Rethinking microbial diversity analysis in the high throughput sequencing era

The analysis of amplified and sequenced 16S rRNA genes has become the most important single approach for microbial diversity studies. The new sequencing technologies allow for sequencing thousands of reads in a single run and a cost-effective option is split into a single run across many samples. However for this type of investigation the key question that needs to be answered is how many samples can be sequenced without biasing the results due to lack of sequence representativeness? In this work we demonstrated that the level of sequencing effort used for analyzing soil microbial communities biases the results and determines the most effective type of analysis for small and large datasets. Many simulations were performed with four independent pyrosequencing-generated 16S rRNA gene libraries from different environments. The analysis performed here illustrates the lack of resolution of OTU-based approaches for datasets with low sequence coverage. This analysis should be performed with at least 90% of sequence coverage. Diversity index values increase with sample size making normalization of the number of sequences in all samples crucial. An important finding of this study was the advantage of phylogenetic approaches for examining microbial communities with low sequence coverage. However, if the environments being compared were closely related, a deeper sequencing would be necessary to detect the variation in the microbial composition.     

Characterization of microbial community structure during continuous anaerobic digestion of straw and cow manure

Responses of bacterial and archaeal communities to the addition of straw during anaerobic digestion of manure at different temperatures (37°C, 44°C and 52°C) were investigated using five laboratory-scale semi-continuous stirred tank reactors. The results revealed that including straw as co-substrate decreased the species richness for bacteria, whereas increasing the operating temperature decreased the species richness for both archaea and bacteria, and also the evenness of the bacteria. Taxonomic classifications of the archaeal community showed that Methanobrevibacter dominated in the manure samples, while Methanosarcina dominated in all digesters regardless of substrate. Increase of the operating temperature to 52°C led to increased relative abundance of Methanoculleus and Methanobacterium. Among the bacteria, the phyla Firmicutes and Bacteroidetes dominated within all samples. Compared with manure itself, digestion of manure resulted in a higher abundance of an uncultured class WWE1 and lower abundance of Bacilli. Adding straw to the digesters increased the level of Bacteroidia, while increasing the operating temperature decreased the level of this class and instead increased the relative abundance of an uncultured genus affiliated to order MBA08 (Clostridia). A considerable fraction of bacterial sequences could not be allocated to genus level, indicating that novel phylotypes are resident in these communities.     

Composting of tannery effluent with cow manure and wheat straw

Wastewater from the leather industry in León (Guanajuato, México) is discharged into the Turbio river without treatment. Tannery wastewater contains utilizable nutrients, but also toxic organic compounds which might affect soil processes and plant growth, and pathogens, which might pose a threat to the local farming community. Tannery effluent was composted with cow manure and wheat straw for 90 days to reduce pathogens and toxic organic compounds and monitored. The compost was characterized by an electrolytic conductivity (EC) of 28.1 ms cm(-1), cation exchange capacity of 17.7 meq 100 g(-1), an absorbance at 645 nm of 0.0175, a respiration rate of 0.062 mg CO2-C kg(-1) compost-C day(-1), pH 8.5 and C:N ratio 7:1 with a germination index for cress (Lepidium sativum) of 48% after 90 days. Less than 10 faecal coliforms and no Salmonella sp., Shigella sp. or eggs of helminthes were detected in the compost while total coliforms decreased by log10 of 2. Total concentrations of lead (Pb) were 8.9 mgkg(-1) dry compost, chromium (Cr) 77 mg kg(-1) dry compost, cadmium (Cd) 0.4 mg kg(-1) dry compost, copper (Cu) 10.3 mg kg(-1) dry compost and sodium (Na) 14,377 mg kg(-1) dry compost. The compost characteristics indicated that it was mature, but the germination index for cress of less than 50% suggested possible remaining phytotoxic compounds. However, the large salt concentrations (especially Na), might have inhibited cress development and thus reduced the germination index. The large salt concentration might thus limit the use of this kind of compost.     

Rapid genotyping of soybean cultivars using high throughput sequencing

Soybean (Glycine max) breeding involves improving commercially grown varieties by introgressing important agronomic traits from poor yielding accessions and/or wild relatives of soybean while minimizing the associated yield drag. Molecular markers associated with these traits are instrumental in increasing the efficiency of producing such crosses and Single Nucleotide Polymorphisms (SNPs) are particularly well suited for this task, owing to high density in the non-genic regions and thus increased likelihood of finding a tightly linked marker to a given trait. A rapid method to develop SNP markers that can differentiate specific loci between any two parents in soybean is thus highly desirable. In this study we investigate such a protocol for developing SNP markers between multiple soybean accessions and the reference Williams 82 genome. To restrict sampling frequency reduced representation libraries (RRLs) of genomic DNA were generated by restriction digestion followed by library construction. We chose to sequence four accessions Dowling (PI 548663), Dwight (PI 597386), Komata (PI200492) and PI 594538A for their agronomic importance as well as Williams 82 as a control.MseI was chosen to digest genomic DNA based on predictions that it will cut sparingly in the mathematically defined high-copy-number regions of the genome. All RRLs were sequenced on the Illumina genome analyzer. Reads were aligned to the Glyma1 reference assembly and SNP calls made from the alignments. We identified from 4294 to 14550 SNPs between the four accessions and the Williams 82 reference. In addition a small number of SNPs (1142) were found by aligning Williams 82 reads to the reference assembly (Glyma1) suggesting limited genetic variation within the Williams 82 line. The SNP data allowed us to estimate genetic diversity between the four lines and Williams 82. Restriction digestion of soybean genomic DNA with MseI followed by high throughput sequencing provides a rapid and reproducible method for generating SNP markers.     

Molecular diet analysis of two african free-tailed bats (molossidae) using high throughput sequencing

Given the diversity of prey consumed by insectivorous bats, it is difficult to discern the composition of their diet using morphological or conventional PCR-based analyses of their faeces. We demonstrate the use of a powerful alternate tool, the use of the Roche FLX sequencing platform to deep-sequence uniquely 5' tagged insect-generic barcode cytochrome c oxidase I (COI) fragments, that were PCR amplified from faecal pellets of two free-tailed bat species Chaerephon pumilus and Mops condylurus (family: Molossidae). Although the analyses were challenged by the paucity of southern African insect COI sequences in the GenBank and BOLD databases, similarity to existing collections allowed the preliminary identification of 25 prey families from six orders of insects within the diet of C. pumilus, and 24 families from seven orders within the diet of M. condylurus. Insects identified to families within the orders Lepidoptera and Diptera were widely present among the faecal samples analysed. The two families that were observed most frequently were Noctuidae and Nymphalidae (Lepidoptera). Species-level analysis of the data was accomplished using novel bioinformatics techniques for the identification of molecular operational taxonomic units (MOTU). Based on these analyses, our data provide little evidence of resource partitioning between sympatric M. condylurus and C. pumilus in the Simunye region of Swaziland at the time of year when the samples were collected, although as more complete databases against which to compare the sequences are generated this may have to be re-evaluated.     

Fixed-bed fermentation of rice straw and chicken manure using a mixed culture of marine mesophilic microorganisms

A mixture of rice straw (80%) and chicken manure (20%) was pretreated and fermented to carboxylic acids by using a mixed culture of marine mesophilic microorganisms. Two sets of four fermentors, built from PVC pipes, were used for both biomass pretreatment and fermentation. Four 1L fermentors (F1-F4) were arranged in series, where liquid fermentation products were transferred from one fermentor to the other, to form a train. A liquid volume of 10mL and 15mL were transferred every four days for Trains A and B, respectively. The maximum total acid concentration for F1 in Train A was 34.2g/L and the maximum acid concentration in F2-F4 was approximately 44g/L. The maximum total acid concentration in F1 in Train B was 30.5g/L and the maximum acid concentration in F2-F4 was approximately 48g/L. The conversion in each of the fermentors in Train A varied from 0.821 to 0.879g VS digested/g VS fed and the yield was in the range 0.489-0.609g total acids/g VS fed. The conversion and yield in Train B were 0.741-0.914g VS digested/g VS fed and 0.563-0.669g total acids/g VS fed, respectively. The continuum particle distribution model (CPDM) predicted acid concentrations and retention times in the fixed-bed fermentation system with R(2) of 0.67-0.84 in Trains A and B.     

Hydrocarbon degradation capacity and population dynamics of a microbial consortium obtained using a sequencing batch reactor in the presence of molasses

A native microbial consortium capable of degrading hydrocarbons was employed as an inoculum source in a sequencing batch reactor (SBR) using molasses as a carbon source. The microbial biomass in the SBR was able to grow in the presence of molasses, degrading 88% of the reducing sugar. Moreover, the consortium produced in the SBR was capable of maintaining 75% of the capacity for biodegradation of oil with respect to the original capacity of the native microbial consortium. Monitoring of the microbial population structure was accomplished using PCR-DGGE. The results indicated that the microbial populations grown in molasses were stable during crude oil degradation, as judged by comparison to the population structure of the native microbial consortium. The results obtained demonstrated that molasses could be used as a carbon source to promote the growth of biomass with oildegrading capacity.     

DNA-based faecal dietary analysis: a comparison of qPCR and high throughput sequencing approaches

The genetic analysis of faecal material represents a relatively non-invasive way to study animal diet and has been widely adopted in ecological research. Due to the heterogeneous nature of faecal material the primary obstacle, common to all genetic approaches, is a means to dissect the constituent DNA sequences. Traditionally, bacterial cloning of PCR amplified products was employed; less common has been the use of species-specific quantitative PCR (qPCR) assays. Currently, with the advent of High-Throughput Sequencing (HTS) technologies and indexed primers it has become possible to conduct genetic audits of faecal material to a much greater depth than previously possible. To date, no studies have systematically compared the estimates obtained by HTS with that of qPCR. What are the relative strengths and weaknesses of each technique and how quantitative are deep-sequencing approaches that employ universal primers? Using the locally threatened Little Penguin (Eudyptula minor) as a model organism, it is shown here that both qPCR and HTS techniques are highly correlated and produce strikingly similar quantitative estimates of fish DNA in faecal material, with no statistical difference. By designing four species-specific fish qPCR assays and comparing the data to the same four fish in the HTS data it was possible to directly compare the strengths and weaknesses of both techniques. To obtain reproducible quantitative data one of the key, and often overlooked, steps common to both approaches is ensuring that efficient DNA isolation methods are employed and that extracts are free of inhibitors. Taken together, the methodology chosen for long-term faecal monitoring programs is largely dependent on the complexity of the prey species present and the level of accuracy that is desired. Importantly, these methods should not be thought of as mutually exclusive, as the use of both HTS and qPCR in tandem will generate datasets with the highest fidelity.     

微生物处理对秸秆结构的影响

使用红外光谱、X射线衍射及扫描电镜对4种经固态培养的微生物降解稻草秸秆的效果进行了研究,并与原稻草粉进行结构对比分析。结果表明：经过高碳低氮培养,秸秆木质素均有明显降解,其中黄孢原毛平革菌达到37.17%。扫描电镜发现秸秆的表面形态和内部结构发生了明显改变,红外光谱中芳香环与醚键吸收明显减少,X射线衍射得到的结晶度最大下降了5.60%。     

Genetic analysis of colorectal carcinoma using high throughput single nucleotide polymorphism genotyping technique within the population of Jammu and Kashmir

Molecular Biology Reports - SNP genotyping has become increasingly more common place to understand the genetic basis of complex diseases like cancer. SNP-genotyping through MassARRAY? is a...     

降解水稻秸秆兼抑制水稻纹枯病菌多功能复合菌系的构建

目的针对稻草直接还田需要,构建能够高效降解水稻秸秆同时又能抑带l水稻纹枯病菌的多功能复合菌系。方法通过将具有高效降解纤维素的天然复合菌群与具有抑制水稻纹枯病菌效果的菌株组合,构建多功能复合菌系;采用失重法检测该复合菌系对水稻秸杆的腐解作用,荧光定量PER法检测其对水稻纹枯病菌的抑制效果。结果成功地构建了一组多功能复合菌系,腐解12d后,水稻秸秆干物质总失重率为41．4％,其中半纤维素降解率为59．5％,纤维素降解率为52．5％,木质素降解率为15．3％,腐解过程中平均CMC酶活为8．1IU／g。该复合菌系对水稻纹枯病菌的抑制效果明显,发酵40d后对水稻纹枯病菌的抑制率为27．1％,对照组抑制率为2．7％。结论该复合菌系能高效降解水稻秸秆,同时又能较好地抑制水稻纹枯病菌,适宜在水稻秸秆直接还田过程中使用。     

Influences of rice straw biochar and organic manure on forage soybean nutrient and Cd uptake

Abstract

This pot experiment aimed to investigate the influence of rice straw biochar (BC 0, 1, and 3%, w/w) and organic manure (OM 0, 1, and 2%, w/w) addition on the growth, nutrient and cadmium (Cd) uptake of forage soybean in 10 mg Cd kg^?1 contaminated soils. Compared with non-biochar treatments, biochar decreased shoot biomass, height and nitrogen (N) contents. Organic manure markedly increased the shoot biomass, shoot phosphorus (P), potassium (K), calcium (Ca) and magnesium (Mg) concentration, and root N, P, Ca contents without biochar addition treatments, while in the case of 3% biochar, there were no significant effects on N, K, Ca, and Mg contents of shoot and root among organic manure treatments. In comparison with other treatments, the minimum Cd content of shoots and roots both occurred in the treatment of BC3%+OM2%, while shoot Cd content reached the maximum value in OM2% treatment. Thus, these results suggested that organic manure addition can elevate forage soybean yield and nutrient content, while biochar had no positive effects. High biochar (3%) addition in combination with highest dose of organic manure (2%) can decline the Cd content of soybean and contribute to the agricultural product safety.     

混合菌群发酵秸秆合成菌体蛋白及其动力学分析

混合菌群发酵秸秆可有效提高秸秆纤维的降解率及菌体蛋白的转化率,对拓广蛋白饲料来源、减少环境污染起到积极的作用。本研究以小麦秸秆为原料,在纤维素酶水解预处理的基础上,以米曲霉作为先导菌,进一步分解残留的粗纤维,为后期发酵提供充足的碳源。根据不同微生物的代谢特征和协同机理,试验确定了发酵阶段混合菌群的组成为:米曲霉、产朊假丝酵母和枯草芽胞杆菌;接种顺序为:先接种米曲霉,再接种产朊假丝酵母,最后接种枯草芽胞杆菌。正交试验表明,影响发酵主要因素的主次顺序为:秸秆与麸皮配比>接种比例>发酵时间>接种量>发酵温度;发酵的最适条件为:米曲霉的接种量2.5%,发酵12h后接入5%的产朊假丝酵母,继续发酵8h后接入2.5%的枯草芽胞杆菌,发酵温度为28℃,秸秆与麸皮的配比为4∶1,尿素添加量为1.2%;结合动力学分析,将混合菌群的发酵时间优化为35h,发酵产物中粗蛋白含量由原来的5.47%提高到25%左右。对最适发酵条件下的动力学过程进行了探讨,建立了以Logistic方程为基础的数学模型和动力学方程。本研究表明,混合菌群发酵秸秆提高了发酵产物中的粗蛋白含量。动力学分析对于了解发酵机理、掌握整个发酵过程中混合菌群生长的动态变化、优化发酵工艺具有重要的指导意义。