Peer-reviewed Articles - Biology

49 downloads
256 views

Background Bacteria, archaea, viruses and fungi live in various plant compartments including leaves and roots. These plant-associated microbial communities have many effects on host fitness and function. Global climate change is impacting plant species distributions,...

["Ecology","Genomics","Microbiology","Plant Science","Climate Change Biology"]
doi:10.7717/peerj.5293
111 downloads
849 views

High-depth sequencing of universal marker genes such as the 16S rRNA gene is a common strategy to profile microbial communities. Traditionally, sequence reads are clustered into operational taxonomic units (OTUs) at a defined identity threshold to avoid sequencing...

["Ecology","Genomics","Microbiology","Mycology","Data Science"]
doi:10.7717/peerj.5364
72 downloads
267 views

Microbes are ubiquitous and often occur in functionally and taxonomically complex communities. Unveiling these community dynamics is one of the main challenges of microbial research. Combining a robust, cost effective and widely used method such as Terminal Restriction...

["Ecology","Microbiology","Molecular Biology"]
doi:10.7717/peerj.5289
61 downloads
355 views

The microbial diversity and function of terrestrial lichens have been well studied, but knowledge about the non-photosynthetic bacteria associated with marine lichens is still scarce. 16S rRNA gene Illumina sequencing was used to assess the culture-independent...

["Biodiversity","Ecology","Microbiology"]
doi:10.7717/peerj.5208
81 downloads
550 views

Black Band Disease (BBD) is a widely distributed and destructive coral disease that has been studied on a global scale, but baseline data on coral diseases is missing from many areas of the Arabian Seas. Here we report on the broad distribution and prevalence of...

["Biogeography","Ecology","Marine Biology","Microbiology"]
doi:10.7717/peerj.5169
63 downloads
632 views

Next-generation sequencing has provided powerful tools to conduct microbial ecology studies. Analysis of community composition relies on annotated databases of curated sequences to provide taxonomic assignments; however, these databases occasionally have errors...

["Bioinformatics","Ecology","Marine Biology","Microbiology","Taxonomy"]
doi:10.7717/peerj.5248
144 downloads
424 views

Natural products from the unique environments of sea water and oceans represent a largely unfamiliar source for isolation of new microbes, which are potent producers of secondary bioactive metabolites. These unique life-forms from the marine ecosphere have served...

["Ecology","Marine Biology","Microbiology","Ecotoxicology","Green Chemistry"]
doi:10.7717/peerj.5049
88 downloads
574 views

Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present in a reduced number of housekeeping genes (typically seven) along the genome. This methodology assigns arbitrary integer...

["Bioinformatics","Ecology","Genomics","Microbiology","Population Biology"]
doi:10.7717/peerj.5098
82 downloads
533 views

Soil microbial communities’ assembly is strongly tied to changes in temperature and moisture. Although microbial functional redundancy seems to overcome taxonomical composition changes, the sensitivity and resilience of soil microbial communities from subtropical...

["Agricultural Science","Biodiversity","Bioinformatics","Ecology","Microbiology"]
doi:10.7717/peerj.4991
125 downloads
818 views

Sponge-associated prokaryotic diversity has been studied from a wide range of marine environments across the globe. However, for certain regions, e.g., Vietnam, Thailand, Cambodia, and Singapore, an overview of the sponge-associated prokaryotic communities is still...

["Ecology","Marine Biology","Microbiology"]
doi:10.7717/peerj.4970
79 downloads
858 views

Sponges belonging to genus Mycale are common and widely distributed across the oceans and represent a significant component of benthic communities in term of their biomass, which in many species is largely composed by bacteria. However, the microbial communities...

["Ecology","Marine Biology","Microbiology"]
doi:10.7717/peerj.4935
144 downloads
709 views

Fungi play a critical role in a range of ecosystems; however, their interactions and functions in marine hosts, and particular sponges, is poorly understood. Here we assess the fungal community composition of three co-occurring sponges (Cymbastela concentrica,...

["Ecology","Marine Biology","Microbiology","Mycology"]
doi:10.7717/peerj.4965
2 citations
146 downloads
1,403 views

High-throughput amplicon sequencing (HTAS) of conserved DNA regions is a powerful technique to characterize microbial communities. Recently, spike-in mock communities have been used to measure accuracy of sequencing platforms and data analysis pipelines. To assess...

["Biodiversity","Bioinformatics","Ecology","Microbiology","Mycology"]
doi:10.7717/peerj.4925
96 downloads
366 views

Insect gut microbiota contribute significantly to host nutritional ecology. Disrupting insect gut microbial assemblages impacts nutrient provisioning functions, and can potentially affect host standard metabolic rate (SMR), a measure of host energy balance. In...

["Ecology","Entomology","Microbiology"]
doi:10.7717/peerj.4717
120 downloads
891 views

The beetle genus Cephaloleia has evolved in association with tropical ginger plants and for many species their specific host plant associations are known. Here we show that the core microbiome of six closely related Costa Rican Cephaloleia species comprises only...

["Biodiversity","Ecology","Entomology","Microbiology"]
doi:10.7717/peerj.4793

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