How much do phenotypic plasticity and local genetic variation contribute to phenotypic divergences along environmental gradients in widespread invasive plants? A meta‐analysis

For introduced species that have spread across a wide distributional range, phenotypic plasticity (PLA) has often been proposed as an important contributor to invasion success, because it increases the survival rate during initial colonization. In contrast, local genetic variation (LOC) has also been proposed to be important, because it could allow invaders to evolve high performance in a new habitat. While evolutionary ecologists have long been interested in understanding genetic mechanisms that allow rapid colonization and spread of species, until recently experimental tests of these concepts have been limited. As a step towards generalization in our understanding of the importance of PLA and LOC, we review the current state of the literature on this topic using meta‐analysis. Here, we focused on three fundamental questions: 1) which strategy, PLA or LOC, better explains the phenotypic divergences during invader range expansion across different environmental gradients? 2) Which species characteristics correlate with the occurrence of these different phenomena? And 3) does the detection of PLA versus LOC depend on the trait studied? Using meta‐analysis we found that plasticity explained a higher proportion of phenotypic variation regardless of the environmental gradients studied or plant growth forms. PLA predominated in clonal, self‐compatible and perennial species, while LOC predominated in annual species. The patterns were trait‐dependent: LOC was significantly more important than PLA in phenology, while opposite patterns were found in fecundity and biomass allocation. The frequent simultaneous detection of PLA and genotypic variation in PLA among invasive populations suggested that PLA might benefit from LOC to some extent. Our results also indicate that the contribution of plasticity to the competitive advantages of invasive plants may be more informative than the level of plasticity itself. Synthesis For invasive plants that spread across a wide distributional range, understanding the mechanisms that allow rapid colonization and spread is crucial. Phenotypic plasticity (PLA) and local genetic variation (LOC) are both believed to play important roles in promoting range expansion. However, it is not clear which mechanism, PLA or LOC, contributes more to this process. According to our meta–analysis, PLA explained a higher proportion of adaptive phenotypic variation in most cases. Nevertheless, the predominance of an expansion mechanism depends on species characteristics and the trait studied. PLA may benefit from LOC to some extent. We suggest that the contribution of PLA to range expansion may better explain plant invasion success than the level of PLA itself.     

基因芯片技术在环境微生物群落研究中的应用

基因芯片技术作为一种快速、敏感、高通量的检测技术,近几年来在环境微生物群落研究中的应用越来越广泛并且得到充分的发展.它不仅可以研究环境微生物群落的微生物分布、种类、功能、动力学变化,还能分析环境污染等环境因素改变对其微生物生态的影响.本文按照基因芯片探针的设计方法,将环境样品群落研究基因芯片分为系统寡核苷酸芯片、功能基因芯片、群落基因组芯片、宏基因组芯片,并简要综述了该技术在活性污泥、土壤、水等环境样品微生物群落研究上的应用,最后,本文展望了该技术的研究方向和在寻找不同环境微生物群落之间差异微生物、差异基因或差异表达基因研究中的应用前景.     

Shifting sources of soil labile organic carbon after termination of plant carbon inputs in a subtropical moist forest of southwest China

Labile organic carbon (LOC) is a critical component of soil organic carbon (C) because of its intimate association with soil heterotrophic respiration and role in the decomposition of resistant soil organic matter. In a subtropical moist evergreen broad-leaved forest of southwest China, we examined changes of LOC and its potential turnover time, microbial biomass C (MBC), and soil microbial activity of the organic and the 0–10 cm mineral soil layers with aboveground plant litter and belowground root treatments. In February of 2004, removal of organic layer, root-trenching, and tree-girdling treatments were applied alone and in combination to manipulate plant-C inputs. In 2006, root-trenching and tree-girdling treatments did not significantly change LOC in the organic layer. In the 0–10 cm mineral soil layer, LOC increased substantially due to tree-girdling treatment, especially in the plots of tree-girdling and the combinations of three treatments, but this increase was absent in 2007. Soil MBC in these two layers generally did not change markedly after plant-C inputs manipulations except significant increase under tree-girdling treatment in 2006. The potential turnover times of LOC increased in all plots with the plant-C inputs manipulations. The lack of influence of plant-C inputs manipulations on LOC pools is likely due to high total soil organic C here, while insignificant changes of MBC suggest the soil microbes are not C limited in this forest. The changes of the potential turnover time of LOC imply that the sources of LOC have been shifted from fresh plant litter or root exudates to old soil organic C. Our results suggest that LOC recently derived from plants is preferred by microbes when available, but microbes can also use LOC from soil organic matter when fresh plant C is not available.     

武夷山不同海拔高度土壤活性有机碳变化

采用连续熏蒸 培养法,测定了福建武夷山自然保护区不同海拔高度具有代表性的中亚热带常绿阔叶林、针叶林、亚高山矮林以及高山草甸土壤中有效碳含量,分析了土壤有效碳（LOC）与微生物量碳（MBC）、土壤总有机碳（TOC）、细根生物量（FRB）和土壤全氮（TN）之间的关系.结果表明：土壤有效碳占总有机碳的3.40%～7.46%;微生物量碳只是土壤有效碳中的一部分,占土壤有效碳26.87%～80.38%; 不同林分土壤有效碳含量随海拔增高而显著增大,随土层深度的增加而降低;土壤有效碳与微生物量碳、土壤总有机碳、细根生物量、土壤全氮之间呈极显著的相关关系.高海拔土壤有效碳含量显著高于低海拔土壤.     

江西官山常绿阔叶林土壤有机碳组分沿海拔的变化

对江西官山国家级自然保护区不同海拔(400、600、800、1000、1200 m)常绿阔叶林土壤总有机碳、惰性有机碳和活性有机碳进行分析,研究土壤有机碳的海拔分布特征。结果表明: 土壤总有机碳、惰性有机碳及活性有机碳含量在土壤表层最高,随土层加深而逐渐下降。随海拔升高,土壤总有机碳、惰性有机碳、易氧化有机碳、微生物生物量碳及0～20 cm土层土壤颗粒有机碳含量均出现先增后降的趋势, 且在海拔1000 m达到峰值,而土壤水溶性有机碳及20～40 cm土层土壤颗粒有机碳含量无明显变化。在0～10 cm土层,土壤惰性有机碳占总有机碳的比例在海拔800和1200 m显著高于海拔400和1000 m,而土壤活性有机碳占总有机碳的比例在海拔400 m最高;土壤惰性有机碳和活性有机碳占总有机碳的比例在10～40 cm土层随海拔的增加均呈先增加后降低的趋势,峰值分别在1000和600 m处。各组分有机碳与土壤湿度、微生物生物量氮、可溶性有机氮均呈显著正相关,而且活性有机碳与铵态氮呈显著正相关。海拔显著影响常绿阔叶林土壤有机碳组分的分布,惰性有机碳、易氧化有机碳和微生物生物量碳对海拔变化的响应更敏感。高海拔土壤惰性有机碳和活性有机碳在水分和氮素充足条件下易发生分解与转化,降低土壤碳库的稳定性。在全球气温持续升高背景下,要加强高海拔地区森林土壤有机碳的动态变化研究。     

Environmental conditions influence the plant functional diversity effect on potential denitrification

Global biodiversity loss has prompted research on the relationship between species diversity and ecosystem functioning. Few studies have examined how plant diversity impacts belowground processes; even fewer have examined how varying resource levels can influence the effect of plant diversity on microbial activity. In a field experiment in a restored wetland, we examined the role of plant trait diversity (or functional diversity, (FD)) and its interactions with natural levels of variability of soil properties, on a microbial process, denitrification potential (DNP). We demonstrated that FD significantly affected microbial DNP through its interactions with soil conditions; increasing FD led to increased DNP but mainly at higher levels of soil resources. Our results suggest that the effect of species diversity on ecosystem functioning may depend on environmental factors such as resource availability. Future biodiversity experiments should examine how natural levels of environmental variability impact the importance of biodiversity to ecosystem functioning.     

Characterizing man-made and natural modifications of microbial diversity and activity in coastal ecosystems

The impacts of growing coastal pollution and habitat alteration accompanying human encroachment are of great concern at the microbial level, where much of the ocean's primary production and biogeochemical cycling takes place. Coastal ecosystems are also under the influence of natural perturbations such as major storms and flooding. Distinguishing the impacts of natural and human stressors is essential for understanding environmentally-induced change in microbial diversity and function. The objective of this paper is to discuss the applications and merits of recently developed molecular, ecophysiological and analytical indicators and their utility in examining anthropogenic and climatic impacts on the structure and function of coastal microbial communities. The nitrogen-limited Neuse River Estuary and Pamlico Sound, North Carolina are used as examples of ecosystems experiencing both anthropogenic (i.e., accelerating eutrophication) and climatic stress (increasing frequencies of tropical storms and hurricanes). Additional examples are derived from a coastal monitoring site (LEO) on the Atlantic coast of New Jersey and Galveston Bay, on the Gulf of Mexico. In order to assess structure, function, and trophic state of these and other coastal ecosystems, molecular (DNA and RNA-based) characterizations of the microbial taxa involved in carbon, nitrogen and other nutrient transformations can be combined with diagnostic pigment-based indicators of primary producer groups. Application of these methods can reveal process-level microbial community responses to environmental variability over a range of scales. Experimental approaches combined with strategic monitoring utilizing these methods will facilitate: (a) understanding organismal and community responses to environmental change, and (b) synthesizing these responses in the context of ecosystem models that integrate physical, chemical and biotic variability with environmental controls. This revised version was published online in August 2006 with corrections to the Cover Date.     

Development of a small-scale bioreactor method to monitor the molecular diversity and environmental impacts of bacterial biofilm communities from an acid mine drainage impacted creek

Shamokin Creek is a tributary of the Susquehanna River in central Pennsylvania that is heavily impacted by the acid mine drainage (AMD) caused by the oxidation of pyrite from the region's extensive anthracite coal mining industry. Recent studies have begun to characterize the microbial communities present in this and other AMD-impacted waters, but varying environmental conditions have complicated attempts to determine the ecological impacts of individual bacterial species within these communities. This study developed a small-scale biofilm reactor protocol that allowed us to simultaneously monitor the development of bacterial biofilm communities in AMD-impacted creek collected water using terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes, while assessing the impacts that the developing biofilms were having on water quality. Our analysis confirmed that the diversity and composition of these small in situ biofilm communities could be monitored using molecular methods, and indicated the possible presence of many taxa frequently found in AMD environments, including Sulfobacillus, Nitrospira, Desulfovibrio, Geobacter, and Leptothrix species. A significant increase in the total sulfate was observed in the bioreactor, and as most likely due to the accumulation of sulfur-oxidizing bacteria such as Sulfobacillus in the biofilms. This system will allow us to study the microbial ecology of Shamokin Creek through controlled experiments that will ultimately integrate microscopic, molecular, physiological and chemical analyses, and that can be utilized to develop more effective and cost-efficient environmental remediation techniques for AMD-impacted areas.     

The LOC387715 gene, smoking, body mass index, environmental associations with advanced age-related macular degeneration

BACKGROUND AND AIMS: Age-related macular degeneration (AMD) is the leading cause of blindness in the Western World. It is now evident that both genetic and environmental factors contribute to disease susceptibility. We tested the hypotheses that (a) a common coding SNP in the LOC387715 gene is associated with advanced AMD (geographic atrophy or choroidal neovascularization), and (b) that modifiable environmental exposures alter AMD susceptibility associated with this SNP. METHODS: A case-control association analysis was performed on participants (530 advanced AMD cases and 280 controls) ascertained as part of the multi-center Age-Related Eye Disease Study. AMD status was determined by the reading center from fundus photographs using the AREDS AMD grading categorization. Environmental risk factor exposure data was collected from participants whose DNA was also genotyped for the LOC387715 gene SNP rs10490924. Multivariate logistic regression analyses were performed. RESULTS AND CONCLUSIONS: The number of risk alleles at the LOC387715 SNP was associated with advanced AMD, with odds ratios (OR) = 3.0 (95% confidence interval (CI) 2.1-4.3) for the GT heterozygous genotype and OR = 12.1 (5.6-26.5) for the homozygous TT risk genotype, after controlling for demographic and behavioral risk factors. The LOC387715 SNP was associated with both forms of advanced AMD. Current cigarette smoking and body mass index were independently related to AMD, controlling for genotype. However, there was no statistical interaction between LOC387715 genotype and smoking with regard to advanced AMD development.     

Grass Invasions Across a Regional Gradient are Associated with Declines in Belowground Carbon Pools

The composition of plant communities everywhere now likely comprises alien as well as native species, and those aliens that become invasive have wide-ranging impacts on the structure and function of recipient ecosystems. These impacts include perturbations to soil carbon (C) cycling, but the direction and magnitude of impacts are species and climate dependent, making it difficult to generalize whether a specific invader will promote losses or gains in soil C stocks. Generalizations of a specific invader??s impacts are necessary; however, because the range of an invader can encompass thousands of square kilometers, meaning their effects can have broad, regional consequences. To quantify broad-scale and context-dependent impacts of a specific invader, multi-site investigations that capture and measure local and regional environmental heterogeneity are necessary. Using this approach, we show that a widespread grass invader of forest understories is associated with declines in soil C during infilling (spreading within the invaded range). Across the 36 study sites, total soil C stocks declined (P?=?0.113) by approximately 12% (estimated mean?±?SD, uninvaded: 2,429?±?512.9 vs. invaded: 2,140?±?520.7?g?C?m^?2). The decline in total soil C is driven by a significant (P?=?0.047) reduction in the native-derived, mineral-associated soil C fraction. This fraction, whose mass and slow turnover makes it an important C store, is approximately 15% lower in invaded (estimated mean?±?SD: 1,560?±?400.4?g?C?m^?2) than uninvaded plots (1,826?±?398.1?g?C?m^?2). Notably, declines in this C fraction are only apparent at 21 of the sites, reflecting how environmental heterogeneity in other variables (specifically pH, soil moisture, and clay content) are important to quantify to determine invader impacts across a region. The 26% decline in microbial biomass with invasion (P?=?0.011; estimated mean?±?SD, uninvaded: 10.05?±?1.79 vs. invaded: 7.40?±?1.80?g?C?m^?2) is also dependent on site characteristics (pH), and reductions are greater where the invader occurs at higher densities. Reductions in microbial biomass and soil C with invasion suggest that grass invasion will alter soil C cycling and decrease forest-C stores across the study region, although invader effects at a specific-site will be dependent on environmental context.     

Long‐term dynamics in microbial eukaryotes communities: a palaeolimnological view based on sedimentary DNA

Assessing the extent to which changes in lacustrine biodiversity are affected by anthropogenic or climatic forces requires extensive palaeolimnological data. We used high‐throughput sequencing to generate time‐series data encompassing over 2200 years of microbial eukaryotes (protists and Fungi) diversity changes from the sedimentary DNA record of two lakes (Lake Bourget in French Alps and Lake Igaliku in Greenland). From 176 samples, we sequenced a large diversity of microbial eukaryotes, with a total 16 386 operational taxonomic units distributed within 50 phylogenetic groups. Thus, microbial groups, such as Chlorophyta, Dinophyceae, Haptophyceae and Ciliophora, that were not previously considered in lacustrine sediment record analyses appeared to be potential biological markers of trophic status changes. Our data suggest that shifts in relative abundance of extant species, including shifts between rare and abundant taxa, drive ecosystem responses to local and global environmental changes. Community structure shift events were concomitant with major climate variations (more particularly in Lake Igaliku). However, this study shows that the impacts of climatic fluctuations may be overpassed by the high‐magnitude eutrophication impacts, as observed in the eutrophicated Lake Bourget. Overall, our data show that DNA preserved in sediment constitutes a precious archive of information on past biodiversity changes.     

Earthworms and eco-consequences: Considerations to soil biological indicators and plant function: A review

Earthworms have been well reported to have a beneficial effect on soil microbes, soil microbial biomass (SMB), fungal community, soil structure, water retention and plant growth in different terrestrial ecosystems. However, the interactions between environmental stressors and various species of earthworms and the subsequent effect on soil microbes, organic matter, soil structure and plant growth are still uncertain. The purpose of this analysis was to test 1- the impact of environmental stressors on earthworm behaviour. 2- the effect of various earthworms on soil microbes, plant growth, soil structure and the carbon cycle. We noted that less fatal temperatures are generally unknown, but higher fatal temperatures range from 25 to 48 °C. Earthworms have a role to play, depending on the nature of organic residues, in both the formation and degradation of soil aggregates. Improvements in microbial biomass and plant growth have been established according to temperature, soil toxicity, soil type, earthworms abundance, organic residues types and field conditions. We observed that although the summer temperature in the arid area was approximately (°C 48), it was found that a particular type of earthworm (Namalycastis indica) was responsible for improving soil characteristics.While a great deal of analysis has been carried out on the role of earthworms within the soil ecology, such a review identifies important knowledge gaps, particularly in the determination of the impacts of earthworm species on the soil structure, microbial biomass and plant productivity, in particular since most papers focused on European species and overlooked the role of earthworms in the arid landscape. Further research is recommended to compare the impacts of different earthworms species on soil microbes and plant growth in various soil types, earthworm abundance, field conditions, organic residues locations, inorganic fertilizers, pesticides, fertile or non-fertile soils and diverse conditions of drought and moisture.     

The influence of rainfall on the incidence of microbial faecal indicators and the dominant sources of faecal pollution in a Florida river

AIMS: An assessment of microbial densities in an urbanized Florida watershed was performed during a period of changing rainfall patterns to investigate the role of climate coupled with urbanization in declining water quality. METHODS AND RESULTS: Concentrations of traditional and alternative faecal indicators were assessed by standard methods over 24 months. Sources of faecal contamination were determined by antibiotic resistance analysis (ARA) of faecal coliform (FC) bacteria. Composite indices of indicator organisms based on a suite of microbial measurements were used to quantify pollution impacts in the river. ARA results found that FC from wild animal sources dominated during the drought, and the relative frequency of FC from human sources increased after cumulative rainfall increased to near-normal levels. CONCLUSIONS: Changes observed in faecal indicator densities and in FC sources during changing rainfall patterns strongly suggest a role of precipitation on the sources and extent of microbial pollution in urbanized coastal watersheds. SIGNIFICANCE AND IMPACT OF THE STUDY: Bacterial source tracking coupled with a composite index of microbial contamination resulted in a more complete picture of microbial pollution within the river, as opposed to the general practice of reliance on one indicator organism. Improved land use decisions in urban areas are necessary to insure maintenance of coastal environmental health under changing climate patterns and population density.     

An automated point-of-care system for immunodetection of staphylococcal enterotoxin B

An automated point-of-care (POC) immunodetection system for immunological detection of staphylococcal enterotoxin B (SEB) was designed, fabricated, and tested. The system combines several elements: (i) enzyme-linked immunosorbent assay–lab-on-a-chip (ELISA–LOC) with fluidics, (ii) a charge-coupled device (CCD) camera detector, (iii) pumps and valves for fluid delivery to the ELISA–LOC, (iv) a computer interface board, and (v) a computer for controlling the fluidics, logging, and data analysis of the CCD data. The ELISA–LOC integrates a simple microfluidic system into a miniature 96-well sample plate, allowing the user to carry out immunological assays without a laboratory. The analyte is measured in a sandwich ELISA assay format combined with a sensitive electrochemiluminescence (ECL) detection method. Using the POC system, SEB, a major foodborne toxin, was detected at concentrations as low as 0.1 ng/ml. This is similar to the reported sensitivity of conventional ELISA. The open platform with simple modular fluid delivery automation design described here is interchangeable between detection systems, and because of its versatility it can also be used to automate many other LOC systems, simplifying LOC development. This new POC system is useful for carrying out various immunological and other complex medical assays without a laboratory and can easily be adapted for high-throughput biological screening in remote and resource-poor areas.     

Non-target impacts of forest defoliator management options: Decision for no spraying may have worse impacts on non-target Lepidoptera than Bacillus thuringiensis insecticides

Management programs for major forest defoliators such as gypsy moths or forest tent caterpillars, and crop pests such as the European corn borer have shifted from broad-spectrum insecticides to more environmentally benign microbial pesticides such as Bacillus thuringiensis (foliage sprays and transgenic toxin expression in plant tissues). Phytochemically resistant host plants and natural enemies have been used as alternative pest management strategies (including generalist tachinid flies such as Compsilura, viruses, microsporidians, and fungi), but all of these have some non-target impacts, as described from literature review. A sequence of lab and field studies were conducted to determine non-target impacts on native Lepidoptera in North America. The conclusions reached are that a decision not to spray Bt pesticides (i.e. to allow defoliation and natural pest outbreaks to run their course) could be as bad or worse for non-target Lepidoptera as the microbial insecticides would be. The important concept that must be maintained is that all pest management programs have some risk of negative non-target impacts, but it is the magnitude and relative importance that will remain the most critical issue for environmental impacts and pest management.     

全球变暖背景下土壤微生物呼吸的热适应性:证据、机理和争议

土壤微生物呼吸的热适应性被认为是决定陆地生态系统对全球变暖反馈作用的潜在重要机制,可能显著改变未来的气候变化趋势,然而学术界对于这一机制是否真实存在尚有分歧。阐述了土壤微生物呼吸的热适应性概念,从证据、机理和争议3方面对已有研究进展进行了综述和分析。土壤微生物呼吸的热适应性是微生物在群落尺度上对温度变化的适应性,具有坚实的生物学与生态学理论基础,研究者们运用各类指标已在许多实验中证实土壤微生物物种及群落的呼吸过程能够在高温环境产生适应性变化。土壤微生物呼吸的热适应性机理涉及生物膜结构变化、酶活性变化、微生物碳分配比例变化和微生物群落结构变化等方面。关于土壤微生物呼吸热适应性的争议可能是由研究方法、微生物物种及环境条件的差异引起的。根据对已有研究的分析,认为土壤微生物呼吸的热适应性是真实存在的,未来的研究可进一步探索土壤微生物呼吸的热适应性机理,深入研究环境和全球变化对土壤微生物呼吸的热适应性影响,定量评估土壤微生物呼吸的热适应性对陆地生态系统反馈过程的影响。     

Rapid filtration separation-based sample preparation method for Bacillus spores in powdery and environmental matrices

Authorities frequently need to analyze suspicious powders and other samples for biothreat agents in order to assess environmental safety. Numerous nucleic acid detection technologies have been developed to detect and identify biowarfare agents in a timely fashion. The extraction of microbial nucleic acids from a wide variety of powdery and environmental samples to obtain a quality level adequate for these technologies still remains a technical challenge. We aimed to develop a rapid and versatile method of separating bacteria from these samples and then extracting their microbial DNA. Bacillus atrophaeus subsp. globigii was used as a simulant of Bacillus anthracis. We studied the effects of a broad variety of powdery and environmental samples on PCR detection and the steps required to alleviate their interference. With a benchmark DNA extraction procedure, 17 of the 23 samples investigated interfered with bacterial lysis and/or PCR-based detection. Therefore, we developed the dual-filter method for applied recovery of microbial particles from environmental and powdery samples (DARE). The DARE procedure allows the separation of bacteria from contaminating matrices that interfere with PCR detection. This procedure required only 2 min, while the DNA extraction process lasted 7 min, for a total of <10 min. This sample preparation procedure allowed the recovery of cleaned bacterial spores and relieved detection interference caused by a wide variety of samples. Our procedure was easily completed in a laboratory facility and is amenable to field application and automation.     

Surviving the heat: heterogeneity of response in Saccharomyces cerevisiae provides insight into thermal damage to the membrane

Environmental heat stress impacts on the physiology and viability of microbial cells with concomitant implications for microbial activity and diversity. Previously, it has been demonstrated that gradual heating of Saccharomyces cerevisiae induces a degree of thermal resistance, whereas a heat shock results in a high level of cell death. Here, we show that the impact of exogenous nutrients on acquisition of thermal resistance differs between strains. Using single‐cell methods, we demonstrate the extent of heterogeneity of the heat‐stress response within populations of yeast cells and the presence of subpopulations that are reversibly damaged by heat stress. Such cells represent potential for recovery of entire populations once stresses are removed. The results show that plasma membrane permeability and potential are key factors involved in cell survival, but thermal resistance is not related to homeoviscous adaptation of the plasma membrane. These results have implications for growth and regrowth of populations experiencing environmental heat stress and our understanding of impacts at the level of the single cell. Given the important role of microbes in biofuel production and bioremediation, a thorough understanding of the impact of stress responses of populations and individuals is highly desirable.