Predicting root biomass from branching patterns of Douglas-fir root systems

There are many examples of branching networks in nature, such as tree crowns, river systems, arteries and lungs. These networks have often been described as being self-similar, or following scale-invariant branching rules, and this property has been used to derive several scaling laws. In this paper we model root systems of Douglas-fir ( Pseudotsuga menziesii var. glauca (Beissn.) Franco) as branching networks following several simple branching rules. Our objective is to establish a relationship between trunk diameter and root biomass. We explore the effect of the self-similar branching assumption on this relationship. Using data collected from a mature stand in British Columbia, we find that branching asymmetry and the rate of root taper change with root size, thereby violating the assumption of self-similarity. However, the data are in general agreement with Leonardo da Vinci's area-preserving branching hypothesis. We use the field data to parameterize two models, one assuming self-similar branching and a second incorporating the measured size dependencies of branching parameters. The two models differ by only a small amount (≈8%) in their predictions. For both models, the predicted relationship between trunk diameter and root biomass is in good concordance with previously published empirical data. We conclude that the assumption of self-similar branching, although violated by the data, nevertheless provides a useful tool for predicting the allometric relationship between trunk diameter and root biomass. Finally, we use our models to show that the geometric properties of individual bifurcations fundamentally change the root biomass cost of different root topologies.     

Effect of interstage mixing in multistage culture systems on continuous biomass production

The significance of the interstage mixing on important process parameters of biomass production was studied. The experiments were performed in a multistage tower fermentor and in fermentors in series. The interstage mixing effect can be evaluated under conditions of geometrical similarity, identity of oxygen transfer rate, and identity of dilution rate per stage in the individual stages of both culture systems. Candida utilis was cultivated on a synthetic medium with ethanol as the sole carbon and energy source in the concentration range 10–100 g/liter. Dilution rate, temperature, and pH in each stage of both culture systems were kept constant. It was demonstrated that in the multistage tower fermentor the definite backflow which ensures the permanent reinoculation by adapted cells significantly decreases the inhibitory effect of higher ethanol concentrations on the cell growth and on the rate of ethanol utilization.     

High root biomass production in anchored Arabidopsis plants grown in axenic sucrose supplemented liquid culture

There are many benefits to growing Arabidopsis in solution-based media, especially when large amounts of root tissue are required for molecular and biochemical studies. Roots grown in soil are brittle and tend to break easily when removed from their substrate. We have developed an axenic liquid culture system that simplifies growing large amounts of roots from intact plants. This technique consists of germinating 15 seeds on 2.5 cm2 stainless steel screens placed on half-strength semisolid Murashige and Skoog medium containing 1% or 2% sucrose. The screens anchor and support the plantlets in an upright position while keeping the roots and shoots separate. The seedlings are transferred with forceps to 125-mL wide-mouth Erlenmeyer flasks containing 10 mL of half-strength Murashige and Skoog liquid medium and 1% sucrose. The flasks are placed onto a floor rotary shaker under fluorescent lights. After 3 days, the sucrose is increased to 3% and the volume to 15 mL for 7 days. During any further experimental manipulations, sucrose is not supplied. The media is changed every 3-4 days to replenish the nutrients. The presence of sucrose in the media dramatically increases the biomass, and large amounts of root tissue can easily be harvested.     

Fine root biomass and turnover of two fast-growing poplar genotypes in a short-rotation coppice culture

Background and aims

The quantification of root dynamics remains a major challenge in ecological research because root sampling is laborious and prone to error due to unavoidable disturbance of the delicate soil-root interface. The objective of the present study was to quantify the distribution of the biomass and turnover of roots of poplars (Populus) and associated understory vegetation during the second growing season of a high-density short rotation coppice culture.

Methods

Roots were manually picked from soil samples collected with a soil core from narrow (75 cm apart) and wide rows (150 cm apart) of the double-row planting system from two genetically contrasting poplar genotypes. Several methods of estimating root production and turnover were compared.

Results

Poplar fine root biomass was higher in the narrow rows than in the wide rows. In spite of genetic differences in above-ground biomass, annual fine root productivity was similar for both genotypes (ca. 44 g DM m^?2 year^?1). Weed root biomass was equally distributed over the ground surface, and root productivity was more than two times higher compared to poplar fine roots (ca. 109 g DM m^?2 year^?1).

Conclusions

Early in SRC plantation development, weeds result in significant root competition to the crop tree poplars, but may confer certain ecosystem services such as carbon input to soil and retention of available soil N until the trees fully occupy the site.     

An analysis of dorsal root ganglia differentiation using three tissue culture systems

Summary The histogenesis of the dorsal root ganglia of chick embryos (ages 3 to 9 days) was followed in three different tissue culture systems. Organotypic explants included dorsal root ganglia connected to the lumbosacral segment of the spinal cord or isolated explants of the contralateral ganglia. Additionally, dissociated monolayer cultures of ganglia tissue were established. The gradual differentiation of progenitor neuroblasts into distinct populations of large ventrolateral and small dorsomedial neurons was observed in vivo and in vitro. Neurites developed after 3 days in the presence or absence of nerve growth factor in the medium. In contrast, autoradiographic analysis indicates that [³H]thymidine incorporation in neuronal cultures differed significantly from intact embryos. In vivo, the number of neuronal progenitor cells labeled with [³H]thymidine decreased in older embryos; in vitro, uptake of [³H]thymidine label was not observed in ganglionic progenitor cells regardless of the age of the donor embryo or the type of culture system. Lack of proliferation in ganglionic progenitor cells was not due to degeneration because vital staining and uptake of [³H]deoxyglucose indicated that neurons were metabolically active. Furthermore, the block in mitotic activity in vitro was limited to presumptive ganglionic neuronal cells. In the ependyma of the spinal cord segment connected to the dorsal root ganglia, neuronal progenitor cells were heavily labeled as were non-neuronal cells within both spinal cord and ganglia. Our results suggest that in vitro conditions can promote the differentiation of sensory neurons from early embryos (E3.5–4.5) without proliferation of progenitor cells.     

Efficiency of neural network-based combinatorial model predicting optimal culture conditions for maximum biomass yields in hairy root cultures

Key message

ANN-based combinatorial model is proposed and its efficiency is assessed for the prediction of optimal culture conditions to achieve maximum productivity in a bioprocess in terms of high biomass.

Abstract

A neural network approach is utilized in combination with Hidden Markov concept to assess the optimal values of different environmental factors that result in maximum biomass productivity of cultured tissues after definite culture duration. Five hidden Markov models (HMMs) were derived for five test culture conditions, i.e. pH of liquid growth medium, volume of medium per culture vessel, sucrose concentration (%w/v) in growth medium, nitrate concentration (g/l) in the medium and finally the density of initial inoculum (g fresh weight) per culture vessel and their corresponding fresh weight biomass. The artificial neural network (ANN) model was represented as the function of these five Markov models, and the overall simulation of fresh weight biomass was done with this combinatorial ANN–HMM. The empirical results of Rauwolfia serpentina hairy roots were taken as model and compared with simulated results obtained from pure ANN and ANN–HMMs. The stochastic testing and Cronbach’s α-value of pure and combinatorial model revealed more internal consistency and skewed character (0.4635) in histogram of ANN–HMM compared to pure ANN (0.3804). The simulated results for optimal conditions of maximum fresh weight production obtained from ANN–HMM and ANN model closely resemble the experimentally optimized culture conditions based on which highest fresh weight was obtained. However, only 2.99 % deviation from the experimental values could be observed in the values obtained from combinatorial model when compared to the pure ANN model (5.44 %). This comparison showed 45 % better potential of combinatorial model for the prediction of optimal culture conditions for the best growth of hairy root cultures.     

Biotechnology of algal biomass production: a review of systems for outdoor mass culture

Microalgae are very efficient solar energy converters and they can produce a great variety of metabolites. Man has always tried to take advantage of these proporties through algal mass culture. Despite the fact that many applications for microalgae have been described in the literature, these micro-organisms are still of minor economic importance. Industrial reactors for algal culture are at present, all designed as open race-ways (shallow open ponds where culture is circulated by a paddle-wheel). Technical and biological limitations of these open systems have given rise to the development of enclosed photoreactors (made of transparent tubes, sleeves or containers and where light source may be natural or artificial). The present review surveys advances in these two technologies for cultivation of microalgae. Starting from published results, the advantages and disadvantages of open systems and closed photobioreactors are discussed. A few open systems are presented for which particularly reliable results are available. Emphasis is then put on closed systems, which have been considered as capital intensive and are justified only when a fine chemical is to be produced.     

Fine root biomass and turnover in southern taiga estimated by root inclusion nets

Fine roots play an important part in forest carbon, nutrient and water cycles. The turnover of fine roots constitutes a major carbon input to soils. Estimation of fine root turnover is difficult, labour intensive and is often compounded by artefacts created by soil disturbance. In this work, an alternative approach of using inclusion nets installed in an undisturbed soil profile was used to measure fine root production and was compared to the in-growth core method. There was no difference between fine root production estimated by the two methods in three southern taiga sites with contrasting soil conditions and tree species compositions in the Central Forest State Biosphere Reserve, Russia. Expressed as annual production over standing biomass, Norway spruce fine root turnover was in the region of 0.10 to 0.24 y^-1. The inclusion net technique is suitable for field based assessment of fine root production. There are several advantages over the in-growth core method, due to non-disturbance of the soil profile and its potential for very high rate of replication.     

Co-ordinated growth between aerial and root systems in young apple plants issued from in vitro culture

BACKGROUND AND AIMS: In several species exhibiting a rhythmic aerial growth, the existence of an alternation between root and shoot growth has been demonstrated. The present study aims to investigate the respective involvement of the emergence of new organs and their elongation in relation to this phenomenon and its possible genotypic variation in young apple plants. METHODS: Two apple varieties, X6407 (recently named 'Ariane') and X3305 ('Chantecler' x 'Baujade'), were compared. Five plants per variety, issued from in vitro culture, were observed in minirhizotrons over 4 months. For each plant, root emergence and growth were observed twice per week. Growth rates were calculated for all roots with more than two segments and the branching density was calculated on primary roots. On the aerial part, the number of leaves, leaf area and total shoot length were observed weekly. KEY RESULTS: No significant difference was observed between varieties in any of the final characteristics of aerial growth. Increase in leaf area and shoot length exhibited a 3-week rhythm in X3305 while a weaker signal was observed in Ariane. The primary root growth rate was homogeneous between the plants and likewise between the varieties, while their branching density differed significantly. Secondary roots emerged rhythmically, with a 3-week and a 2-week rhythm, respectively, in X3305 and 'Ariane'. Despite a high intra-variety variability, significant differences were observed between varieties in the secondary root life span and mean length. A synchronism between leaf emergence and primary root growth was highlighted in both varieties, while an opposition phase was observed between leaf area increments and secondary root emergence in X3305 only. CONCLUSION: A biological model of dynamics that summarizes the interactions between processes and includes the assumption of a feedback effect of lateral root emergence on leaf emergence is proposed.     

A neural network approach for the prediction of in vitro culture parameters for maximum biomass yields in hairy root cultures

The present study deals with ANN based prediction of culture parameters in terms of inoculum density, pH and volume of growth medium per culture vessel and sucrose content of the growth medium for Glycyrrhiza hairy root cultures. This kind of study could be a model system in exploitation of hairy root cultures for commercial production of pharmaceutical compounds using large bioreactors. The study is aimed to evaluate the efficiency of regression neural network and back propagation neural network for the prediction of optimal culture conditions for maximum hairy root biomass yield. The training data for regression and back propagation networks were primed on the basis of function approximation, where final biomass fresh weight (f_wt) was considered as a function of culture parameters. On this basis the variables in culture conditions were described in the form of equations which are for inoculum density: y=0.02x+0.04, for pH of growth medium: y=x+2.8, for sucrose content in medium: y=9.9464x+(−9.7143) and for culture medium per culture vessel: y=10x. The fresh weight values obtained from training data were considered as target values and further compared with predicted fresh weight values. The empirical data were used as testing data and further compared with values predicted from trained networks. Standard MATLAB inbuilt generalized regression network with radial basis function radbas as transfer function in layer one and purelin in layer two and back propagation having purelin as transfer function in output layer and logsig in hidden layer were used. Although in comparative assessment both the networks were found efficient for prediction of optimal culture conditions for high biomass production, more accuracy in results was seen with regression network.     

Growth of the toxic dinoflagellate Alexandrium minutum (Dinophyceae) using high biomass culture systems

Toxic dinoflagellates are important in natural ecosystems and are ofglobal economic significance because of the impact of toxic blooms onaquaculture and human health. Both the organisms and the toxins they producehave potential for biotechnology applications. We investigated autotrophicgrowth of a toxic dinoflagellate, Alexandrium minutum, inthree different high biomass culture systems, assessing growth, productivityandtoxin production. The systems used were: aerated and non-aerated2-L Erlenmeyer flasks; 0.5-L glass aerated tubes; anda 4-L laboratory scale alveolar panel photobioreactor. A range ofindicators was used to assess growth in these systems. Alexandriumminutum grew well in all culture conditions investigated, with amarked increase in both biomass and productivity in response to aeration. Thehighest cell concentration (4.9 × 10⁵ cellsmL^–1) and productivity (2.6 ×10⁴cells mL^–1d^–1) was achieved inthe aerated glass culture tubes. Stable growth of A.minutum in the laboratory scale alveolar panel photobioreactor wasmaintained over a period of five months, with a maximum cell concentration of3.3 × 10⁵ cells mL^–1, a meanproductivity of 1.4 × 10⁴ cells mL^–1d^–1, and toxin production of approximately 20g L^–1 d^–1 with weeklyharvesting.     

Competition in tree row agroforestry systems. 1. Distribution and dynamics of fine root length and biomass

Complementarity in the distribution of tree and crop root systems is important to minimise competition for resources whilst maximising resource use in agroforestry systems. A field study was conducted on a kaolinitic Oxisol in the sub-humid highlands of western Kenya to compare the distribution and dynamics of root length and biomass of a 3-year-old Grevillea robusta A. Cunn. ex R. Br. (grevillea) tree row and a 3-year-old Senna spectabilis DC. (senna) hedgerow grown with Zea mays L. (maize). Tree roots were sampled to a 300 cm depth and 525 cm distance from the tree rows, both before and after maize cropping. Maize roots were sampled at two distances from the tree rows (75–150 cm and 450–525 cm) to a maximum depth of 180 cm, at three developmental stages. The mean root length density (L_rv) of the trees in the upper 15 cm was 0.55 cm cm⁻³ for grevillea and 1.44 cm cm⁻³ for senna, at the start of the cropping season. The L_rv of senna decreased at every depth during the cropping season, whereas the L_rv of grevillea only decreased in the crop rooting zone. The fine root length of the trees decreased by about 35% for grevillea and 65% for senna, because of maize competition, manual weeding, seasonal senescence or pruning regime (senna). At anthesis, the L_rv of maize in the upper 15 cm was between 0.8 and 1.5 cm cm⁻³. Maize root length decreased with greater proximity to the tree rows, potentially reducing its ability to compete for soil resources. However, the specific root length (m g⁻¹) of maize was about twice that of the trees, so may have had a competitive uptake advantage even when tree root length was greater. Differences in maize fine root length and biomass suggest that competition for soil resources and hence fine root length may have been more important for maize grown with senna than grevillea. This revised version was published online in June 2006 with corrections to the Cover Date.     

水曲柳根系生物量、比根长和根长密度的分布格局

采用连续钻取土芯法在生长季内对东北林业大学帽儿山实验林场17年生水曲柳人工林根系取样,研究水曲柳不同直径根系现存生物量、比根长和根长密度及垂直分布状况.结果表明,水曲柳人工林根系总生物量为1 637.6 g·m^-2,其中活根生物量占85%,死根占15%.在活根生物量当中,粗根(直径5～30 mm)占的比例最高（69.95%）,其次为活细根（直径<1 mm,13.53%）,小根(1～2 mm)和中等直径的根(2～5 mm)比例较小（分别为7.21%和9.31%）.直径<1 mm活细根的比根长为32.20 m·g^-1,直径5～30 mm粗根的比根长为0.08 m·g^-1.单位面积上活根的总长度为6 602.54 m·m^-2,其中直径<1 mm的细根占92.43%,其它直径等级则不到活根总长度的8%.直径<1 mm的细根生物量与根长密度具显著线性关系（R²=0.923）,但与比根长无显著相关关系（R²=0.134）.     

青杨人工林根系生物量、表面积和根长密度变化

在植物生长季节,采用钻取土芯法对秦岭北坡50年生青杨人工林根径≤2 mm和2～5 mm根系的生物量、表面积和根长密度进行测定.结果表明：在青杨人工林根系(＜5 mm)中,根径≤2 mm根系占总生物量的77.8%,2～5 mm根系仅占22.2%;根径≤2 mm根系表面积和根长密度占根系总量的97%以上,而根径2～5 mm根系不足3%.随着土层的加深,根径≤2 mm根系生物量、表面积和根长密度数量减少,根径2～5 mm根系生物量、表面积和根长密度最小值均分布在20～30 cm土层.≤2 mm根系生物量、表面积和根长密度与土壤有机质、有效氮呈极显著相关,而根径2～5 mm根系的相关性不显著.     

实验增温对陆地生态系统根系生物量的影响

根系是植物吸收土壤水分和养分的重要器官, 驱动着多个生态系统过程, 该研究揭示了实验增温对根系生物量的影响及机制, 可为气候变暖背景下土壤碳动态和生态系统过程的变化提供理论依据。该研究从已发表的151篇国内外研究论文中收集到611组数据, 通过整合分析(meta-analysis)方法研究了实验增温对根系生物量(根系总生物量、粗根生物量、细根生物量、根冠比)的影响, 并探讨了增温幅度、增温年限、增温方式的影响, 以及根系生物量对增温的响应与本底环境条件(生态系统类型、年平均气温、年降水量、干旱指数)的关系。结果表明: (1)模拟增温使细根生物量显著增加8.87%, 而对根系总生物量、粗根生物量、根冠比没有显著影响; (2)中等强度增温(1-2 ℃)使得细根生物量和根冠比分别提高14.57%和23.63%; 中短期增温实验(<5年)对细根生物量具有促进影响, 而长期增温实验(≥5年)使细根生物量有降低的趋势; 开顶箱增温和红外辐射增温分别使细根生物量显著提高了17.50%和12.16%, 而电缆加热增温使细根生物量和粗根生物量显著降低了23.44%和43.23%; (3)不同生态系统类型对于增温响应不一致, 模拟增温使苔原生态系统细根生物量显著提高了21.03%, 细根生物量对增温的响应与本底年平均气温、年降水量、干旱指数均呈显著负相关关系。     

中国区域植被地上与地下生物量模拟

应用大气-植被相互作用模型AVIM2在0.1°×0.1°经纬度网格上估算了中国区域植被总生物量、地下和地上生物量以及根茎比的空间分布格局。研究了植被生物量和根茎比的空间分布与水热限制条件的关系。研究表明:中国植被总生物量、地下和地上生物量受水热条件影响明显,空间分布趋势基本相似,即在暖湿的东南和西南地区生物量大,而在干冷的西部地区生物量小。同类植被生物量的空间分布有显著区域差异,气温高、降水量大的区域植被生物量大;低温和干旱地区的植被生物量小。除灌木以外,植被生物量大小的空间分布受水分的影响大于温度。中国区域植被根茎比的空间分布存在明显区域差异,全国大致以大兴安岭、太行山、秦岭以及青藏高原东南侧一线为界线,界线东南植被根茎比较小;界线以西,植被根茎比较大。植被根茎比的空间分布与年平均气温、土壤湿度和年降水量显著反相关,水分因子对根茎比空间分布的影响大于温度。     

An unusual root tip formation in hairy root culture of Hyoscyamus muticus

Summary Hairy root cultures of Hyoscyamus muticus were established using Agrobacterium rhizogenes ATCC 15834. In one out of 8 clones established, an unusual root tip formation was observed after transfer of cultures from half-strength Murashige and Skoog (1962) to White's medium (1939). This phenomenon was associated with the production of a fine brownish cell suspension culture. Hairy root development resumed after transfer of the root tips from White to half-strength Murashige and Skoog medium. After plating the isolated brownish cells on hormone-free half-strength Murashige and Skoog or White solid medium, callus proliferation was observed, and then redifferentiation of hairy roots occurred. The polymerase chain reaction analysis of the H. muticus hairy root (clone Z2) revealed that only the tl region of the T-DNA was integrated. The growth and the production of five tropane alkaloids by this clone were examined.Abbreviations PCR Polymerase Chain Reaction - MS medium Murashige and Skoog Medium - 1/2 MS medium half-strength MS medium - WP medium Woody Plant medium - RC medium Root Culture medium - WH medium White medium - HPLC High Performance Liquid Chromatography - wt. weight     

Optimal control of biomass growth in a mixed culture

It is shown that, in a mixed culture, under realistic assumptions, the optimal temperature profile maximizing the final biomass production under the constraint of the final relative proportions of the two populations is constant. This result is illustrated with a simulation experiment on a lactic fermentation model.