Abstract:
:The soil microbiome is inherently complex with high biological diversity, and spatial heterogeneity typically occurring on the submillimetre scale. To study the microbial ecology of soils, and other microbiomes, biomolecules, that is, nucleic acids and proteins, must be efficiently and reliably co-recovered from the same biological samples. Commercial kits are currently available for the co-extraction of DNA, RNA and proteins but none has been developed for soil samples. We present a new protocol drawing on existing phenol-chloroform-based methods for nucleic acids co-extraction but incorporating targeted precipitation of proteins from the phenol phase. The protocol is cost-effective and robust, and easily implemented using reagents commonly available in laboratories. The method is estimated to be eight times cheaper than using disparate commercial kits for the isolation of DNA and/or RNA, and proteins, from soil. The method is effective, providing good quality biomolecules from a diverse range of soil types, with clay contents varying from 9.5% to 35.1%, which we successfully used for downstream, high-throughput gene sequencing and metaproteomics. Additionally, we demonstrate that the protocol can also be easily implemented for biomolecule co-extraction from other complex microbiome samples, including cattle slurry and microbial communities recovered from anaerobic bioreactors, as well as from Gram-positive and Gram-negative pure cultures.
journal_name
Mol Ecol Resourjournal_title
Molecular ecology resourcesauthors
Thorn CE,Bergesch C,Joyce A,Sambrano G,McDonnell K,Brennan F,Heyer R,Benndorf D,Abram Fdoi
10.1111/1755-0998.12979subject
Has Abstractpub_date
2019-03-01 00:00:00pages
439-455issue
2eissn
1755-098Xissn
1755-0998journal_volume
19pub_type
杂志文章abstract::The pygmy grasshopper Tetrix japonica is a common insect distributed throughout the world, and it has the potential for use in studies of body colour polymorphism, genomics and the biology of Tetrigoidea (Insecta: Orthoptera). However, limited biological information is available for this insect. Here, we conducted a d...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12553
更新日期:2017-05-01 00:00:00
abstract::The public availability of large quantities of gene sequence data provides a valuable resource of the mining of Simple Sequence Repeat (SSR) molecular genetic markers for genetic analysis. These markers are inexpensive, require minimal labour to produce and can frequently be associated with functionally annotated gene...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12078
更新日期:2013-05-01 00:00:00
abstract::Our understanding of Glossina fuscipes fuscipes, a major vector of sleeping sickness, has been severely constrained by a lack of genetic markers for mapping and population genetic studies. Here we present 10 newly developed microsatellite loci for this tsetse species. Heterozygosity levels in Moyo, an Ugandan populati...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02328.x
更新日期:2008-11-01 00:00:00
abstract::We describe 15 polymorphic microsatellite loci from the white-ruffed manakin Corapipo altera, a common understory bird of Neotropical lowland and montane evergreen forests from eastern Honduras to northwestern Colombia. These markers were developed in order to assess population structure and genetic diversity in a fra...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1471-8286.2007.01929.x
更新日期:2008-01-01 00:00:00
abstract::Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant archived skeletal mater...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12580
更新日期:2017-05-01 00:00:00
abstract::Thirteen polymorphic microsatellite markers were isolated and characterized from the great hornbill, Buceros bicornis. In analyses of 20 individuals, the numbers of alleles per locus varied from two to 11. The expected and observed heterozygosities ranged from 0.22 to 0.88 and from 0.20 to 1.00, respectively. The mean...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02447.x
更新日期:2009-03-01 00:00:00
abstract::Long a major focus of genetic research and breeding, sunflowers (Helianthus) are emerging as an increasingly important experimental system for ecological and evolutionary studies. Here, we review the various attributes of wild and domesticated sunflowers that make them valuable for ecological experimentation and descr...
journal_title:Molecular ecology resources
pub_type: 杂志文章,评审
doi:10.1111/1755-0998.12023
更新日期:2013-01-01 00:00:00
abstract::The emergence of third-generation sequencing (3GS; long-reads) is bringing closer the goal of chromosome-size fragments in de novo genome assemblies. This allows the exploration of new and broader questions on genome evolution for a number of nonmodel organisms. However, long-read technologies result in higher sequenc...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13176
更新日期:2020-09-01 00:00:00
abstract::DNA barcoding has become an important current scientific trend to the understanding of the world biodiversity. In the case of mega-diverse hot spots like Mexico, this technique represents an important tool for taxonomists, allowing them to concentrate in highlighted species by the barcodes instead of analyzing entire ...
journal_title:Molecular ecology resources
pub_type:
doi:10.1111/1755-0998.12149
更新日期:2013-11-01 00:00:00
abstract::The interbreeding of individuals coming from genetically differentiated but incompletely isolated populations can lead to the formation of admixed populations, having important implications in ecology and evolution. In this simulation study, we evaluate how individual admixture proportions estimated by the software st...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13234
更新日期:2020-11-01 00:00:00
abstract::Mitochondrial DNA (mtDNA) has formed the backbone of phylogeographic research for many years; however, recent trends focus on genome-wide analyses. One method proposed for calibrating inferences from noisy next-generation data, such as RAD sequencing, is to compare these results with analyses of mitochondrial sequence...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12953
更新日期:2019-01-01 00:00:00
abstract::Microsatellites are valuable markers for the analysis of genetic diversity, linkage mapping or genotyping. The limited availability of microsatellites for the genus Potentilla (Rosaceae) stipulated the isolation of markers from a representative (Potentilla pusilla Host) of the Potentilla core group that constitutes th...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2012.03134.x
更新日期:2012-07-01 00:00:00
abstract::Estimation of demographic history from nucleotide sequences represents an important component of many studies in molecular ecology. For example, knowledge of a population's history can allow us to test hypotheses about the impact of climatic and anthropogenic factors. In the past, demographic analysis was typically li...
journal_title:Molecular ecology resources
pub_type: 杂志文章,评审
doi:10.1111/j.1755-0998.2011.02988.x
更新日期:2011-05-01 00:00:00
abstract::The use of dominant markers such as amplified fragment length polymorphism (AFLP) for population genetics analyses is often impeded by the lack of appropriate computer programs and rarely motivated by objective considerations. The point of the present note is twofold: (i) we describe how the computer program Geneland ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2010.02864.x
更新日期:2010-11-01 00:00:00
abstract::In noninvasive genetic sampling, when genotyping error rates are high and recapture rates are low, misidentification of individuals can lead to overestimation of population size. Thus, estimating genotyping errors is imperative. Nonetheless, conducting multiple polymerase chain reactions (PCRs) at multiple loci is tim...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1471-8286.2007.01992.x
更新日期:2008-03-01 00:00:00
abstract::Plastid sequencing is an essential tool in the study of plant evolution. This high-copy organelle is one of the most technically accessible regions of the genome, and its sequence conservation makes it a valuable region for comparative genome evolution, phylogenetic analysis and population studies. Here, we discuss re...
journal_title:Molecular ecology resources
pub_type: 杂志文章,评审
doi:10.1111/1755-0998.12626
更新日期:2017-09-01 00:00:00
abstract::Identification of the juveniles of economically important thrips species on imports by morphology alone can be challenging and culturing is usually required. In the case of EU quarantine species such as Thrips palmi, rapid and accurate identification is essential. DNA barcoding using the Cytochrome oxidase I (COI) gen...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02723.x
更新日期:2010-01-01 00:00:00
abstract::As coral populations decline worldwide in the face of ongoing environmental change, documenting their distribution, diversity and conservation status is now more imperative than ever. Accurate delimitation and identification of species is a critical first step. This task, however, is not trivial as morphological varia...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13241
更新日期:2021-01-01 00:00:00
abstract::DNA microarrays are a popular technique for the detection of microorganisms. Several approaches using specific oligomers targeting one or a few marker genes for each species have been proposed. Data analysis is usually limited to call a species present when its oligomer exceeds a certain intensity threshold. While thi...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02199.x
更新日期:2009-01-01 00:00:00
abstract::We developed four multiplex panels comprising 19 microsatellite loci and tested their amplification in 21 rodent species important for agricultural and conservation management (Microtus, Arvicola, Chionomys). On average, 17.6 loci amplified per species. Number of alleles ranged from 1 to 19 per locus. We report an add...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02521.x
更新日期:2009-05-01 00:00:00
abstract::To determine the visual sensitivities of an organism of interest, quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is often used to quantify expression of the light-sensitive opsins in the retina. While qRT-PCR is an affordable, high-throughput method for measuring expression, it comes with inher...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13062
更新日期:2019-11-01 00:00:00
abstract::Biodiversity analyses based on next-generation sequencing (NGS) platforms have developed by leaps and bounds in recent years. A PCR-free strategy, which can alleviate taxonomic bias, was considered as a promising approach to delivering reliable species compositions of targeted environments. The major impediment of suc...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12472
更新日期:2016-03-01 00:00:00
abstract::Avian malaria and related haemosporidians (Plasmodium, [Para]Haemoproteus and Leucocytoozoon) represent an exciting multihost, multiparasite system in ecology and evolution. Global research in this field accelerated after the publication in 2000 of PCR protocols to sequence a haemosporidian mitochondrial (mtDNA) barco...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12977
更新日期:2019-03-01 00:00:00
abstract::We present 25 polymorphic microsatellite loci for Intsia palembanica, a highly valued timber species in the Indo-Malayan region, Australia and western Pacific islands. Microsatellite loci were tested for polymorphism across a total of 76 individuals from three natural populations from Irian Jaya, Indonesia. The averag...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02491.x
更新日期:2009-01-01 00:00:00
abstract::Two of the five subspecies of the western big-eared bat, Corynorhinus townsendii, are listed as federally endangered with the remaining three being of conservation concern. Knowing the degree of connectivity among populations would aid in the establishment of sound conservation and management plans for this taxon. For...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02243.x
更新日期:2009-01-01 00:00:00
abstract::A novel set of microsatellite markers for mungbean [Vigna radiata (L.) Wilczek] was developed from the public sequence database. Seventy-eight primers were designed and evaluated for polymorphism among 22 cultivated accessions. Eight polymorphic loci detected two to three alleles per locus with an average of 2.25. The...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02655.x
更新日期:2009-05-01 00:00:00
abstract::DNA extraction from minute hymenopterans and their larvae is difficult and challenging because of their small size indicating a low amount of starting material. Hence, 11 DNA extraction methods were compared to determine their efficacy in isolating DNA. Success of each method was scored on a 2% agarose gel after PCR o...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2011.03074.x
更新日期:2012-01-01 00:00:00
abstract::Understanding how landscape features affect gene flow has implications for numerous fields including molecular and evolutionary ecology. Despite this, modelling landscape resistance surfaces has remained a significant challenge. The R package resistancega was developed to provide a framework for optimizing landscape r...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13217
更新日期:2020-11-01 00:00:00
abstract::QST , a measure of quantitative genetic differentiation among populations, is an index that can suggest local adaptation if QST for a trait is sufficiently larger than the mean FST of neutral genetic markers. A previous method by Whitlock and Guillaume derived a simulation resampling approach to statistically test for...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12303
更新日期:2015-03-01 00:00:00
abstract::Type specimens have high scientific importance because they provide the only certain connection between the application of a Linnean name and a physical specimen. Many other individuals may have been identified as a particular species, but their linkage to the taxon concept is inferential. Because type specimens are o...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12474
更新日期:2016-03-01 00:00:00