Development of microsatellite markers and a preliminary assessment of population structuring in the rice weevil,Sitophilus oryzae (L.)

The rice weevil, Sitophilus oryzae is one of the primary pests of stored grains worldwide. To develop and implement an effective integrated pest management strategy, an understanding of the population structuring of this destructive pest is vital. In this study we used Illumina paired-end sequencing to develop S. oryzae species-specific microsatellite markers, and used these markers to conduct a preliminary assessment of population structuring in four populations of S. oryzae from three countries (Australia, China, and USA). 7,635,996 raw sequencing reads were produced, with 11,794 microsatellites detected and 214,257 primer options designed. 48 microsatellite markers were selected for further validation, with 10 markers amplifying consistently across the four S. oryzae populations. These markers displayed a high level of polymorphism overall (6.67 alleles/locus), though this was slightly lower within populations (3.10–4.88 alleles/locus). We used the markers to conduct a preliminary assessment of genetic structuring among the four S. oryzae populations: three laboratory cultures (New South Wales, Queensland, and Santai) and a field collected population from Kansas. Analyses suggest high levels of genetic differentiation between the sample locations, with a global F_ST of 0.239, and pairwise F_ST values ranging from 0.100 to 0.395. Bayesian clustering analyses suggest these four populations formed four distinct clusters, with a similar pattern identified by Principal Coordinate Analysis. These microsatellite markers, together with our preliminary population genetic analyses, will provide a valuable resource for population genetic research, and contribute to effective integrated pest management strategies in the future.     

基于Illumina PE300高通量测序的海南糟粕醋微生物多样性分析

目的 研究海南糟粕醋中微生物的多样性,分析海南糟粕醋在自然条件下贮藏时的优势菌及风险菌。方法 采用Illumina PE300高通量测序技术对海南糟粕醋中细菌和真菌群落进行多样性分析,扩增糟粕醋中细菌的16S rDNA和真菌的ITS序列。结果 细菌多样性测序获得306,600条序列, 130,745,424碱基(base pair, bp),505操作分类单元(operational taxonomic units, OTU),可归属为23门(phylum)、51纲(class)、115目(order)、191科(family)、312属(genus)、432种(species);真菌多样性测序获得612,015条序列, 132,784,567 bp, 27 OTU,可归属为3 phylum、7 class、12 order、18 family、24 genus、25 species。糟粕醋在自然条件下贮藏时,主要细菌属为:乳酸菌属(Lactobacillus)、棒杆菌属(Corynebacteriums)、乳酪短杆菌属(Brevibacterium)、芽孢杆菌属(Bacillus)、...     

Sulfate- and pH-driven metabolic flexibility in sugarcane vinasse dark fermentation stimulates biohydrogen evolution,sulfidogenesis or homoacetogenesis

Dark fermentation of sugarcane vinasse can be used as a “cleaning” step to remove sulfate prior to methanogenesis because sulfidogenic conditions can be successfully established in parallel with biohydrogen production. Using a 2² central composite rotational design (CCRD) and response surface methodology (RSM), this study assessed the impacts of bicarbonate and sulfate availability on the establishment of sulfidogenesis in the thermophilic (55 °C) fermentation of vinasse in batch reactors, equally assessing the impacts on biohydrogen evolution. CCRD-RSM results indicated the favoring of biohydrogen production at the lowest sulfate and bicarbonate concentrations, whilst the opposite was observed for sulfidogenesis. Glycerol, lactate, and hydrogen were the preferential electron donors utilized by sulfate-reducing bacteria (SRB), whilst ethanol was markedly consumed only at high sulfate concentrations. SRB were inhibited by sodium when dosing excess NaHCO₃ and Na₂SO₄. Complementary tests revealed maximum biohydrogen production (2.40 mmol) out of the CCRD, at pH exceeding 7.5 with no interference of sulfidogenesis. Non-efficient biohydrogen production was observed at low pH (<5.0; ～1.90 mmol) because the uptake of lactate was inhibited. Meanwhile, homoacetogenesis was established under intermediate pH range (5.5–6.5), as revealed by the accumulation of acetate (up to 2.5 g L^?1). 16S rRNA gene amplicon sequencing further revealed the genera Thermoanaerobacterium/Pseudoclostridium, Desulfotomaculum/Desulfohalotomaculum and Sporomusaceae/Moorella as the main biohydrogen-producing, sulfate-removing and biohydrogen-consuming (homoacetogens) microbial groups, respectively. Hence, using a single inoculum source, vinasse may provide a butyrate-rich (along with biohydrogen-rich biogas) or a sulfate-free and acetate-rich fermented effluent, depending mainly on proper pH control.     

Changes in rumen bacterial and archaeal communities over the transition period in primiparous Holstein dairy cows

In the present study, we hypothesized that the rumen bacterial and archaeal communities would change significantly over the transition period of dairy cows, mainly as an adaptation to the classical use of low-grain prepartum and high-grain postpartum diets. Bacterial 16S rRNA gene amplicon sequencing of rumen samples from 10 primiparous Holstein dairy cows revealed no changes over the transition period in relative abundance of genera such as Ruminococcus, Butyrivibrio, Clostridium, Coprococcus, and Pseudobutyrivibrio. However, other dominant genus-level taxa, such as Prevotella, unclassified Ruminococcaceae, and unclassified Succinivibrionaceae, showed distinct changes in relative abundance from the prepartum to the postpartum period. Overall, we observed individual fluctuation patterns over the transition period for a range of bacterial taxa that, in some cases, were correlated with observed changes in the rumen short-chain fatty acids profile. Combined results from clone library and terminal-restriction fragment length polymorphism (T-RFLP) analyses, targeting the methyl-coenzyme M reductase α-subunit (mcrA) gene, revealed a methanogenic archaeal community dominated by the Methanobacteriales and Methanomassiliicoccales orders, particularly the genera Methanobrevibacter, Methanosphaera, and Methanomassiliicoccus. As observed for the bacterial community, the T-RFLP patterns showed significant shifts in methanogenic community composition over the transition period. Together, the composition of the rumen bacterial and archaeal communities exhibited changes in response to particularly the dietary changes of dairy cows over the transition period.     

Illumina高通量测序技术分析中周羌稞养生酒窖泥细菌多样性

以不同窖龄（5年、10年、20年和30年）的中周羌稞养生酒窖泥为研究对象,利用Illumina高通量测序技术对窖泥细菌16S rRNA V4～V5区进行测序,分析其细菌多样性。结果表明,窖泥中细菌多样性（Shannon指数）和丰富度（Chao指数）随着窖龄的增加而显著提高（P＜0.05）。不同窖龄窖泥的细菌群落组成存在差异,盐扁菌科（Haloplasmataceae）、乳酸杆菌科（Lactobacillaceae）,瘤胃球菌属（Ruminococcaceae）和梭菌属（Clostridium）为不同窖龄窖泥的共有细菌;类芽孢杆菌属（Paemibacillus）、芽孢杆菌属（Bacillus）、消化球菌科（Peptococcaceae）、喜盐芽孢杆菌属（Haloballus）和链球菌属（Streptococcus）只出现在30年窖龄窖泥中;PCA结果分析表明,相同窖龄窖泥中的细菌具有更高的相似性,说明窖龄是影响窖泥细菌群落组成的重要因素之一。     

应用Illumina MiSeq测序解析O3-BAC水处理技术生产饮用水中细菌多样性

采用切向流超滤技术(TFF)大量富集浓缩饮用水,提取其基因组DNA,扩增16SrDNA片段的V4+V5区,共获得45 093条序列,序列平均长度395.65bp,经高通量测序和物种注释、评估、组成分析、β-多样性分析、物种差异分析、RDA分析等进行生物信息学分析,获得饮用水中细菌多样性组成及丰度信息。结果发现,饮用水中可能含有的细菌多样性具有不确定性和随机性,对其影响最大的水质指标为浊度和余氯,经Illumina MiSeq高通量测序获得基因信息的细菌可能存在无活性或者处于VBNC状态的可能,难以采用纯培养方式培养,Illumina MiSeq高通量测序可作为饮用水细菌分析的前置技术加以推广和应用。     

应用Illumina MiSeq高通量测序技术分析来凤地区腌制大头菜叶中微生物多样性

该研究利用Illumina MiSeq高通量测序技术对腌制大头菜叶样品中微生物多样性进行了研究,进而分析其中的微生物群落组成和差异。结果表明,在门分类水平上,以硬壁菌门（Firmicutes,52.28%）和变形菌门（Proteobacteria,38.40%）为主要优势细菌门;子囊菌门（Ascomycota,88.19%）和担子菌门（Basidiomycota,11.15%）为优势真菌门。在属分类水平上,注释到明确分类地位的细菌属和真菌属分别有382个和31个,其中平均相对含量＞1%的分别有12个和8个。在操作分类单元（OTU）水平上,共发现17个核心细菌OTUs和11个核心真菌OTUs。综上,腌制大头菜叶具有较高的微生物多样性,且细菌群落物种数高于真菌。     

低分子质量壳寡糖对鲢鱼冷藏过程中鱼肉品质及菌相的影响

分析低分子质量壳寡糖（分子质量≤1 000 Da,脱乙酰度≥90%）对鲢鱼片4 ℃冷藏过程中菌相组成及品质变化的影响。将鲢鱼片随机分为对照组与壳寡糖（0.5 g/100 mL）处理组,测定其感官评分、菌落总数、总挥发性盐基氮含量、三磷酸腺苷关联物含量及K值等指标,并采用Illumina MiSeq高通量测序技术分析菌相组成,评价壳寡糖对鲢鱼片的保鲜作用。结果表明：壳寡糖能够改变鲢鱼冷藏过程中的菌相组成且抑制其优势腐败菌属假单胞菌和气单胞菌的生长;壳寡糖处理能够显著抑制鱼肉菌落总数和挥发性盐基氮的生成,同时显著延缓肌苷酸及次黄嘌呤核苷酸的降解,进而减少次黄嘌呤的生成。壳寡糖能够显著提高鲢鱼贮藏过程中的品质,这主要通过抑制优势腐败菌属的生长实现。     

烟草种子附生真菌群落结构与多样性

为了解烟草种子附生真菌的群落结构和多样性。采用Illumina MiSeq高通量测序技术测定K326、云烟85、L8、301种子的附生真菌。结果表明K326种子的优势属为链格孢属（Alternaria）、赤霉菌属（Gibberella）、隐球菌属（Cryptococcus）、镰刀菌属（Fusarium）及红酵母属（Rhodotorula）等;云烟85的优势属为赤霉菌属、小画线壳属（Monographella）、链格孢属、红酵母属及镰刀菌属;301的优势属为链格孢属;L8的优势属为链格孢属、曲霉菌属、镰刀菌属、赤霉菌属及隐球菌属等。