiejskie lake was based on the characteristic architecture of particular macrophyte species, where the plant length was the strongest predictor. Moreover, the character of the zooplankton communities was also influenced by the concentrations of chlorophyll ‘a’ and the chemical variables, with the strongest impact of P_tot, of periphyton received from a particular macrophyte habitat and from water filling the spaces between plant stems.