A comparison of taxon co-occurrence patterns for macro- and microorganisms

We examine co-occurrence patterns of microorganisms to evaluate community assembly "rules". We use methods previously applied to macroorganisms, both to evaluate their applicability to microorganisms and to allow comparison of co-occurrence patterns observed in microorganisms to those found in macroorganisms. We use a null model analysis of 124 incidence matrices from microbial communities, including bacteria, archaea, fungi, and algae, and we compare these results to previously published findings from a meta-analysis of almost 100 macroorganism data sets. We show that assemblages of microorganisms demonstrate nonrandom patterns of co-occurrence that are broadly similar to those found in assemblages of macroorganisms. These results suggest that some taxon co-occurrence patterns may be general characteristics of communities of organisms from all domains of life. We also find that co-occurrence in microbial communities does not vary among taxonomic groups or habitat types. However, we find that the degree of co-occurrence does vary among studies that use different methods to survey microbial communities. Finally, we discuss the potential effects of the undersampling of microbial communities on our results, as well as processes that may contribute to nonrandom patterns of co-occurrence in both macrobial and microbial communities such as competition, habitat filtering, historical effects, and neutral processes.     

Disappearing plants: why they hide and how they return

Prolonged dormancy is a life-history stage in which mature plants fail to resprout for one or more growing seasons and instead remain alive belowground. Prolonged dormancy is relatively common, but the proximate causes and consequences of this intriguing strategy have remained elusive. In this study we tested whether stored resources are associated with remaining belowground, and investigated the resource costs of remaining belowground during the growing season. We measured stored resources at the beginning and end of the growing season in Astragalus scaphoides, an herbaceous perennial in southwest Montana, USA. At the beginning of the growing season, dormant plants had lower concentrations of stored mobile carbon (nonstructural carbohydrates, NSC) than did emergent plants. Surprisingly, during the growing season, dormant plants gained as much NSC as photosynthetically active plants, an increase most likely due to remobilization of structural carbon. Thus, low levels of stored NSC were associated with remaining belowground, and remobilization of structural carbon may allow for dormant plants to emerge in later seasons. The dynamics of NSC in relation to dormancy highlights the ability of plants to change their own resource status somewhat independently of resource assimilation, as well as the importance of considering stored resources in understanding plant responses to the environment.     

Individual-based modelling of carbon and nitrogen dynamics in soils: Parameterization and sensitivity analysis of microbial components

The fate of soil carbon and nitrogen compounds in soils in response to climate change is currently the object of significant research. In particular, there is much interest in the development of a new generation of micro-scale models of soil ecosystems processes. Crucial to the elaboration of such models is the ability to describe the growth and metabolism of small numbers of individual microorganisms, distributed in a highly heterogeneous environment. In this context, the key objective of the research described in this article was to further develop an individual-based soil organic matter model, INDISIM-SOM, first proposed a few years ago, and to assess its performance with a broader experimental data set than previously considered. INDISIM-SOM models the dynamics and evolution of carbon and nitrogen associated with organic matter in soils. The model involves a number of state variables and parameters related to soil organic matter and microbial activity, including growth and decay of microbial biomass, temporal evolutions of easily hydrolysable N, mineral N in ammonium and nitrate, CO₂ and O₂. The present article concentrates on the biotic components of the model. Simulation results demonstrate that the model can be calibrated to provide good fit to experimental data from laboratory incubation experiments performed on three different types of Mediterranean soils. In addition, analysis of the sensitivity toward its biotic parameters shows that the model is far more sensitive to some parameters, i.e., the microbial maintenance energy and the probability of random microbial death, than to others. These results suggest that, in the future, research should focus on securing better measurements of these parameters, on environmental determinants of the switch from active to dormant states, and on the causes of random cell death in soil ecosystems.     

Mapping the niche space of soil microorganisms using taxonomy and traits

The biodiversity of microbial communities has important implications for the stability and functioning of ecosystem processes. Yet, very little is known about the environmental factors that define the microbial niche and how this influences the composition and activity of microbial communities. In this study, we derived niche parameters from physiological response curves that quantified microbial respiration for a diverse collection of soil bacteria and fungi along a soil moisture gradient. On average, soil microorganisms had relatively dry optima (0.3 MPa) and were capable of respiring under low water potentials (-2.0 MPa). Within their limits of activity, microorganisms exhibited a wide range of responses, suggesting that some taxa may be able to coexist by partitioning the moisture niche axis. For example, we identified dry-adapted generalists that tolerated a broad range of water potentials, along with wet-adapted specialists with metabolism restricted to less-negative water potentials. These contrasting ecological strategies had a phylogenetic signal at a coarse taxonomic level (phylum), suggesting that the moisture niche of soil microorganisms is highly conserved. In addition, variation in microbial responses along the moisture gradient was linked to the distribution of several functional traits. In particular, strains that were capable of producing biofilms had drier moisture optima and wider niche breadths. However, biofilm production appeared to come at a cost that was reflected in a prolonged lag time prior to exponential growth, suggesting that there is a trade-off associated with traits that allow microorganisms to contend with moisture stress. Together, we have identified functional groups of microorganisms that will help predict the structure and functioning of microbial communities under contrasting soil moisture regimes.     

Orchids do not pay costs at emergence for prolonged dormancy

In plants, prolonged dormancy is often considered a response to resource depletion or environmental stress that comes at a fitness cost. However, apparent costs of dormancy could reflect the state in which plants entered dormancy, rather than effects of dormancy per se. We tested this hypothesis for a terrestrial orchid, Epipactis atrorubens, by analyzing differences in vital rates of dormant and emergent plants using generalized linear mixed models, applied to eight years of demographic data. Dormant E. atrorubens plants did not form one homogeneous stage class. Instead, the vital rates of dormant plants mirrored performance of plants in their life stage before dormancy. Plants emerging from dormancy were slightly (albeit only marginally statistically significantly) larger than plants transitioning from the matching aboveground stage class, especially for smaller and younger stage classes. Because small plants were most likely to go dormant, plants emerging from dormancy were also smaller than average, if one were to compare all previously dormant plants to all previously emergent plants. Therefore, misclassifying all dormant plants into a single stage class changes whether we view dormancy as intrinsically costly, in terms of future performance upon emergence. We suggest that prolonged dormancy may be a form of phenotypic plasticity in which plants distribute their performance and reproductive effort through time, rather than a simple stress response.     

Influence of invasive plant Coreopsis grandiflora on functional diversity of soil microbial communities

Biological invasions are increasingly attracting the ecologists' attention. Invasive plants threaten the natural ecosystems not only by competing with the native plants, but also by altering the structure and function of soil microbial communities belowground. In this study, we studied the effects of the invasive plant Coreopsis grandiflora (C. grandiflora) on the functional diversity of soil microbial communities in Laoshan mountain in the province of Shandong, North of China. We sampled soil from plots that were invaded or not invaded by C. grandiflora. The functional diversity of microbial communities in the sampled soils was assessed by the Biolog procedure test. By the ANOVA analysis of average well color development (AWCD), Shannon index (H'), Shannon evenness (E), principle components analysis of the level physiological profiles (CLPP) and correlation analysis between the studied parameters, we found that the invasive species C. grandiflora enhanced the functional diversity of soil microbial communities where the habitat was invaded by the C. grandiflora. The study indicated thatthe successful invasive plants have profound effects on the function of soil microbial communities.     

Compositional divergence and convergence in arbuscular mycorrhizal fungal communities

In spite of the controversy that they have generated, neutral models provide ecologists with powerful tools for creating dynamic predictions about beta-diversity in ecological communities. Ecologists can achieve an understanding of the assembly rules operating in nature by noting when and how these predictions are met or not met. This is particularly valuable for those groups of organisms that are challenging to study under natural conditions (e.g., bacteria and fungi). Here, we focused on arbuscular mycorrhizal fungal (AMF) communities and performed an extensive literature search that allowed us to synthesize the information in 19 data sets with the minimal requisites for creating a null hypothesis in terms of community dissimilarity expected under neutral dynamics. In order to achieve this task, we calculated the first estimates of neutral parameters for several AMF communities from different ecosystems. Communities were shown either to be consistent with neutrality or to diverge or converge with respect to the levels of compositional dissimilarity expected under neutrality. These data support the hypothesis that divergence occurs in systems where the effect of limited dispersal is overwhelmed by anthropogenic disturbance or extreme biological and environmental heterogeneity, whereas communities converge when systems have the potential for niche divergence within a relatively homogeneous set of environmental conditions. Regarding the study cases that were consistent with neutrality, the sampling designs employed may have covered relatively homogeneous environments in which the effects of dispersal limitation overwhelmed minor differences among AMF taxa that would lead to environmental filtering. Using neutral models we showed for the first time for a soil microbial group the conditions under which different assembly processes may determine different patterns of beta-diversity. Our synthesis is an important step showing how the application of general ecological theories to a model microbial taxon has the potential to shed light on the assembly and ecological dynamics of communities.     

DNA damage induced by ultraviolet radiation in coral-reef microbial communities

Ultraviolet radiation (UVR) has been implicated in coral-bleaching processes and UVR may create stress to marine organisms by damage to DNA. Absorption of energy from UVB (280 to 320 nm) induces direct damage to DNA via cyclobutane pyrimidine dimer photoproduct-formation. We examined the extent of DNA damage created by UVR in coral reef microbial communities and whether the coral-surface microlayer (CSM) provides protection from UVR to the microorganisms found there. Diel patterns and depth profiles of UVR effects were examined in coral mucus (coral-surface microlayer, CSM) from Montastraea faveolata and Colpophyllia natans, and water-column samples of similar depths. UV-induced photodamage was determined using a radioimmunoassay specific for cyclobutane pyrimidine dimers (thymine dimers). Significant photodamage was detected in water-column and CSM samples, although the level of damage in CSM samples was consistently lower than in water-column samples collected from the same depth, suggesting the presence of photoprotective mechanisms within the CSM. Diel patterns of photodamage were detected in both water-column and CSM samples, but peak damage occurred earlier in the day for the CSM samples, suggesting differences in damage and repair kinetics between the water column and CSM. The results suggest that microorganisms within the CSM are afforded some protection from UVR stress and that changes in the amount of DNA damage in these organisms may be an indicator of changing UVR stress to corals. Received: 10 January 1997 / Accepted: 15 September 1997     

Extinction, recolonization, and dispersal through time in a planktonic crustacean

Dormant propagule banks are important reservoirs of biological and genetic diversity of local communities and populations and provide buffering mechanisms against extinction. Although dormant stages of various plant and animal species are known to remain viable for decades and even centuries, little is known about the effective influence of recolonization from such old sources on the genetic continuity of intermittent populations under natural conditions. Using recent and old dormant eggs recovered from a dated lake sediment core in Kenya, we traced the genetic composition of a local population of the planktonic crustacean Daphnia barbata through a sequence of extinction and recolonization events. This was combined with a phylogeographic and population-genetic survey of regional populations. Four successive populations, fully separated in time, inhabited Lake Naivasha from ca. 1330 to 1570 AD, from ca. 1610 to 1720 AD, from ca. 1840 to 1940 AD, and from 1995 to the present (2001 AD). Our results strongly indicate genetic continuity between the 1840-1940 and 1995-2001 populations, which are separated in time by at least 50 years, and close genetic relatedness of them both to the 1330-1580 population. A software tool (Colonize) was developed to find the most likely source population of the refounded 1995-2001 population and to test the number of colonists involved in the recolonization event. The results confirmed that the 1995-2001 population most probably developed out of a limited number of surviving local dormant eggs from the previous population, rather than out of individuals from regional (central and southern Kenya) or more distant (Ethiopia, Zimbabwe) populations that may have immigrated to Lake Naivasha through passive dispersal. These results emphasize the importance of prolonged dormancy for the natural long-term dynamics of crustacean zooplankton in fluctuating environments and suggest an important role of old local dormant egg banks in aquatic habitat restoration.     

Microbial relationships in surface-mine revegetation

The establishment and interrelationships of microorganisms with soil and plant processes during reclamation are greatly influenced by the composition of the planting medium and vegetation practices. While in some instances the parent material may be used as the vegetation medium, the practice of topsoiling, particularly the direct haul method, may be beneficial in introducing microorganisms and improving the quality of the plant growth medium of spoils that are chemically or physically less desirable than the native soils. The influence of different vegetation types on soil development on surface mines may be a reflection of physioiogical differences that affect microbial development in the rhizosphere. Such differences include levels of carbohydrate translocated to the root system and/or released into the surrounding soil; the plant's effectiveness as a mycorrhizal host; and the rate of degradation of plant residues. It has become apparent that microbial interactions are an important part of plant and soil processes in reclamation. While some of the microorganisms important in plant growth and soil development can be introduced readily by management practices, the majority usually are disseminated by natural means and only gradually become a part of the microbial population. More research is needed on developing new methods or refining current procedures for early introduction of these microorganisms in reclamation practices.     

油藏微生物群落分布及提高采收率的模拟实验研究

对取自大庆油田各类油藏的126个地层油水样品中部分微生物进行了培养计数和分析,检测出大庆油田地层水中含有好氧和厌氧微生物9类.在此基础上,进行了微生物提高石油采收率的物理模拟试验.结果表明,通过激活油藏地层水中的微生物,可以使油藏压力上升0.2MPa,并提高采收率幅度9%以上.     

Annual life cycle of Chattonella spp., causative flagellates of noxious red tides in the Inland Sea of Japan

Effects of storage temperature on the dormancy and maturation of dormant cells of Chattonella spp. were investigated by the extinction dilution method using sediment samples collected in 1984 after the blooming in Harima-Nada. Seasonality of germinability in fresh sediments was also studied in 1985. A storage period of more than 4 months with a low temperature (11°C) was essential for the maturation to induce the germination capacity of dormant cells. The optimal temperature for germination (22°C) had no effects on the maturation. Using fresh Suo-Nada sediments, a marked seasonality of germinability was confirmed. It was weak from autumn to early winter, then strengthened gradually up to a high level, which was maintained between spring and early summer, and again decreased rapidly during summer. The annual life cycle of Chattonella spp., including vetetative and dormant phases, was summarized as follows: (1) vegetative cells in early summer originate from germination of dormant cells in sediments; (2) they form overwintering dormant cells during the summer season; (3) dormant cells spend a period of spontaneous dormancy until next spring; (4) the duration of post dormancy, an enforced one due to low temperatures, follows until early summer. The life cycle of Chattonella spp. is therefore well adapted to the temperature regime in temperate seas such as the Seto Inland Sea of Japan.     

肠道微生物受环境污染的影响及其对宿主疾病的调控作用

宿主肠道内存在的大量微生物与其健康状况直接相关,这些微生物是人和动物健康成长不可或缺的。肠道微生物通过多种途径调节人体生理功能的同时也受到人体内外环境的影响。因此,分析建立肠道微生物、相关疾病的产生原因和作用机制以及环境影响因子之间的联系具有重要意义。本文首先针对肠道微生物对人体的物质与能量代谢、先天和获得性免疫、胃肠道功能等方面的影响进行综述。然后重点分析了近年来有关肠道微生物对环境污染所致健康效应的影响及作用机制的研究进展。以期加深肠道微生物与人类健康之间相互作用机理的理解,并为环境毒理学与肠道微生物之间关系的研究提供新的思路。     

Microbial stress-response physiology and its implications for ecosystem function

Microorganisms have a variety of evolutionary adaptations and physiological acclimation mechanisms that allow them to survive and remain active in the face of environmental stress. Physiological responses to stress have costs at the organismal level that can result in altered ecosystem-level C, energy, and nutrient flows. These large-scale impacts result from direct effects on active microbes' physiology and by controlling the composition of the active microbial community. We first consider some general aspects of how microbes experience environmental stresses and how they respond to them. We then discuss the impacts of two important ecosystem-level stressors, drought and freezing, on microbial physiology and community composition. Even when microbial community response to stress is limited, the physiological costs imposed on soil microbes are large enough that they may cause large shifts in the allocation and fate of C and N. For example, for microbes to synthesize the osmolytes they need to survive a single drought episode they may consume up to 5% of total annual net primary production in grassland ecosystems, while acclimating to freezing conditions switches Arctic tundra soils from immobilizing N during the growing season to mineralizing it during the winter. We suggest that more effectively integrating microbial ecology into ecosystem ecology will require a more complete integration of microbial physiological ecology, population biology, and process ecology.     

Microbial relationships in surface-mine revegetation

The establishment and interrelationships of microorganisms with soil and plant processes during reclamation are greatly influenced by the composition of the planting medium and vegetation practices. While in some instances the parent material may be used as the vegetation medium, the practice of topsoiling, particularly the direct haul method, may be beneficial in introducing microorganisms and improving the quality of the plant growth medium of spoils that are chemically or physically less desirable than the native soils. The influence of different vegetation types on soil development on surface mines may be a reflection of physioiogical differences that affect microbial development in the rhizosphere. Such differences include levels of carbohydrate translocated to the root system and/or released into the surrounding soil; the plant's effectiveness as a mycorrhizal host; and the rate of degradation of plant residues. It has become apparent that microbial interactions are an important part of plant and soil processes in reclamation. While some of the microorganisms important in plant growth and soil development can be introduced readily by management practices, the majority usually are disseminated by natural means and only gradually become a part of the microbial population. More research is needed on developing new methods or refining current procedures for early introduction of these microorganisms in reclamation practices.     

土壤微生物污染诱导群落耐性研究进展

污染诱导群落耐性(PICT)是指生物群落为了在污染环境中继续生存,通过生理生化与遗传特征的改变或以耐性类群生物代替敏感类群,从而使整个群落产生耐性.目前人们已将PICT作为一项指标,从群落耐性方面来评价污染生态学的效应.目前PICT研究已涵盖了水生生物、陆地植物、微生物等,其中土壤微生物是PICT研究的重要群落对象.对土壤微生物群落PICT的研究始于上世纪90年代,并已在多方面取得进展,包括在研究方法上的一些突破和改进.在PICT产生和变化机理等方面也有新发现,如发现了土壤微生物群落PICT与污染物浓度存在较好的正相关关系,并且污染物能够引起土壤微生物群落对其他污染物的共耐性等.在PICT影响因素研究方面发现不仅环境因素会影响PICT的形成,而且检测方法也会影响对PICT的判断.论文较为全面地综述了国际上针对土壤微生物群落PICT的研究进展,包括PICT的概念、研究方法、污染物影响PICT的内在机制及影响PICT的关键因素等,最后提出了研究展望.     

Unexpected similar stability of soil microbial CO2 respiration in 20-year manured and in unmanured tropical soils

Soil respiration is one of the main CO₂ sources from terrestrial ecosystems. Soil respiration is therefore a major source of greenhouse gas. Knowledge of the impact of agronomic practices such as manuring on the stability, for example resistance and resilience, of heterotrophic C–CO₂ respiration to disturbance is scarce. Here, we studied the stability of soil microbial heterotrophic respiration of two tropical soils from plots annually enriched or not with manure applications during more than 20 years. Stability was quantified after heating soils artificially. We hypothesized that field manuring would change the stability of the microbial community. Additionally, the impact of both manured and unmanured soils to addition of an organic cocktail was assessed under controlled conditions in order to discriminate the metabolic capacity of the microbial community, and to link the metabolic capacity up with the microbial heterotrophic soil respiration. Our results show that total respiration was not significantly different in manured and unmanured pots. Moreover, contrary to our hypothesis, manure amendment did not affect the stability (resistance, resilience) of the microbial abundance or the basal metabolism, in our experimental conditions. By contrast, the diversity of the bacterial community in heated soils was different from that in unheated soils. After heating, surviving microorganisms showed different carbon utilization efficiency, manuring stimulating the growth of different resistant communities, that is, r-strategist or K-strategist. Microbial community of manured soils developed in the presence of the organic cocktail was less resistant to heating than microbial community of unmanured plots.     

Water-dispersible nano-pollutions reshape microbial metabolism in type-specific manners: A metabolic and bacteriological investigation in Escherichia coli

• Water-dispersible nano-pollutions exhibit type-specific toxic effects on E. coli. • Global metabolite profiling was used to characterize metabolic disruption patterns. • Key dysregulated metabolites responsive to nano-pollution exposures were found. • Amino acid metabolism and purine metabolism are perturbed at nano-pollutions. Incomplete separation and recycling of nanoparticles are causing undesirable nanopollution and thus raising great concerns with regard to nanosafety. Since microorganisms are important regulator of physiological processes in many organisms, the interaction between nanopollution and microbial metabolomics and the resultant impact on the host’s health are important but unclear. To investigate how typical nanopollution perturbs microbial growth and metabolism, Escherichia coli (E. coli) in vitro was treated with six water-dispersible nanomaterials (nanoplastic, nanosilver, nano-TiO₂, nano-ZnO, semiconductor quantum dots (QDs), carbon dots (CDs)) at human-/environment-relevant concentration levels. The nanomaterials exhibited type-specific toxic effects on E. coli growth. Global metabolite profiling was used to characterize metabolic disruption patterns in the model microorganism exposed to different nanopollutants. The percentage of significant metabolites (p<0.05, VIP>1) accounted for 6%–38% of the total 293 identified metabolites in each of the nanomaterial-contaminated bacterial groups. Metabolic results also exhibited significant differences between different nanopollutants and dose levels, revealing type-specific and untypical concentration-dependent metabolic responses. Key metabolites responsive to nanopollution exposures were mainly involved in amino acid and purine metabolisms, where 5, 4, and 7 significant metabolic features were included in arginine and proline metabolism, phenylalanine metabolism, and purine metabolism, respectively. In conclusion, this study horizontally compared and demonstrated how typical nanopollution perturbs microbial growth and metabolomics in a type-specific manner, which broadens our understanding of the ecotoxicity of nanopollutants on microorganisms.     

Interactive effects of disturbance and dispersal directionality on species richness and composition in metacommunities

Dispersal among ecological communities is usually assumed to be random in direction, or to vary in distance or frequency among species. However, a variety of natural systems and types of organisms may experience dispersal that is biased by directional currents or by gravity on hillslopes. We developed a general model for competing species in metacommunities to evaluate the role of directionally biased dispersal on species diversity, abundance, and traits. In parallel, we tested the role of directionally biased dispersal on communities in a microcosm experiment with protists and rotifers. Both the model and experiment independently demonstrated that diversity in local communities was reduced by directionally biased dispersal, especially dispersal that was biased away from disturbed patches. Abundance of species (and composition) in local communities was a product of disturbance intensity but not dispersal directionality. High disturbance selected for species with high intrinsic growth rates and low competitive abilities. Overall, our conclusions about the key role of dispersal directionality in (meta)communities seem robust and general, since they were supported both by the model, which was set in a general framework and not parameterized to fit to a specific system, and by a specific experimental test with microcosms.