基因组规模代谢网络模型构建及其应用

微生物制造产业的发展迫切需要进一步提高认识、设计和改造微生物细胞代谢的能力,以推动工业生物技术快速发展。随着微生物全基因组序列等高通量数据的不断积聚和生物信息学策略的持续涌现,使全局性、系统化地解析、设计、调控微生物生理代谢功能成为可能。而基于基因组序列注释和详细生化信息整合的基因组规模代谢网络模型(GSMM)构建为全局理解和理性调控微生物生理代谢功能提供了最佳平台。以下在详述GSMM的应用基础上,描述了如何构建一个高精确度的GSMM,并展望了未来的发展方向。     

Predictors of Introduction Success in the South Florida Avifauna

Biological invasions are an increasing global challenge, for which single-species studies and analyses focused on testing single hypotheses of causation in isolation are unlikely to provide much additional insight. Species interact with other species to create communities, which derive from species interactions and from the interactions of species with the scale specific elements of the landscape that provide suitable habitat and exploitable resources. I used logistic regression analysis to sort among potential intrinsic, community and landscape variables that theoretically influence introduction success. I utilized the avian fauna of the Everglades of South Florida, and the variables body mass, distance to nearest neighbor (in terms of body mass), year of introduction, presence of congeners, guild membership, continent of origin, distribution in a body mass aggregation or gap, and distance to body-mass aggregation edge (in terms of body mass). Two variables were significant predictors of introduction success. Introduced avian species whose body mass placed them nearer to a body-mass aggregation edge and further from their neighbor were more likely to become successfully established. This suggests that community interactions, and community level phenomena, may be better understood by explicitly incorporating scale.     

Recent advances in the study of long-distance dispersal of aquatic invertebrates via birds

Although Darwin pioneered the study of long‐distance dispersal (LDD) of aquatic invertebrates via waterbirds, it remains in its infancy as a modern discipline. A handful of recent studies have quantified internal or external transport in the field, confirming that a variety of long‐distance migrants carry invertebrates both internally and externally. These studies show that variation in the morphology of vectors influences the frequency and size of propagules transported, and suggest that more invertebrate groups disperse via birds than was previously thought. Dispersal limitation has mainly been investigated for zooplankton in small experimental systems from which waterbirds were effectively excluded, and the extent of such limitation for invertebrate populations in wetlands interconnected by waterbird movements remains unclear. We expect that the spatial and temporal scales at which dispersal limitation constrains geographical ranges, species richness and genetic structure of invertebrates depends partly on the density of migratory birds using the area. Birds may have a major role in the expansion of exotic species. We propose several avenues for future research. There is a particular need for more quantitative studies of LDD by birds that will enable modellers to assess its role in maintaining invertebrate biodiversity among increasingly fragmented wetlands and in the face of climate change, as well as in the spread of invasive species.     

基于RS和GIS的开封市土地覆盖分形

以RS和GIS为技术手段,利用开封市0.61m空间分辨率的QuickBird卫星遥感数据,采用分形几何方法研究了斑块的面积效应和覆盖类型分形的关系,并对覆盖类型的分形特征差异等进行了分析。结果表明,开封市防护林地和农田的平均斑块面积较大,分维数也较大,而水体的分维数较小,说明防护林和农田斑块的边界结构特征比水体更为复杂。斑块的分维值具有尺度依赖性,同一类型中大的斑块往往具有较大的分维值,其原因是大斑块经常出现不同类型的斑块相互嵌套,小斑块则很少出现甚至不出现这种现象。     

The influence of cultivation methods on Shewanella oneidensis physiology and proteome expression

High-throughput analyses that are central to microbial systems biology and ecophysiology research benefit from highly homogeneous and physiologically well-defined cell cultures. While attention has focused on the technical variation associated with high-throughput technologies, biological variation introduced as a function of cell cultivation methods has been largely overlooked. This study evaluated the impact of cultivation methods, controlled batch or continuous culture in bioreactors versus shake flasks, on the reproducibility of global proteome measurements in Shewanella oneidensis MR-1. Variability in dissolved oxygen concentration and consumption rate, metabolite profiles, and proteome was greater in shake flask than controlled batch or chemostat cultures. Proteins indicative of suboxic and anaerobic growth (e.g., fumarate reductase and decaheme c-type cytochromes) were more abundant in cells from shake flasks compared to bioreactor cultures, a finding consistent with data demonstrating that “aerobic” flask cultures were O₂ deficient due to poor mass transfer kinetics. The work described herein establishes the necessity of controlled cultivation for ensuring highly reproducible and homogenous microbial cultures. By decreasing cell to cell variability, higher quality samples will allow for the interpretive accuracy necessary for drawing conclusions relevant to microbial systems biology research.     

Biological soil crusts in ecological restoration: emerging research and perspectives

Drylands encompass over 40% of terrestrial ecosystems and face significant anthropogenic degradation causing a loss of ecosystem integrity, services, and deterioration of social‐ecological systems. To combat this degradation, some dryland restoration efforts have focused on the use of biological soil crusts (biocrusts): complex communities of cyanobacteria, algae, lichens, bryophytes, and other organisms living in association with the top millimeters of soil. Biocrusts are common in many ecosystems and especially drylands. They perform a suite of ecosystem functions: stabilizing soil surfaces to prevent erosion, contributing carbon through photosynthesis, fixing nitrogen, and mediating the hydrological cycle in drylands. Biocrusts have emerged as a potential tool in restoration; developing methods to implement effective biocrust restoration has the potential to return many ecosystem functions and services. Although culture‐based approaches have allowed researchers to learn about the biology, physiology, and cultivation of biocrusts, transferring this knowledge to field implementation has been more challenging. A large amount of research has amassed to improve our understanding of biocrust restoration, leaving us at an opportune time to learn from one another and to join approaches for maximum efficacy. The articles in this special issue improve the state of our current knowledge in biocrust restoration, highlighting efforts to effectively restore biocrusts through a variety of different ecosystems, across scales and utilizing a variety of lab and field methods. This collective work provides a useful resource for the scientific community as well as land managers.     

保护性耕作对稻田土壤有机质的影响

研究使用常规犁耕-休闲(DTF),常规犁耕-小麦(DTW),保护耕作-休闲(CTF),保护耕作-小麦(CTW)4个处理,评价连续实验10a后保护性耕作对稻作区SOM的影响。结果表明:垄作、免耕和小麦种植的结合是稻作区一种较好的保护性耕作实践。它不仅显著增加SOM在土壤表层的聚集,而且它也通过改变SOM的组成和结构显著影响土壤胡敏酸的光谱和热解特性。相比其他处理,垄作免耕(稻麦)在0～10cm土层拥有最多的SOM含量,但随着土层厚度的增加,这一含量下降的也较为迅速。垄作免耕(稻麦)土壤胡敏酸在波长665nm处的光密度为0.122,465nm处为0.705,而常规平作(中稻)在这两个波长处却分别为0.062和0.321。垄作免耕土壤胡敏酸DTA曲线在360～365℃处放热峰的焓变值比常规平作低,1000～1050cm-1吸收峰常规平作也比垄作免耕强。垄作免耕土壤腐殖质的氧化稳定系数增高,表明长期垄作免耕土壤腐殖酸的缩合度增高,芳构化程度增强。通过保护性耕作和作物实践可以管理稻田土壤,维持充分的SOM积累,缓解土壤有机碳的丢失。     

流域尺度土地利用与土壤类型空间分布的相关性研究

随着人类活动日益加强,土地利用变化及其驱动力研究已经成为国际地理学界研究的热点。但目前更多的工作侧重于研究人为因子,如人口增长、政策变化等因子对土地利用变化的影响,其实土地利用在宏观尺度上的变化一定程度上取决于自然环境背景,因此研究土地利用变化的自然环境背景特征对于进一步探讨土地利用变化的自然驱动力具有重要意义。土壤类型的空间分布在一定程度将影响土地利用的空间分布格局和变化过程。本文利用遥感、地理信息系统,通过选取景观格局指标,以于桥水库流域为例,研究了土地利用与土壤类型空间分布之间的相互关系。结果表明：(1)受人类活动干扰较弱的土地利用类型,如有林地、稀疏林地、灌木林地、其他林地和草地,主要分布在淋溶褐土、褐土性土以及棕壤地区;而与人类活动密切的土地利用类型,如山区旱耕地、丘陵区水田、丘陵区旱耕地和平原区旱耕地主要分布在淋溶褐土、褐土性土和潮土地区;(2)同类地区土地利用的多样性指数要比土壤的低。并且土地利用和土壤类型多样性均表现出明显的地形梯度效应,从中低山区、低山丘陵区、丘陵平原区到山间盆地区,土壤多样性指数从小到大有规律地变化。而土地利用类型多样性变化较为复杂,反映出人类活动对土地利用格局的影响较强,而对土壤类型的影响相对较小;(3)随着平均斑块面积的增加,流域多样性指数将呈下降趋势。土地利用多样性指数与流域总面积之间的相关性较差,但土壤多样性指数与流域总面积表现出的相关性较好;(4)土地利用类型与土壤类型之间,平均斑块面积上没有明显的相关关系,但在多样性指数之间存在着较好的相关性。土壤类型丰富多样的地区,土地利用的多样性指数也相对较高。     

黑河下游地下水波动带地下水与植被动态耦合模拟

采用对数正态分布模型,基于2006年黑河下游的野外实测数据,建立了研究区胡杨和柽柳植被盖度与地下水埋深的模型,并模拟了研究区的潜在植被.结果表明：黑河下游胡杨的最适宜地下水位和平均地下水位分别为2.6和3.6 m,柽柳则分别为2.0和3.0 m;胡杨的高盖度分布区主要集中在河道两侧的区域,而柽柳则可以在研究区的大部分区域以较高的盖度生存,对于研究区当前的地下水埋深而言,柽柳应该是最适宜生存的物种之一;研究区胡杨和柽柳的潜在植被空间分布与现状分布的相似性分别为43.4%和55.6%,导致相似程度不高的主要原因为土壤中存在的石膏盐盘层阻碍了土壤水分的垂直运动.     

Localization of genes for bacterial canker resistance in Lycopersicon peruvianum using RFLPs

A backcross population of the L. peruvianum accession LA 2157, which is resistant to bacterial canker caused by Clavibacter michiganensis ssp. michiganensis, with the susceptible L. peruvianum accession LA 2172 was evaluated for the segregation of C. michiganenis resistance and of RFLP markers in order to map the loci involved in this resistance. The development of symptoms of the disease was scored using an ordinal scale. The mapping of the disease resistance was hampered by distorted segregation ratios of a large number of markers and unexpected quantitative inheritance of the resistance. By means of the Kruskal-Wallis rank-sum test, five regions on chromosomes 1, 6, 7, 8 and 10 were identified that may be involved in C. michiganensis resistance.