Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by geographic features

Here, we examine soil-borne microbial biogeography as a function of the features that define an American Viticultural Area (AVA), a geographically delimited American wine grape-growing region, defined for its distinguishing features of climate, geology, soils, physical features (topography and water), and elevation. In doing so, we lay a foundation upon which to link the terroir of wine back to the soil-borne microbial communities. The objective of this study is to elucidate the hierarchy of drivers of soil bacterial community structure in wine grape vineyards in Napa Valley, California. We measured differences in the soil bacterial and archaeal community composition and diversity by sequencing the fourth variable region of the small subunit ribosomal RNA gene (16S V4 rDNA). Soil bacterial communities were structured with respect to soil properties and AVA, demonstrating the complexity of soil microbial biogeography at the landscape scale and within the single land-use type. Location and edaphic variables that distinguish AVAs were the strongest explanatory factors for soil microbial community structure. Notably, the relationship with TC and TN of the <53 μm and 53–250 μm soil fractions offers support for the role of bacterial community structure rather than individual taxa on fine soil organic matter content. We reason that AVA, climate, and topography each affect soil microbial communities through their suite of impacts on soil properties. The identification of distinctive soil microbial communities associated with a given AVA lends support to the idea that soil microbial communities form a key in linking wine terroir back to the biotic components of the soil environment, suggesting that the relationship between soil microbial communities and wine terroir should be examined further.     

内蒙古岩画中的动物群落结构及其生态环境的研究——以阴山和乌兰察布两地岩画对比研究为例

动物岩画是内蒙古地区古代动物的图解,通过岩画中的动物群落结构对比,可以推测相同地域范围内,不同时期的动物分布情况,进而推断当地的自然环境变迁的过程。     

Response of the soil fungal community to multi-factor environmental changes in a temperate forest

Both environmental and climatic changes are known to influence soil microbial biomes in terrestrial ecosystems. However, there are limited data defining the interactive effects of multi-factor environmental disturbances, including N-deposition, precipitation, and air temperature, on soil fungal communities in temperate forests. A 3-year outdoor pot experiment was conducted to examine the temporal shifts of soil fungal communities in a temperate forest following N-addition, precipitation and air temperature changes. The shifts in the structure and composition of soil fungal communities were characterized by denaturing gradient gel electrophoresis and DNA sequencing. N-addition regimen induced significant alterations in the composition of soil fungal communities, and this effect was different at both higher and lower altitudes. The response of the soil fungal community to N-addition was much stronger in precipitation-reduced soils compared to soils experiencing enhanced precipitation. The combined treatment of N-addition and reduced precipitation caused more pronounced changes in the lower altitude versus those in the higher one. Certain fungal species in the subphylum Pezizomycotina and Saccharomycotina distinctively responded to N fertilization and soil water control at both altitudes. Redundancy discrimination analysis showed that changes in environmental factors and soil physicochemical properties explained 43.7% of the total variability in the soil fungal community at this forest ecosystem. Variations in the soil fungal community were significantly related to the altitude, soil temperature, total soil N content (TN) and pH value (P < 0.05). We present evidence for the interactive effects of N-addition, water manipulation and air temperature to reshape soil fungal communities in the temperate forest. Our data could provide new insights into predicting the response of soil micro-ecosystem to climatic changes.     

白三叶返园对苹果园土壤微生物群落的影响

为了解苹果(Malus pumila)园中覆盖和埋置白三叶(Trifolium repens)对土壤微生物群落的影响,采用尼龙袋法将新鲜的白三叶覆盖和埋置到苹果园中,分别在白三叶降解1、3、6个月时,利用Biolog微平板法检测土壤微生物群落的功能多样性。结果表明,覆盖和埋置白三叶均可使苹果园土壤微生物代谢活性显著提高(P0.05),微生物的多样性除6个月外显著增加、丰富度显著增加,均匀度显著降低(P0.05),群落结构发生变化,且覆草处理大于埋草,同时,白三叶降解时间的长短也影响土壤微生物群落。土壤微生物群落主成分分析结果显示,不同返园方式间主要对羧酸类碳源的利用有差异,而导致不同降解时间土壤微生物群落代谢差异的主要是糖类。说明在苹果园覆盖和埋置白三叶可改变土壤微生物群落,而覆盖白三叶对微生物群落结构的改善情况显著优于埋置白三叶。     

Analysis of Inter-Individual Bacterial Variation in Gut of Cicada Meimuna mongolica (Hemiptera: Cicadidae)

Intestinal bacterial community plays a crucial role in the nutrition, development, survival, and reproduction of insects. When compared with other insects with piercing-sucking mouthparts, the habitats of cicada nymphs and adults are totally different. However, little is known about the differences in the gut bacterial communities in the nymphs and adults within any cicada species. The diversity of bacteria in the gut of nymphs and adults of both genders of Meimuna mongolica (Distant) was studied using the denaturing gradient gel electrophoresis (DGGE) method. Few inter-individual variations among gut microbiota were observed, suggesting that M. mongolica typically harbors a limited and consistent suite of bacterial species. Bacteria in the genera Pseudomonas and Enterobacter were the predominant components of the gut microflora of M. mongolica at all life stages. Bacteria of Pantoea, Streptococcus, and Uruburuella were also widespread in the cicada samples but at relatively lower concentrations. The relative stability and similarity of the PCR-DGGE patterns indicate that all individuals of this cicada species harbor a characteristic bacterial community which is independent from developmental stages and genders. Related endosymbionts that could be harbored in bacteromes of cicadas were not detected in any gut samples, which could be related to the cicada species and the distribution of these endosymbionts in the cicada cavity, or due to some of the possible limitations of PCR-DGGE community profiling. It is worthwhile to further address if related cicada endosymbiont clades distribute in the alimentary canals and other internal organs through diagnostic PCR using group-specific primer sets.     

Responses of soil nematode community structure to soil carbon changes due to different tillage and cover crop management practices over a nine-year period in Kanto,Japan

The response of the soil food web structure to soil quality changes during long-term anthropogenic disturbance due to farming practices has not been well studied. We evaluated the effects of three tillage systems: moldboard plow/rotary harrow (MP), rotary cultivator (RC), and no-tillage (NT), three winter cover-crop types (fallow, FL; rye, RY; and hairy vetch, HV), and two nitrogen fertilization rates (0 and 100 kg N ha⁻¹ for upland rice, and 0 and 20 kg N ha⁻¹ for soybean production) on changes in nematode community structure. Sixty-nine taxa were counted, total nematode abundance (ALL), bacterial feeders (BAC), predators (PRD), omnivores (OMN), and obligatory root feeders (ORF) were more abundant in NT than in MP and RC, but fungal feeders and facultative root feeders (FFR) were more abundant in RC than in NT and MP. Cover crop also influenced nematode community structure; rye and hairy vetch were always higher in ALL, BAC, FFR, ORF, and OMN than fallow. Seasonal changes in nematode community structure were also significant; in particular, as soil carbon increased, nematode abundance also increased. The relationship between nematode indices and soil carbon was significant only in NT, but not in MP and RC. In NT, with increasing soil carbon, enrichment index and structure index (SI) were positive and significant and channel index was negative. Bulk density was significantly negatively correlated with FFR and ORF. Seasonal difference in nematode community between summer and autumn was larger in an upland rice rotation than in a soybean rotation. Over the nine-year experiment, SI increased not only in NT but also in MP and RC, suggesting that repeated similar tillage inversions in agroecosystems may develop nematode community structures adapted to specific soil environmental conditions. Because NT showed the highest values of both SI and soil carbon, the increase of soil carbon in NT is expected to have a great impact on developing a more diverse nematode community structure.     

关于植物群丛划分的探讨

在传统的植物群落分类系统中,群丛是植物群落分类的基本单位.从群丛分类的必要性出发,综述了传统植物群落分类系统中对群丛的定义及其划分方法,即在群丛的划分中主要依据群落中不同层片的优势种或特征种；但是在利用传统植物群落分类方法划分群丛时也存在一些不确定性因素,主要表现在确定群丛的特征种(组)时需要人为确定；同时,论述了当前植物群落数量分类的研究现状,分析了利用双向指示种分析法(TWINSPAN)、主成分分析(PCA)等数量分类方法划分群丛时存在的一些问题,主要表现在数量分类结果与传统分类单位的对应关系不能达到协调一致,无法判断是否划分到了群丛的水平.最后提出了群丛划分方法的展望:数量方法是基础,特征种(组)是及其数量特征是关键.     

Black soldier fly and yellow mealworm live larvae for broiler chickens: Effects on bird performance and health status

The commercial broiler chicken strains are the result of successful selection programmes. Most of the problems related to welfare arise from the high growth rate and body weight. The use of environmental enrichments in intensive farming could have a positive effect on birds by increasing animal welfare. The aim of the study was to evaluate the effects of Hermetia illucens (HI) and Tenebrio molitor (TM) live larvae in the diets of broiler chickens on growth performance, carcass yield and health status. A total of 180 four-day-old male broiler chickens (Ross 308) were randomly allotted to 18 pens. Each pen was assigned to one of the three dietary treatments (6 replicates/treatment, 10 birds/replicate) as follows: (i) control diet (C): commercial feed (two feeding phases: starter [4–11 days] and grower [12–38 days]), (ii) HI: C + 5% of the expected daily feed intake (DFI) HI live larvae (calculated on dry matter [DM]) and (iii) TM: C + 5% of DFI TM live larvae (DM). At 39 days of age, birds were slaughtered. Growth performance parameters were overall not affected by dietary treatments, except for the grower phase feed conversion ratio (FCR) and the overall FCR being better in the TM broilers than the others (p < 0.01). No differences were observed for slaughtering performance and haematological and serum parameters, except for the spleen relative weight being higher (p < 0.01) in the birds administered with larvae when compared to the C group. Gut morphometric indexes and histopathological alterations were not influenced by insect larvae administration. In conclusion, the administration in limited quantities of HI and TM live larvae as environmental enrichment has no negative effects on broiler chicken growth performance and health status. A behavioural study could confirm that live insect larvae represent a novel natural environmental enrichment in broiler farming.     

抗菌肽粗提物对肉鸡生长性能、粪便微生物菌群结构及经济效益的影响

为分析抗菌肽粗提物对肉鸡生长性能、粪便微生物菌群结构及经济效益的影响,试验选择体重相近的21日龄白羽肉鸡600只,随机分成4组,每组15个重复,每个重复10只,1组为空白对照组饲喂基础日粮,试验2、3、4组在基础日粮中分别添加1.0%、1.5%、2.0%的抗菌肽粗提物,试验期为21 d。结果表明：（1）试验2、3、4组的平均采食均高于1组（P > 0.05）|试验3、4组的平均日增重较1组比分别提高11.0%、9.4%（P ＜ 0.05）,料重比较1组比分别降低18.5%、15.2% （P ＜ 0.05）|（2）试验3、4组粪便中大肠杆菌的含量较1组分别降低14.3%、18.0%（P ＜ 0.05）,试验3、4组粪便中乳酸杆菌、双歧杆菌的含量较1组比分别提高4.6%、6.7%、14.5%、12.3%（P ＜ 0.05）|（3）试验3、4组每只肉鸡经济效益较1组比分别提高19.3%、17.7%。综上,1.5%抗菌肽粗提物添加可以提高白羽肉鸡生长性能,改善粪便微生物菌群结构,提高其经济效益。 [关键词] 抗菌肽粗提物|白羽肉鸡|生长性能|粪便微生物菌群结构|经济效益     

口蹄疫病毒VP1基因密码子偏好性分析

VP1蛋白是口蹄疫病毒(FMDV)的主要结构蛋白,可诱导机体产生中和抗体以及激发保护性免疫应答。为探究VP1基因密码子偏好性,筛选出其最佳体外表达系统,使用Visual Gene Developer、CodonW、GraphPad Prism等软件,对VP1基因进行密码子偏好性分析,同时将VP1基因密码子使用频率与大肠杆菌、毕赤酵母、昆虫杆状病毒和哺乳动物细胞表达系统作了比较。结果显示,VP1基因的CAI为0.21,ENC为55.43,GC3S为65.26%,表明该基因密码子使用偏好较弱并且密码子偏好以G/C碱基结尾。结合VP1基因与各表达系统密码子使用频率比值,发现其与昆虫杆状病毒表达系统频率比值差异最小且CAI最大,因此推断昆虫杆状病毒表达系统是FMDV VP1基因最适体外表达系统。本研究为FMDV亚单位疫苗研制等提供了技术基础。