The microbial diversity and structure in peatland forest in Indonesia

The microbial community structure and function under forest in tropical peatlands are poorly understood. In this study, we investigated the microbial community structure and diversity in natural peat swamp forest soil, disturbed peat soil and mineral soil in Central Kalimantan, Indonesia, using 454 pyrosequencing. The results showed that the natural peat soil had the greatest fungal species richness (Chao1), which was significantly (p < .05) larger than that in the other two soils. Community structure of both fungi and bacteria in natural peat soil differed significantly from that in the disturbed peat soil (p = .039 and p = .045, respectively). Ascomycota (40.5%) was the most abundant phylum across the three soils followed by Basidiomycota (18.8%), Zygomycota (<0.1%) and Glomeromycota (<0.1%). The linear discriminant analysis with effect size (LEfSe) showed that Ascomycota (p < .05) and genus Gliocephalotrichum (p < .05) dominated in natural peat soil. Functionally, pathotrophs were more abundant in disturbed peat soil (p < .05). Proteobacteria (43.8%) were the most abundant phylum followed by Acidobacteria (32.6%), Actinobacteria (9.8%), Planctomycetes (1.7%). Methylocystis, Telmatospirillum, Syntrophobacter, Sorangium and Opitutus were the more abundant genera in disturbed peat soil, whereas Nevskia and Schlesneria were more abundant in mineral soil and natural peat soil, respectively. The natural peat forest soil supported a more diverse microbiology; however, the land use of such a soil can change its microbial community structure. The results provide evidence that the disturbance of tropical peat land could lead to the introduction and spread of a large number of fungal diseases     

Soil conditions and land use intensification effects on soil microbial communities across a range of European field sites

Intensive land use practices necessary for providing food and raw materials are known to have a deleterious effect on soil. However, the effects that such practices have on soil microbes are less well understood. To investigate the effects of land use intensification on soil microbial communities we used a combined T-RFLP and pyrosequencing approach to study bacteria, archaea and fungi in spring and autumn at five long term observatories (LTOs) in Europe; each with a particular land use type and contrasting levels of intensification (low and high). Generally, due to large gradients in soil variables, both molecular methods revealed that soil microbial communities were structured according to differences in soil conditions between the LTOs, more so than land use intensity. Moreover, variance partitioning analysis also showed that soil properties better explained the differences in microbial communities than land use intensity effects. Predictable responses in dominant bacterial, archaeal and fungal taxa to edaphic conditions (e.g. soil pH and resource availability) were apparent between the LTOs. Some effects of land use intensification at individual field sites were observed. However, these effects were manifest when land use change affected soil conditions. Uniquely, this study details the responses of different microbial groups to soil type and land use intensification, and their relative importance across a range of European field sites. These findings reinforce our understanding of drivers impacting soil microbial community structure at both field and larger geographic scales.     

Fine root decomposition,nutrient mobilization and fungal communities in a pine forest ecosystem

Despite its importance to energy flow and nutrient cycling the process of fine root decomposition has received comparatively little detailed research. Disruption of the fine root-soil interface during preparation of root litterbags for decomposition studies could affect decay rates and nutrient mobilization in part by altering the community of decay organisms. We compared rates of decomposition and nutrient release from fine roots of pine between litterbags and intact cores and characterized the fungal community in the decomposing roots. Fine root decomposition was about twice as fast overall for intact cores than litterbags, and rapid mobilization of N and P was observed for roots in cores whereas nutrients were immobilized in litterbags. Fungal communities characterized using 454 pyrosequencing were considerably different between decaying roots in intact cores and litterbags. Most interesting, taxa from ectomycorrhizal fungal orders such as Boletales, Thelephorales and Cantharellales appeared to be more common in decaying roots from cores than litterbags. Moreover, the rate of N and P mobilization from decaying fine roots was highly correlated with taxa from two orders of ectomycorrhizal fungi (Thelephorales, Cantharellales). Although we caution that DNA identified from the decaying roots cannot be conclusively ascribed to active fungi, the results provide tentative support for a significant role of ectomycorrhizal fungi in decomposition and nutrient mobilization from fine roots of pine.     

Within‐ and across‐breed imputation of high‐density genotypes in dairy and beef cattle from medium‐ and low‐density genotypes

The objective of this study was to evaluate, using three different genotype density panels, the accuracy of imputation from lower‐ to higher‐density genotypes in dairy and beef cattle. High‐density genotypes consisting of 777 962 single‐nucleotide polymorphisms (SNP) were available on 3122 animals comprised of 269, 196, 710, 234, 719, 730 and 264 Angus, Belgian Blue, Charolais, Hereford, Holstein‐Friesian, Limousin and Simmental bulls, respectively. Three different genotype densities were generated: low density (LD; 6501 autosomal SNPs), medium density (50K; 47 770 autosomal SNPs) and high density (HD; 735 151 autosomal SNPs). Imputation from lower‐ to higher‐density genotype platforms was undertaken within and across breeds exploiting population‐wide linkage disequilibrium. The mean allele concordance rate per breed from LD to HD when undertaken using a single breed or multiple breed reference population varied from 0.956 to 0.974 and from 0.947 to 0.967, respectively. The mean allele concordance rate per breed from 50K to HD when undertaken using a single breed or multiple breed reference population varied from 0.987 to 0.994 and from 0.987 to 0.993, respectively. The accuracy of imputation was generally greater when the reference population was solely comprised of the breed to be imputed compared to when the reference population comprised of multiple breeds, although the impact was less when imputing from 50K to HD compared to imputing from LD.     

白菜型油菜和菜薹的InDel 标记开发及其RILs群体遗传连锁图谱的构建

 通过白菜型油菜‘R-O-18’和菜薹‘L58’的基因组重测序数据与白菜基因组的参考序列（‘Chiifu-401-42’的基因组序列）的比对,在全基因组范围内检测到了18 479 个短插入缺失变异位点（≤5 bp）。从中挑选了500 个插入/缺失片段为4 ~ 5 bp 的InDel 变异位点,将其设计成InDel 分子标记并进行试验验证,结果有452 个标记通过PCR 扩增出单一条带,但仅有106 个在‘R-O-18’和‘L58’间表现出多态性,346 个没有多态性,48 个在PCR 中没有扩增。亲本间具有多态性的106 个InDel 标记可用来检测以‘R-O-18’和‘L58’为亲本构建的RILs 基因型,并构建了一张包含99 个标记的遗传连锁图谱。     

石灰联合碳铵熏蒸对连作香蕉生长和根际微生物群落结构的影响

摘 要：由于长期连作导致香蕉枯萎病大量爆发，造成香蕉种植面积锐减，已严重影响海南香蕉产业的发展，因而急需寻求能够缓解或克服香蕉连作障碍的有效措施。本实验旨在探究使用绿色土壤熏蒸剂对长期连作蕉园的香蕉枯萎病的防控效果，特别是对植株生长发育、土壤化学性质和根际微生物区系的影响。田间试验共设置两个处理：石灰碳铵熏蒸处理（LAB）和对照处理（CK）。结果表明: LAB处理可以显著降低香蕉枯萎病发病率，与CK处理相比两季分别降低40%和46.62%，显著增加香蕉亩产量，与CK处理相比两季分别增产45.56%和75.99%。LAB处理可以显著提高土壤pH，改善土壤酸化，使酸性土壤维持中性水平，同时，增加土壤有机质含量，并且显著提高土壤速效磷（两季分别提高28.33%和89.14%）和速效钾含量（23.92%和38.67%）。并且LAB处理明显改变香蕉根际微生物群落结构，可以显著降低变形菌门和子囊菌门相对丰度，显著增加放线菌门等相对丰度，同时显著降低病原菌镰刀菌属相对丰度，并且显著提高部分土壤拮抗菌属的相对丰度，如链霉菌属、红球菌属和曲霉属。因此，石灰碳铵熏蒸有效改善香蕉根际微生物群落结构，有效防控香蕉枯萎病的发生并促进其植株生长。     

Intestinal Microbiota in Large Yellow Croaker,Larimichthys crocea,at Different Ages

The polymerase chain reaction–denaturing gradient gel electrophoresis (PCR‐DGGE) of 16S ribosomal RNA gene was used to investigate bacterial communities in the intestines of large yellow croaker at six different ages (12 d, 18 d, 26 d, 40 d, 3 mo, and 1 yr old) as well as within the corresponding feed and culture water. In addition, Illumina Miseq sequencing was utilized to compare intestinal microbiota between 12‐d‐old and 1‐yr‐old individuals. PCR‐DGGE results revealed that the culture water had the highest bacterial diversity, followed by the feed, while the intestines had the lowest diversity. The intestinal microbiota at six ages changed severely; however, the change did not follow any trend. The large yellow croaker intestines harbored specific bacterial communities that differed from those in both feed and water. Illumina Miseq sequencing results revealed that the diversity of intestinal bacteria in 12‐d‐old fish was higher than that in 1‐yr‐old fish, and the bacterial composition differed significantly between them. γ‐Proteobacteria and Pseudoalteromonas supplied the most abundant phylum and genus in the 12‐d‐old fish intestine. However, in the 1‐yr‐old fish intestine, Firmicutes and Clostridium were the most dominant, respectively. The study may contribute to a better understanding of gut microbiota and dynamics of the large yellow croaker and the relationship with their surrounding environment.     

增氧方式对水芹菜-微生物联合作用处理冬季养殖废水的影响

为探究不同增氧方式对水芹菜-微生物联合作用处理养殖废水消化液及微生物群落结构变化的影响，设置循环和曝气两组试验，以静置处理作为对照，共运行35 d，间隔7 d取样，测定常规水质指标，在试验开始和结束时分别测定水芹菜生长情况，并采用高通量测序技术对微生物群落结构进行分析。结果显示，经过35 d的处理，静置组、曝气组和循环组的DO（溶解氧）分别达到0.60、10.38 mg·L^-1和10.85 mg·L^-1；静置培养的水芹菜长势最好，相对生长速率为0.03 g·g^-1·d^-1；三种处理方式对水质的净化效果差异显著，循环组的水质净化效果最好，COD（化学需氧量）、NH₃-N（氨氮）和TN（总氮）的去除率分别达89.89%、69.40%和77.65%；黄杆菌属（Flavobacterium）的相对丰度从43.21%下降到0.16%，克里斯滕森菌属（Christensenellaceae）和瘤胃球菌属（Ruminococcaceae）的相对丰度则大幅增加。水芹菜在冬季于养殖废水消化液中可以正常生长，曝气和循环处理可以明显提高净化效率；黄杆菌属和假单胞菌属（Pseudononas）是脱氮的功能菌属，梭菌纲（Clostridia）的大量繁殖有利于COD的去除。