Emerging high-throughput approaches to analyze bioremediation of sites contaminated with hazardous and/or recalcitrant wastes

Sustainable development requires the promotion of environmental management and a constant search for new technologies to treat a wide range of aquatic and terrestrial habitats contaminated by increasing anthropogenic activities. Bioremediation, i.e. the elimination of natural or xenobiotic pollutants by living organisms, is an environmentally friendly and cost-effective alternative to physico-chemical cleanup options. However, the strategy and outcome of bioremediation in open systems or confined environments depend on a variety of physico-chemical and biological factors that need to be assessed and monitored. In particular, microorganisms are key players in bioremediation applications, yet their catabolic potential and their dynamics in situ remain poorly characterized. To perform a comprehensive assessment of the biodegradative potential of a contaminated site and efficiently monitor changes in the structure and activities of microbial communities involved in bioremediation processes, sensitive, fast and large-scale methods are needed. Over the last few years, the scientific literature has revealed the progressive emergence of genomic high-throughput technologies in environmental microbiology and biotechnology. In this review, we discuss various high--throughput techniques and their possible--or already demonstrated-application to assess biotreatment of contaminated environments.     

增施氮肥能够缓解麦田土壤线虫群落对O3浓度升高的响应

在辽宁沈阳农田生态系统国家野外科学观测研究站,利用运行2a的开顶式气室,研究了臭氧(O3)浓度升高和不同氮肥施用水平对土壤线虫群落的影响。结果表明:(1)O3浓度升高降低了成熟期小麦根生物量。O3浓度升高和不同氮肥施用水平的交互作用改变了小麦成熟期土壤微生物生物量碳、氮和水溶性有机碳的含量。低氮条件下,O3浓度升高降低了土壤微生物生物量碳、氮和水溶性有机碳的含量;而高氮条件下则表现出相反的趋势。(2)O3浓度升高和不同氮肥施用水平对土壤线虫总数没有产生显著影响,而在灌浆期,食细菌线虫和食真菌线虫中c-p值为4(Ba4 and Fu4)的功能团对O3浓度升高和不同氮肥施用水平的响应敏感;与对照相比,不同氮处理中,O3浓度升高均降低了灌浆期Ba4功能团线虫的数量。灌浆期,O3浓度升高条件下,与对照相比Fu4功能团线虫数量在高氮条件下表现出增加的趋势,而在低氮条件表现出降低的趋势。(3)O3浓度升高和不同氮肥施用水平的交互作用显著影响了小麦灌浆期线虫的成熟度指数(MI)和结构指数(SI)。与对照相比,线虫成熟度指数和结构指数在低氮条件下随O3浓度升高而降低;而在高氮条件下随O3浓度升高而升高。上述结果表明,氮肥的施用能够缓解O3浓度升高对土壤食物网的扰动。     

Developing a Benthic Index of Biological Integrity and Some Relationships to Environmental Factors in the Subtropical Xiangxi River,China

The aim of this study is to develop a benthic index of biotic integrity (B‐IBI) to help understand how the increasing anthropogenic pressure may impact the subtropical Xiangxi River in China. Benthic macroinvertebrate and environmental surveys were conducted at 77 sites in early summer 2004. Each collection site was categorized as reference or impaired based on physical, chemical, biological, and land‐use information. Six non‐redundant metrics from 35 metrics were used to differentiate between reference and impaired sites. We selected six metrics for the final IBI. The scoring criteria of each metric were normalized based on the quadrisection and 0–10 scaling systems. Both scaling methods were used to assess the aquatic health of each site in the Xiangxi River watershed. The results showed that most sites were in fairly poor condition. Furthermore, we identified the relationship between B‐IBI metrics, water‐quality, and land‐use variables with a principal component analysis. A composite of nutrients and land‐use intensity explained most variances. These results suggest that the B‐IBI may be a suitable method for assessing river conditions within the subtropical Xiangxi River in central China (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Cover crops and compost prevent weed seed bank buildup in herbicide‐free wheat–potato rotations under conservation tillage

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Varietal effects of eight paired lines of transgenic Bt maize and near-isogenic non-Bt maize on soil microbial and nematode community structure

A glasshouse experiment was undertaken to provide baseline data on the variation between conventional maize (Zea mays L.) varieties and genetically modified maize plants expressing the insecticidal Bacillus thuringiensis protein (Bt, Cry1Ab). The objective was to determine whether the variation in soil parameters under a range of conventional maize cultivars exceeded the differences between Bt and non-Bt maize cultivars. Variations in plant growth parameters (shoot and root biomass, percentage carbon, percentage nitrogen), Bt protein concentration in shoots, roots and soil, soil nematode abundance and soil microbial community structure were determined. Eight paired varieties (i.e. varieties genetically modified to express Bt protein and their near-isogenic control varieties) were investigated, together with a Bt variety for which no near-isogenic control was available (NX3622, a combined transformant expressing both Bt and herbicide tolerance) and a conventional barley (Hordeum vulgare L.) variety which was included as a positive control. The only plant parameter which showed a difference between Bt varieties and near-isogenic counterparts was the shoot carbon to nitrogen ratio; this was observed for only two of the eight varieties, and so was not attributable to the Bt trait. There were no detectable differences in the concentration of Bt protein in plant or soil with any of the Bt-expressing varieties. There were significant differences in the abundance of soil nematodes, but this was not related to the Bt trait. Differences in previously published soil nematode studies under Bt maize were smaller than these varietal effects. Soil microbial community structure, as determined by phospholipid fatty acid (PLFA) analysis, was strongly affected by plant growth stage but not by the Bt trait. The experimental addition of purified Cry1Ab protein to soil confirmed that, at ecologically relevant concentrations, there were no measurable effects on microbial community structure.     

Integration of Biological Control and Native Seeding to Restore Invaded Plant Communities

Disturbed natural areas frequently experience invasion by introduced plant species that can reduce native biodiversity. Biological control can suppress these introduced species, but without restoration another introduced species can invade. Integration of biological control with concurrent revegetation can both aid in weed reduction via interspecific plant competition and establish a restored native plant community. This 3‐year study investigated an integrated approach to controlling the introduced annual Mile‐a‐minute weed (Persicaria perfoliata [L.] H. Gross [Polygonaceae]) using the biocontrol weevil Rhinoncomimus latipes Korotyaev (Coleoptera: Curculionidae) and restoration planting using a native seed mix. A fully factorial design tested weevils and seeding, separately and together, using insecticide to eliminate weevils. The weevils together with the native seed mix reduced P. perfoliata percent cover in 2009 and 2010, and peak seed cluster production in 2010, compared to the insecticide ? no seed control treatment. Persicaria perfoliata final dry biomass was reduced by 75% in 2010 and by 57% in 2011 in the weevils plus seed treatment compared to the control, with weevils having the greatest effect in 2010 and the seed treatment having the greatest impact in 2011. Results suggest an additive effect of biocontrol and seeding in suppressing P. perfoliata. Seeded treatments also developed the highest native plant species richness and diversity, comprised of spontaneous recolonization in addition to species from the seed mix. Results support the use of integrated management of this invasive weed, with suppression through biological control and native revegetation together helping prevent reinvasion while restoring native plant biodiversity.     

Landscape fragmentation affects responses of avian communities to climate change

Forecasting the consequences of climate change is contingent upon our understanding of the relationship between biodiversity patterns and climatic variability. While the impacts of climate change on individual species have been well‐documented, there is a paucity of studies on climate‐mediated changes in community dynamics. Our objectives were to investigate the relationship between temporal turnover in avian biodiversity and changes in climatic conditions and to assess the role of landscape fragmentation in affecting this relationship. We hypothesized that community turnover would be highest in regions experiencing the most pronounced changes in climate and that these patterns would be reduced in human‐dominated landscapes. To test this hypothesis, we quantified temporal turnover in avian communities over a 20‐year period using data from the New York State Breeding Atlases collected during 1980–1985 and 2000–2005. We applied Bayesian spatially varying intercept models to evaluate the relationship between temporal turnover and temporal trends in climatic conditions and landscape fragmentation. We found that models including interaction terms between climate change and landscape fragmentation were superior to models without the interaction terms, suggesting that the relationship between avian community turnover and changes in climatic conditions was affected by the level of landscape fragmentation. Specifically, we found weaker associations between temporal turnover and climatic change in regions with prevalent habitat fragmentation. We suggest that avian communities in fragmented landscapes are more robust to climate change than communities found in contiguous habitats because they are comprised of species with wider thermal niches and thus are less susceptible to shifts in climatic variability. We conclude that highly fragmented regions are likely to undergo less pronounced changes in composition and structure of faunal communities as a result of climate change, whereas those changes are likely to be greater in contiguous and unfragmented habitats.     

Density‐related effects on the infectivity and aggressiveness of a sterilising smut in a wild population of Digitaria sanguinalis

Understanding host–pathogen evolutionary dynamics needs characterisation and quantification of processes occurring at many spatiotemporal scales. With this aim, the effects of smut on a naturally infected population of the summer annual Digitaria sanguinalis were followed for 4 years in an uncropped field. The main purpose of the study was to quantify the effects of within‐population density on the infectivity and the aggressiveness of the pathogen in a range of densities that occurred naturally. The infectivity‐related variable measured was the proportion of smutted plants at the end of each growing season; proportions were analysed using a generalised linear model with a binomial distribution considering the year, the density and their interaction as effects. The aggressiveness‐related variables chosen were the number of smutted inflorescences per plant and per area, obtained over the last 2 years; they were analysed by means of ancova considering disease status (seeded or smutted), year, density and all the interactions between them. Although the disease is monocyclic, results showed clearly that infectivity increased with plant density. The number of inflorescences per plant was 1.5 times higher in smutted plants than in healthy plants throughout the range of densities. This variable declined when density increased, but as the infectivity increased at a higher rate, the aggressiveness also increased with density. The surprising results on infectivity are discussed in the context of current knowledge of plant–pathogen interaction dynamics, as well as neighbour effects on pathogen aggressiveness. Moreover, the results could be useful to develop weed biological control strategies.     

深圳南山区天然植物群落的聚类分析

运用组平均聚类法,以44个样方中80个种的重要值为数据,对深圳南山区天然植物群落进行聚类分析。根据聚类结果,南山区天然植物群落可划分为8个群系19个群丛,较全面地反映了群落的组成结构以及群落的生境,为南山区植物群落的保护和管理提供了科学依据。