Hierarchical partitioning for selection of microbial and chemical indicators of soil quality

Statistical approaches, especially multivariate techniques such as hierarchical partitioning analysis (HP) and redundancy analysis (RDA), can be used to select appropriate variables for soil quality assessment. HP is usually applied to ecological data from plants and animals, but has not been applied to chemical and microbial properties such as those used as indicators of soil quality. Our aim was to show how these methods can be employed to find soil quality indicators, using soil microbiological, chemical and physical data to compare two forest types (native and reforested Brazilian Araucaria forests) in two locations in Southeast Brazil. We used RDA to investigate relationships among variables. Additionally, we quantified the independent effects of predictor variables: location, forest type, two specific seasons and some soil properties and used HP to examine how these environmental variables interact to influence soil microbial and chemical attributes. RDA showed that acid phosphatase and dehydrogenase activity, NO₂⁻ oxidizer numbers, basal respiration, metabolic quotient, pH, P and sand content were positive and significantly correlated with the native Araucaria forest, whereas arylsulphatase activity, denitrifier numbers, microbial biomass carbon, microbial quotient, TOC, S and clay levels were positively correlated with the reforested Araucaria. These preliminary results suggest that these variables are the best indicators of soil quality for Araucaria forests. However, HP, used as a complementary tool, showed that only dehydrogenase activity, pH and S variations were due more to forest type than to physical and chemical soil properties, and were resistant to the variation in the two seasons. Overall, our results indicated that dehydrogenase activity, pH and S are potential indicators that can be used to assess or monitor soil health in Araucaria forests. In conclusion, we demonstrated the usefulness of HP to find soil quality indicators. Similarly, other statistical methods, as RDA, could complement HP and increase the reliability of studies that consider simultaneous variables in soil science.     

棉花非冗余性EST-SSR新标记的开发及其评价

利用Clustal X等软件对公共数据库现有的393 753条棉花EST序列分析,得到349 815条非冗余EST序列,借助自主开发的SSRmine软件共发掘SSR位点11 372个,分布于10 507条EST中,EST-SSR的频率是3%,平均相隔21 kb出现一个SSR。在2~6 bp的重复基元中,三核苷酸和六核苷酸分别占34.1%、40.6%,二、三、四、五和六核苷酸基序分别以AG/CT、AAG/CTT、AAAT/ATTT、AAAAG/CTTTT和AAAAAG/CTTTTT的类型最多。利用去冗余的且在亚洲棉、陆地棉、海岛棉中没有被开发过的410条EST序列设计开发了200对非冗余性SSR引物,利用自主开发的SSRD软件通过SSR引物序列下载、预处理、Blastn、提取相似性分值≥81%的引物编号、提取引物冗余对、冗余引物写成一行等6个步骤去除来源于自身部分同源序列以及与CMD释放的不同棉种相似性SSR引物,得到了非相似性引物,定名为CRIXXX (CRI即Cotton Research Institute)。并分别选用棉花12个种的代表性材料对其中100对进行引物功效评价,包括多态信息含量(polymorphism information content, PIC)及引物通用性研究。结果显示,从自主开发的100对SSR引物筛选出56对均能在12份材料间扩增出稳定明显的条带, 其中多态性引物35对,多态率占35%。引物的PIC变幅为0.097~0.888,平均为0.482;1对海岛棉EST-SSR引物在12份材料间的通用性为100%,25对亚洲棉引物通用性为81%,74对陆地棉引物通用性为80.1%。     

库车山区新疆假龙胆适生地植物群落多样性及其环境解释

采用相关分析和RDA排序法分析了天山南坡中段库车山区新疆假龙胆适生地植物群落多样性特征及其环境影响因子。结果表明,在新疆假龙胆适生地植物群落的24个样地中,共记录到物种87种,隶属于20科54属;共有10种植物群落类型,其结构组成及物种多样性组成是不同的,分布较广的物种为菊科、禾本科、豆科和蔷薇科。各群落物种多样性指数中,Simpson指数最高,各样地间多样性指数测值变幅较大。群落物种多样性指数及种群数量特征与环境因子的相关性分析表明,群落物种Margalef丰富度指数显著受土壤全N、全P的影响;群落物种Simpson多样性指数显著受海拔、土壤总盐的影响;群落中新疆假龙胆的重要值及其种群数量受pH的显著影响;群落中新疆假龙胆种群高度显著受有效K、海拔和土壤总盐的影响。RDA分析表明,全N、全P、有效K、pH、海拔是影响群落物种多样性的主要环境因素。     

河西走廊荒漠土壤微生物群落结构及环境响应

荒漠土壤中微生物生存适应机制及其生态系统功能对揭示干旱区物质转化过程具有重要意义。本研究沿河西走廊东南至西北自然降水递减梯度下设置16个样地,采用高通量测序技术探究土壤细菌和真菌群落多样性特征,揭示微生物多样性、优势菌群与土壤机械组成、养分关系。结果显示：河西走廊荒漠土壤细菌中厚壁菌门(Firmicutes）、变形菌门（Proteobacteria）、放线菌门（Actinobacteria）、拟杆菌门（Bacteroidetes）为优势群落,部分样地厚壁菌门相对丰度最高达85%;真菌中子囊菌门（Ascomycota）和担子菌门（Basidiomycota）为优势群落,其相对丰度均大于>5%。相关性分析显示：粗粉粒(0.05~0.02 mm)、细粉粒(0.25~0.10 mm)、黏粒(<0.002 mm)、有效磷(AP)和解碱氮(AN)对细菌多样性影响极显著,细粉粒(0.25~0.10 mm)、黏粒(<0.002 mm)、有效磷(AP)和解碱氮(AN)对真菌多样性影响极显著（P<0.01）。冗余分析显示：细粉粒(0.25~0.10 mm)和速效磷(AP)对细菌群落影响显著,黏粒（<0.002mm）和速效磷(AP)对真菌群落影响显著（P<0.05）。研究表明了河西走廊荒漠土壤微生物群落结构的组成、变化及影响因子,解释了土壤环境对微生物分布的影响及微生物对土壤生态系统系统发展的作用,为保护生物多样性及荒漠生态服务提供理论参考。     

Plant parasitic nematodes and spatio-temporal variation in natural vegetation

In this paper, the possible role of plant parasitic nematodes as a driving force of change in natural vegetation is analysed using the succession at coastal foredunes as a model. In pot trials, when grown in natural substrates from mature stands, seedlings of dominant foredune plants showed poor growth when compared to sterilised substrates. In natural substrates from preceding stages, growth reduction was far less, or even non-significant. Chemical soil treatment with nematicides resulted in enhanced growth of the seedlings. Inoculation of ectoparasitic nematodes reduced plant growth, but only at densities much higher than those occurring in control pots with unsterilised field soil. Identification at species level showed that endoparasitic nematodes are specifically associated with particular plant species. Therefore, it is hypothesised that the distribution of endoparasitic nematodes may be an important factor leading to the specific nature of soil pathogen complexes in coastal foredunes. We discuss the role of endoparasitic nematodes as possible key species in soil communities and compare the possible effects of specific vs. generalistic plant parasitic nematodes in soil communities on vegetation processes.     

Spatial and Seasonal Patterns of Cattle Habitat use in a Mountain Wooded Pasture

Management-oriented models of cattle habitat use often treat grazing pressure as a single variable summarizing all cattle activities. This paper addresses the following questions: How does the spatial pattern of cattle effects vary between cattle activities in a highly heterogeneous landscape? Do these patterns change over the grazing season as forage availability decreases? What are the respective roles of natural and management-introduced structures? We estimated the intensity of herbage removal, dung deposition and trampling after each of three grazing periods on a grid of 25 m ×25 m cells covering an entire paddock in the Swiss Jura Mountains. We found no significant positive correlations between cattle effects. Spatial patterns weakened through the season for grazing and trampling, whereas dunging patterns changed little between grazing periods. Redundancy analysis showed that different cattle effects were correlated with different environmental variables and that the importance of management-introduced variables was highest for herbage removal. Autocorrelograms and partial redundancy analyses using principal coordinates of neighbour matrices suggested that dunging patterns were more coarse-grained than the others. Systematic differences in the spatial and seasonal patterns of cattle effects may result in complex interactions with vegetation involving feedback effects through nutrient shift, with strong implications for ecosystem management. In heterogeneous environments, such as pasture-woodland landscapes, spatially explicit models of vegetation dynamics need to model cattle effects separately.     

The effect of target extent on the location of optimal protected areas networks in Canada

Various jurisdictions in Canada are currently undertaking, or have recently completed, planning exercises as part of implementation and expansion of representative reserve networks (networks of provincial parks, national parks, ecological reserves, etc.). These exercises have resulted in recommendations to governments about which areas of land should be set aside as protected areas, and different levels of government have been involved in the process of land acquisition. In some cases, planning exercises have included implementation of new protected areas to complement existing reserve networks. Many of these exercises have applied principles such as complementarity, using heuristic algorithms that are well-described in the literature. These planning exercises may be conducted within politically or ecologically bounded target regions of varying extents. Here, I develop candidate locations for representative reserve areas for disturbance-sensitive mammals across Canada. I use ecologically bounded regions (within the national boundaries of Canada) at three different levels of spatial hierarchy: mammal provinces, ecozones, and ecoregions. I show that the extent of the target region has an effect on the minimum number of protected areas required to achieve representation; a larger region requires fewer protected areas than the sum of the protected areas required to represent its component regions at a lower level of spatial hierarchy. The results illustrate that selection of sites for inclusion in a reserve network is highly scale-dependent, and different spatial extents in the target regions may introduce inefficiencies or redundancies in selecting representative protected areas.     

高通量测序技术下连作植烟土壤细菌群落与土壤环境因子的耦合分析

为了揭示连作条件下植烟土壤细菌群落结构及其与土壤环境间的响应关系,本研究采用了Illumina平台Hiseq2500高通量测序技术,对不同施肥处理(常规施肥,蚯蚓粪肥,微生物菌肥以及蚯蚓粪和微生物菌肥混合)的漯河烟区连作植烟土壤细菌进行16S rRNA V4区测序,结合冗余分析(redundancyanalysis,RDA)研究土壤细菌微生物的群落结构组成、多样性以及与土壤环境间的相关关系.结果表明,测序质控后共获得25 203个操作分类单元(operational taxonomic units,OTUs),计1 600 239条读数.分层聚类图显示,不同施肥处理的连作植烟土壤细菌群落有较大差异,但这种差异不体现在结构多样性上.多样性指数分析表明,连作植烟土壤细菌群落易受环境变化的影响,体现出一定的时间差异性;烤烟成熟期土壤丰度指数明显升高,微生物菌肥和蚯蚓粪肥处理下土壤细菌群落丰度变化较大.主成分分析表明,不同土壤环境因子间有很强的相关关系,可以将原有的11个土壤环境因子按照强正相关关系划分为4类;RDA结果表明,土壤pH既影响土壤细菌群落的多样性,又影响土壤细菌群落的丰度;而有机质主要对土壤细菌群落丰度有积极影响.研究结果为在微生物水平上研究连作植烟障碍的形成机理提供了依据.     

Effects of tree harvesting, forest floor removal, and compaction on soil microbial biomass, microbial respiration, and N availability in a boreal aspen forest in British Columbia

The effects of timber harvesting and the resultant soil disturbances (compaction and forest floor removal) on relative soil water content, microbial biomass C and N contents (C_mic and N_mic), microbial biomass C:N ratio (C_mic-to-N_mic), microbial respiration, metabolic quotient (qCO₂), and available N content in the forest floor and the uppermost mineral soil (0-3 cm) were assessed in a long-term soil productivity (LTSP) site and adjacent mature forest stands in northeastern British Columbia (Canada). A combination of principal component analysis and redundancy analysis was used to test the effects of stem-only harvest, whole tree harvest plus forest floor removal, and soil compaction on the studied variables. Those properties in the forest floor were not affected by timber harvesting or soil compaction. In the mineral soil, compaction increased soil total C and N contents, relative water content, and N_mic by 45%, 40%, 34% and 72%, respectively, and decreased C_mic-to-N_mic ratio by 29%. However, these parameters were not affected by stem only harvesting or whole tree harvesting plus forest floor removal, contrasting the reduction of white spruce and aspen growth following forest floor removal and soil compaction reported in an earlier study. Those results suggest that at the study site the short-term effects of timber harvesting, forest floor removal, and soil compaction are rather complex and that microbial populations might not be affected by the perturbations in the same way as trees, at least not in the short term.     

不同施肥水平对青稞豌豆混作根际土壤真菌群落结构及多样性的影响

采用真菌ITS区的Illumina MiSeq高通量测序技术，并结合NMDS、RDA和Mantel test分析，探讨青稞单作(Q)、豌豆单作(W)、青稞豌豆混作(Q×W)3种模式在不施肥(0NP)、低氮磷(LNP)、高氮磷(HNP)3种施肥水平下根际土壤真菌群落结构组成及多样性的差异，同时测定其土壤理化性质，并与根际土壤真菌群落结构进行了相关性分析。结果表明：青稞、豌豆在3种种植模式下土壤均呈碱性，且在不同施肥水平下土壤理化性质差异显著。不同试验处理下共检测到18个真菌类群，子囊菌门(Ascomycota，63.5%~78.5%)、被孢霉门(Mortierellomycota，3.6%~14%)、担子菌门(Basidiomycota，1.1%~6.9%)为共有优势类群，在属水平上，Penicillium、Mortierella在青稞豌豆混作根际土壤中相对丰度最高，可能是驱动土壤有机氮、磷转化为无机氮、磷的主要真菌群落。Bipolaris、Blumeria、Fusarium、Cladosporium为土壤真菌群落丰度最高的4种潜在致病菌属，在青稞豌豆混作根际土壤中的相对丰度低于青稞单作和豌豆单作，混作模式在不同施肥水平下4种具有潜在致病性的真菌间相对丰度存在显著差异；在LNP、HNP水平下混作模式根际土壤中的真菌丰富度(ACE、Chao1)和多样性(Shannon、Simpson)指数均低于青稞单作，混作模式在LNP水平下丰富度(ACE、Chao1)指数显著低于0NP水平，但多样性(Shannon、Simpson)指数高于0NP水平；从不同试验处理属水平下真菌群落相对丰度来看，混作模式可显著增加根际土壤中有益菌群的相对丰度，通过根际土壤微生物优势种群及α多样性分析，青稞豌豆混作模式较青稞单作、豌豆单作可增加根际土壤中属水平下Penicillium、Mortierella等具有溶磷、氨化作用菌群的相对丰度，降低Bipolaris、Blumeria、Fusarium、Cladosporium等潜在致病菌群的相对丰度；相关分析表明，速效氮、速效磷、有机质是影响混作模式根际土壤真菌群落结构差异的主要驱动因子。