Universal ligation-detection-reaction microarray applied for compost microbes

Background  

Composting is one of the methods utilised in recycling organic communal waste. The composting process is dependent on aerobic microbial activity and proceeds through a succession of different phases each dominated by certain microorganisms. In this study, a ligation-detection-reaction (LDR) based microarray method was adapted for species-level detection of compost microbes characteristic of each stage of the composting process. LDR utilises the specifiCity of the ligase enzyme to covalently join two adjacently hybridised probes. A zip-oligo is attached to the 3'-end of one probe and fluorescent label to the 5'-end of the other probe. Upon ligation, the probes are combined in the same molecule and can be detected in a specific location on a universal microarray with complementary zip-oligos enabling equivalent hybridisation conditions for all probes. The method was applied to samples from Nordic composting facilities after testing and optimisation with fungal pure cultures and environmental clones.     

Environmental impact of two aerobic composting technologies using life cycle assessment

Background, aim, and scope  Composting is a viable technology to treat the organic fraction of municipal solid waste (OFMSW) because it stabilizes biodegradable organic matter and contributes to reduce the quantity of municipal solid waste to be incinerated or land-filled. However, the composting process generates environmental impacts such as atmospheric emissions and resources consumption that should be studied. This work presents the inventory data and the study of the environmental impact of two real composting plants using different technologies, tunnels (CT) and confined windrows (CCW). Materials and methods  Inventory data of the two composting facilities studied were obtained from field measurements and from plant managers. Next, life cycle assessment (LCA) methodology was used to calculate the environmental impacts. Composting facilities were located in Catalonia (Spain) and were evaluated during 2007. Both studied plants treat source separated organic fraction of municipal solid waste. In both installations the analysis includes environmental impact from fuel, water, and electricity consumption and the main gaseous emissions from the composting process itself (ammonia and volatile organic compounds). Results and discussion  Inventory analysis permitted the calculation of different ratios corresponding to resources consumption or plant performance and process yield with respect to 1 t of OFMSW. Among them, it can be highlighted that in both studied plants total energy consumption necessary to treat the OFMSW and transform it into compost was between 130 and 160 kWh/t OFMSW. Environmental impact was evaluated in terms of global warming potential (around 60 kg CO₂/t OFMSW for both plants), acidification potential (7.13 and 3.69 kg SO₂ eq/t OFMSW for CT and CCW plant respectively), photochemical oxidation potential (0.1 and 3.11 kg C₂H₄ eq/t OFMSW for CT and CCW plant, respectively), eutrophication (1.51 and 0.77 kg /t OFMSW for CT and CCW plant, respectively), human toxicity (around 15 kg 1,4-DB eq/t OFMSW for both plants) and ozone layer depletion (1.66 × 10⁻⁵ and 2.77 × 10⁻⁵ kg CFC⁻¹¹ eq/t OFMSW for CT and CCW plant, respectively). Conclusions  This work reflects that the life cycle perspective is a useful tool to analyze a composting process since it permits the comparison among different technologies. According to our results total energy consumption required for composting OFMSW is dependent on the technology used (ranging from 130 to 160 kWh/t OFMSW) as water consumption is (from 0.02 to 0.33 m³ of water/t OFMSW). Gaseous emissions from the composting process represent the main contribution to eutrophication, acidification and photochemical oxidation potentials, while those contributions related to energy consumption are the principal responsible for global warming. Recommendations and perspectives  This work provides the evaluation of environmental impacts of two composting technologies that can be useful for its application to composting plants with similar characteristics. In addition, this study can also be part of future works to compare composting with other OFMSW treatments from a LCA perspective. Likewise, the results can be used for the elaboration of a greenhouse gasses emissions inventory in Catalonia and Spain.     

Profiling of bacterial community in a full-scale aerobic composting plant

Changes in temperature, pH, moisture, C/N ratio, and bacterial community were monitored in Istanbul full-scale composting plant. C/N ratio steadily decreased during composting and final mature compost products had a C/N ratio of less than 20. During the composting process, temperature was mostly above 55 °C and decreased to mesophilic conditions in the matured stages. Different types of bacteria were dominant in every stage of composting and bacterial diversity changed mainly by temperature. Bacillus species were dominant in early stages of composting while Acinetobacter and Sphingobacterium strains were detected in thermophilic and maturing stages. Bacteria were mainly active in the degradation of cellulose and toxic organics while some strains had denitrification ability. Generally, thermophilic stages were more rich in bacterial diversity than mesophilic and hyperthermophilic conditions significantly changed the bacterial community.     

Inhibitory effects of Eucalyptus globulus on understorey plant growth and species richness are greater in non‐native regions

Aim

We studied the novel weapons hypothesis in the context of the broadly distributed tree species Eucalyptus globulus. We evaluated the hypothesis that this Australian species would produce stronger inhibitory effects on species from its non‐native range than on species from its native range.

Location

We worked in four countries where this species is exotic (U.S.A., Chile, India, Portugal) and one country where it is native (Australia).

Time period

2009–2012.

Major taxa studied

Plants.

Methods

We compared species composition, richness and height of plant communities in 20 paired plots underneath E. globulus individuals and open areas in two sites within its native range and each non‐native region. We also compared effects of litter leachates of E. globulus on root growth of seedlings in species from Australia, Chile, the U.S.A. and India.

Results

In all sites and countries, the plant community under E. globulus canopies had lower species richness than did the plant community in open areas. However, the reduction was much greater in the non‐native ranges: species richness declined by an average of 51% in the eight non‐native sites versus 8% in the two native Australian sites. The root growth of 15 out of 21 species from the non‐native range were highly suppressed by E. globulus litter leachates, whereas the effect of litter leachate varied from facilitation to suppression for six species native to Australia. The mean reduction in root growth for Australian plants was significantly lower than for plants from the U.S.A., Chile and India.

Main conclusions

Our results show biogeographical differences in the impact of an exotic species on understorey plant communities. Consistent with the novel weapons hypothesis, our findings suggest that different adaptations of species from the native and non‐native ranges to biochemical compounds produced by an exotic species may play a role in these biogeographical differences.     

畜禽粪便堆肥过程中氮素的损失与控制

堆肥是实现畜禽粪便处理及资源化利用的有效途径,然而畜禽粪便堆肥过程中氮素损失较严重,对氮素损失与控制的研究可为有效控制氮素损失提供理论基础和实践参考.本文简述了畜禽粪便堆肥过程中氮素转化及主要损失途径,总结了影响堆肥氮素损失的主要因素(包括堆肥物料初始特性、堆肥环境参数和堆肥工艺条件),并综述了氮素损失控制措施(调节C、N代谢,改变氮素形态,添加NH₃吸附剂和调节通风与控温措施)的研究进展,此外,对未来的研究方向进行了展望.     

Identification of genic moss SSR markers and a comparative analysis of twenty-four algal and plant gene indices reveal species-specific rather than group-specific characteristics of microsatellites

Background  

The moss Physcomitrella patens is an emerging model in comparative plant science. At present, the Physcomitrella genome is sequenced at the Joint Genome Institute (USA). In this study we present our results on the development of expressed sequence tag-derived microsatellite markers for Physcomitrella patens, their classification and applicability as genetic markers on the intra- as well as on the interspecies level. We experienced severe restrictions to compare our results on Physcomitrella with earlier studies for other plant species due to varying microsatellite search criteria and a limited selection of analysed species. As a consequence, we performed a side by side analysis of expressed sequence tag-derived microsatellites among 24 plant species covering a broad phylogenetic range and present our results on the observed frequencies.     

Variations of culturable thermophilic microbe numbers and bacterial communities during the thermophilic phase of composting

Composting is a process of stabilizing organic wastes through the degradation of biodegradable components by microbial communities under controlled conditions. In the present study, genera and species diversities, amylohydrolysis, protein and cellulose degradation abilities of culturable bacteria in the thermophilic phase of composting of cattle manure with plant ash and rice bran were investigated. The number of culturable thermophilic bacteria and actinomyces decreased with the increasing temperature. At the initiation and end of the thermophilic phase, genera and specie diversities and number of bacteria possessing degradation abilities were higher than during the middle phase. During the thermophilic composting phase, Bacillus, Geobacillus and Ureibacillus were the dominant genera, and Geobacillus thermodenitrificans was the dominant species. In later thermophilic phases, Geobacillus toebii and Ureibacillus terrenus were dominant. Bacillus, at the initiation, and Ureibacillus and Geobacillus, at the later phase, contributed the multiple degradation abilities. These data will facilitate the control of composting in the future.     

添加竹炭对猪粪堆肥过程中升温脱水及氮素损失的影响

堆肥是实现畜禽粪便处理及资源化利用的有效途径,但传统堆肥过程存在升温脱水效果不佳及氮素损失的问题.本文利用猪粪进行堆肥试验,探讨了堆肥过程中添加不同比例竹炭对堆肥升温脱水及氮素损失的影响.结果表明: 与不添加竹炭的对照相比,添加竹炭处理可以使堆体升温时间缩短24～48 h,脱水率提高13.6%～21.4%,堆肥高温期持续时间延长216～264 h;添加竹炭处理可以增加堆肥铵态氮、硝态氮及总氮含量,使氮素固定率提高28.3%～65.4%.
     

Characterisation of microRNAs from apple (<Emphasis Type="Italic">Malus domestica</Emphasis>'Royal Gala') vascular tissue and phloem sap

Background  

Plant microRNAs (miRNAs) are a class of small, non-coding RNAs that play an important role in development and environmental responses. Hundreds of plant miRNAs have been identified to date, mainly from the model species for which there are available genome sequences. The current challenge is to characterise miRNAs from plant species with agricultural and horticultural importance, to aid our understanding of important regulatory mechanisms in crop species and enable improvement of crops and rootstocks.     

Shift from facilitative to neutral interactions by the cushion plant Silene acaulis along a primary succession gradient

Background

The stress‐gradient hypothesis predicts a shift from facilitative to competitive plant interactions with decreasing abiotic stress. This has been supported by studies along elevation and temperature gradients, but also challenged by the hypothesis of a facilitation collapse at extremely harsh sites. Although facilitation is known to be important in primary succession, few studies have examined these hypotheses along primary succession gradients.

Aim

To examine whether there is a relationship between the presence of the circumpolar cushion plant Silene acaulis and other species, and if so, whether there is a shift between positive and negative interactions along a primary succession gradient in a glacier foreland.

Location

Finse, southern Norway.

Methods

We examined the performance of the common alpine forb Bistorta vivipara, species richness of vascular plants, bryophytes and lichens, and the number of seedlings and fertile vascular plants in S. acaulis cushions, and control plots without S. acaulis, along a succession gradient with increasing distance from a glacier front, and thus decreasing abiotic stress. To examine if S. acaulis cushions modify the abiotic environment, we recorded soil temperature, moisture, organic content and pH in cushions and control plots.

Results

Bistorta vivipara performed better, as shown by bigger leaves in S. acaulis cushions compared to control plots in the harshest part of the gradient close to the glacier. There were few differences in B. vivipara performance between cushion and control plots in the more benign environment further away from the glacier. This suggests a shift from facilitative to mainly neutral interactions by S. acaulis on the performance of B. vivipara with decreasing abiotic stress. A trend, although not significant, of higher vascular species richness and fertility inside S. acaulis cushions along the whole gradient, suggests that S. acaulis also facilitates community‐level species richness. The causal mechanism of this facilitation is likely that the cushions buffer extreme temperatures.

Conclusions

Our results support the stress‐gradient hypothesis for the relationship between the cushion plant S. acaulis and the performance of a single species along a primary succession gradient in a glacier foreland. S. acaulis also tended to increase vascular plant species richness and fertility regardless of stress level along the gradient, suggesting facilitation at the community level. We found no collapse of facilitation at the most stressful end of the gradient in this alpine glacier foreland.     

Composting of de-inking sludge from the recycled paper manufacturing industry

Composting of two different types of sludge from the recycled paper manufacturing industry was carried out at laboratory scale. Physico-chemical sludge (PCS) from the de-inking process and biological sludge (BS) from the wastewater treatment plant were composted and co-composted with and without addition of a bulking material. Despite its poor initial characteristics (relatively high C/N ratio, low organic content and moisture), PCS showed excellent behaviour in the composting process, reaching and maintaining thermophilic temperatures for more than 7 days at laboratory scale, and therefore complete hygienization. Pilot scale composting of PCS was also studied, and a respiratory quotient of 1.19 was obtained, indicating a full aerobic biological process. Respiration tests showed a complete stabilization of the material, with final values of the static respiration index in the range of 1.1 mg O2gTOM(-1)h(-1). Composting is proposed as a suitable technology for the effective recycling of this type of sludge from the recycled paper manufacturing industry.     

Effects of fire regime on plant species richness and composition differ among forest,woodland and heath vegetation

Question

Do the effects of fire regimes on plant species richness and composition differ among floristically similar vegetation types?

Location

Booderee National Park, south‐eastern Australia.

Methods

We completed floristic surveys of 87 sites in Sydney Coastal dry sclerophyll vegetation, where fire history records have been maintained for over 55 years. We tested for associations between different aspects of the recent fire history and plant species richness and composition, and whether these relationships were consistent among structurally defined forest, woodland and heath vegetation types.

Results

The relationship between fire regime variables and plant species richness and composition differed among vegetation types, despite the three vegetation types having similar species pools. Fire frequency was positively related to species richness in woodland, negatively related to species richness in heath, and unrelated to species richness in forest. These different relationships were explained by differences in the associations between fire history and species traits among vegetation types. The negative relationship between fire frequency and species richness in heath vegetation was underpinned by reduced occurrence of resprouting species at high fire frequency sites (more than four fires in 55 years). However, in forest and woodland vegetation, resprouting species were not negatively associated with fire frequency.

Conclusions

We hypothesize that differing relationships among vegetation types were underpinned by differences in fire behaviour, and/or biotic and abiotic conditions, leading to differences in plant species mortality and post‐fire recovery among vegetation types. Our findings suggest that even when there is a high proportion of shared species between vegetation types, fires can have very different effects on vegetation communities, depending on the structural vegetation type. Both research and management of fire regimes may therefore benefit from considering vegetation types as separate management units.     

The biosecurity of on-farm mortality composting

Composting is a natural biological decomposition process that takes place under aerobic and thermophilic conditions. It can be used for the day-to-day management of mortalities on farms and for carcass disposal in emergency animal disease (EAD) outbreaks. In mortality composting, carcasses are placed in piles or bins together with supplemental carbon sources such as sawdust, litter, straw or wood shavings. Composting is particularly suitable for broiler-farm mortalities and litter. In the case of emergency disease outbreaks, composting can be conducted either inside or outside the poultry house following killing. Composting has been successfully employed for emergency disposal of carcasses in a few cases in North America, but research is lacking on the biosecurity of the process. Composting is a well-established pathogen reduction technology, but process management and heterogenous pile conditions pose particular challenges for validating the microbiological safety of mortality composting. This paper reviews the available information on the biosecurity of mortality composting, identifies potential sources of risk, and highlights emerging research needs. Reports to date of the use of composting in EAD outbreaks are also discussed.     

Isolation and functional characterization of a cDNA coding a hydroxycinnamoyltransferase involved in phenylpropanoid biosynthesis in <Emphasis Type="Italic">Cynara cardunculus</Emphasis> L

Background  

Cynara cardunculus L. is an edible plant of pharmaceutical interest, in particular with respect to the polyphenolic content of its leaves. It includes three taxa: globe artichoke, cultivated cardoon, and wild cardoon. The dominating phenolics are the di-caffeoylquinic acids (such as cynarin), which are largely restricted to Cynara species, along with their precursor, chlorogenic acid (CGA). The scope of this study is to better understand CGA synthesis in this plant.     

A membrane-bound matrix-metalloproteinase from Nicotiana tabacum cv. BY-2 is induced by bacterial pathogens

Background  

Plant matrix metalloproteinases (MMP) are conserved proteolytic enzymes found in a wide range of monocotyledonous and dicotyledonous plant species. Acting on the plant extracellular matrix, they play crucial roles in many aspects of plant physiology including growth, development and the response to stresses such as pathogen attack.     

Ditches as species‐rich secondary habitats and refuge for meadow species in agricultural marsh grasslands

Questions

Can drainage ditches in agricultural marsh grassland provide a suitable habitat for the persistence of fen meadow species? How does the ditch margin vegetation develop as a function of regular dredging? Is ornithologically oriented management also beneficial for plant biodiversity?

Location

Riparian marshes, Eider‐Treene‐Sorge lowland, Schleswig‐Holstein, Germany.

Methods

We performed vegetation surveys of drainage ditches along with their water body, slope and margin structures annually for 3 years. The data were analysed with respect to date and means of ditch dredging. In addition, we recorded vegetation of the surrounding agricultural grassland, measured nutrient status of the soil and the water body and sampled seed bank of the ditch slopes. We used ANOVA and multivariate methods to describe the development of the ditch vegetation and the persistence of target meadow species.

Results

Vegetation re‐development of ditch margins proceeds quite rapidly after disturbance from dredging. Dominance of mudbank species was observed only in the first year, followed by an increase of reed species and reduction of phytodiversity. Target species of wet meadow communities reach highest abundance in the second and third year and build a significant seed bank before being suppressed by reeds.

Conclusions

In heavily eutrophicated, intensively used marsh grassland, regularly disturbed ditch margins are important secondary habitats for pioneer and subdominant wetland species, which have nearly disappeared in a larger area. Current management cycles of ditch dredging every 3–4 years comply with the successional development, allowing the mudbank and wet meadow species to persist in the vegetation and seed bank. In contrast to the frequency, the form of dredging (ditch profile), which is crucial for bird protection, plays a minor role for plants. We recommend moderate disturbance (mowing of ditch margins) to suppress strong competitors in the years between dredging for additional support to target plant species.     

Plant traits correlated with generation time directly affect inbreeding depression and mating system and indirectly genetic structure

Background  

Understanding the mechanisms that control species genetic structure has always been a major objective in evolutionary studies. The association between genetic structure and species attributes has received special attention. As species attributes are highly taxonomically constrained, phylogenetically controlled methods are necessary to infer causal relationships. In plants, a previous study controlling for phylogenetic signal has demonstrated that Wright's F _ST, a measure of genetic differentiation among populations, is best predicted by the mating system (outcrossing, mixed-mating or selfing) and that plant traits such as perenniality and growth form have only an indirect influence on F _ST via their association with the mating system. The objective of this study is to further outline the determinants of plant genetic structure by distinguishing the effects of mating system on gene flow and on genetic drift. The association of biparental inbreeding and inbreeding depression with population genetic structure, mating system and plant traits are also investigated.     

Structure and evolution of <Emphasis Type="Italic">Apetala3</Emphasis>, a sex-linked gene in <Emphasis Type="Italic">Silene latifolia</Emphasis>

Background  

The evolution of sex chromosomes is often accompanied by gene or chromosome rearrangements. Recently, the gene AP3 was characterized in the dioecious plant species Silene latifolia. It was suggested that this gene had been transferred from an autosome to the Y chromosome.     

Recombination in Glomus intraradices, a supposed ancient asexual arbuscular mycorrhizal fungus

Background  

Arbuscular mycorrhizal fungi (AMF) are important symbionts of most plant species, promoting plant diversity and productivity. This symbiosis is thought to have contributed to the early colonisation of land by plants. Morphological stasis over 400 million years and the lack of an observed sexual stage in any member of the phylum Glomeromycota led to the controversial suggestion of AMF being ancients asexuals. Evidence for recombination in AMF is contradictory.