Preprints (not yet peer-reviewed)

34 downloads
184 views

Metabarcoding and metagenomic approaches are becoming routine techniques in biodiversity assessment and ecological studies. The assignment of taxonomic information to sequences is challenging, as many reference libraries are lacking information on certain taxonomic...

["Biodiversity","Bioinformatics","Ecology","Molecular Biology","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.3133v1
43 downloads
259 views

Background. Viral metagenomics (viromics) is increasingly used to obtain uncultivated viral genomes, evaluate community diversity, and assess ecological hypotheses. While viromic experimental methods are relatively mature and widely accepted by the research community,...

["Bioinformatics","Ecology","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.3053v1
119 downloads
388 views

Symbiotic microalgae (Symbiodinium spp.) strongly influence the performance and stress-tolerance of their coral hosts, making the analysis of Symbiodinium communities in corals (and metacommunities on reefs) advantageous for many aspects of coral reef research....

["Bioinformatics","Ecology","Marine Biology"]
doi:10.7287/peerj.preprints.2925v1
999 downloads
2,711 views

A central challenge in the present era of biodiversity loss is to assess and manage human impacts on freshwater ecosystems. Macroinvertebrates are an important group for bioassessment as many taxa show specific responses to environmental conditions. However, generating...

["Biodiversity","Bioinformatics","Ecology","Genetics","Molecular Biology"]
doi:10.7287/peerj.preprints.2044v5
105 downloads
351 views

Taxonomic markers such as the 16S ribosomal RNA gene are widely used in microbial community analysis. A common first step in marker-gene analysis is grouping genes into clusters to reduce data sets to a more manageable size and potentially mitigate the effects...

["Bioinformatics","Ecology","Microbiology","Computational Science"]
doi:10.7287/peerj.preprints.2879v1
103 downloads
431 views

Metatranscriptomics and metaproteomics make it possible to measure gene expression in microbial communities. So far these approaches were mostly used to get a general overview of the dominant metabolism and physiologies of community members. Recently, environmental...

["Bioinformatics","Ecology","Environmental Sciences","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.2846v1
146 downloads
536 views

Cyanobacteria are major contributors to global biogeochemical cycles. The genetic diversity among Cyanobacteria enables them to thrive across many habitats. However, the taxonomy of Cyanobacteria remains unstable because of an inadequate taxonomic classification...

["Bioinformatics","Ecology","Genomics","Microbiology","Taxonomy"]
doi:10.7287/peerj.preprints.2676v1
192 downloads
554 views

To answer many of the major questions in comparative botany, ecology, and global change biology it is necessary to extrapolate across enormous geographic, temporal and taxonomic scales. Yet much ecological knowledge is still based on observations conducted within...

["Biodiversity","Biogeography","Bioinformatics","Ecology","Computational Science"]
doi:10.7287/peerj.preprints.2615v2
1,860 downloads
853 views

The diversity of complex microbial communities can be rapidly assessed by high-throughput DNA sequencing of marker gene (e.g., 16S) PCR amplicon pools, often yielding many thousands of DNA sequences per sample. However, analysis of such community amplicon sequencing...

["Biodiversity","Bioinformatics","Ecology","Microbiology"]
doi:10.7287/peerj.preprints.2196v3
110 downloads
513 views

Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host’s health and to provide potential defenses against invading pathogens. However, we have little to no understanding of the external bacterial microbiome on bats,...

["Biogeography","Bioinformatics","Ecology","Microbiology"]
doi:10.7287/peerj.preprints.2493v1
287 downloads
545 views

To microbiologists, the term macroecology may conjure iconic images of wildebeests grazing in African savannahs or hummingbirds pollinating flowers in a tropical rain forest. Contrary to what the name implies, macroecology is not the ecological study of macroscopic...

["Biodiversity","Biogeography","Bioinformatics","Ecology","Microbiology"]
doi:10.7287/peerj.preprints.2478v1
334 downloads
509 views

1) DNA metabarcoding is a powerful tool to assess biodiversity by amplifying and sequencing a standardized gene marker region. Its success is often limited due to variable binding sites that introduce amplification biases. Thus the development of optimized primers...

["Bioinformatics","Ecology","Genetics","Molecular Biology","Zoology"]
doi:10.7287/peerj.preprints.2352v1
164 downloads
589 views

Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS) studies are presently generating huge volumes of data to address this biogeographical...

["Bioinformatics","Ecology","Environmental Sciences","Microbiology"]
doi:10.7287/peerj.preprints.2317v1
140 downloads
958 views

Solar salterns are excellent model ecosystems for studying virus-microbial interactions because of their low microbial diversity, environmental stability, and high viral density. By using the power of CRISPR spacers to link viruses to their prokaryotic hosts, we...

["Bioinformatics","Computational Biology","Ecology","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.2106v2
138 downloads
464 views

A variety of methods are available to collapse 16S rRNA gene sequencing reads to the operational taxonomic units (OTUs) used in microbiome analyses. A number of studies have aimed to compare the quality of the resulting OTUs. However, in the absence of a standard...

["Bioinformatics","Ecology","Microbiology"]
doi:10.7287/peerj.preprints.2115v1
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