Preprints (not yet peer-reviewed)

The phylum Actinobacteria constitutes one of the largest and anciently divergent phyla within the Bacteria domain. Actinobacterial diversity has been thoroughly researched in various environments due to its unique biotechnological potential. Such studies have focused...

["Biodiversity","Biogeography","Ecology","Microbiology"]
doi:10.7287/peerj.preprints.2893v1
33 downloads
175 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
15 downloads
55 views

Denitrification is an important part of the nitrogen cycle and the key step to removal of nitrogen in surface-flow wetlands. Denitrifying bacteria also function in denitrification. In this study, we explored space-time analysis with high-throughput sequencing to...

["Ecology","Environmental Sciences","Microbiology"]
doi:10.7287/peerj.preprints.2848v1
39 downloads
223 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
43 downloads
122 views

Aerobic anoxygenic phototrophic bacteria (AAPB) containing bacteriochlorophyll a (BChl a) are photoheterotrophic prokaryotes that are a widely distributed functional bacterial group due to their obligately aerobic and facultative photoheterotrophic abilities. Here,...

["Ecology","Environmental Sciences","Genomics","Marine Biology","Microbiology"]
doi:10.7287/peerj.preprints.2820v1
115 downloads
459 views

Numerous investigations of bacterial communities using sequence analysis of environmental DNA have revealed extensive diversity of microbial taxa in an array of different environmental habitats. Community analysis based solely on DNA, however, does not reveal whether...

["Computational Biology","Ecology","Microbiology"]
doi:10.7287/peerj.preprints.2051v2
54 downloads
168 views

The human microbiome has demonstrated importance for health and functioning in living individuals. However the fate of the microbiome after death is poorly understood. In addition to a better understanding of microbe-mediated decomposition processes, postmortem...

["Ecology","Microbiology"]
doi:10.7287/peerj.preprints.2777v1
18 downloads
148 views

Ecosystem functions of rivers have been greatly impaired due to the negative effects of human actions on river structures in different regions of the Earth during the last decades. It is an urgent task to understand the complete structures and ecosystem functions...

["Ecology","Ecosystem Science","Environmental Sciences","Microbiology"]
doi:10.7287/peerj.preprints.2712v2
100 downloads
304 views

Residence time (τ) is the average amount of time that particles spend in an ecosystem. Often estimated from the ratio of volume to flow rate, τ equates the physical environment with dynamics of growth. Here, we propose that τ is key to understanding relationships...

["Biodiversity","Ecology","Ecosystem Science","Microbiology"]
doi:10.7287/peerj.preprints.2727v1
27 downloads
273 views

Marker gene sequencing of microbial communities has generated big datasets of microbial relative abundances varying across environmental conditions, sample sites and treatments. These data often come with putative phylogenies, providing unique opportunities to...

["Computational Biology","Ecology","Mathematical Biology","Microbiology","Statistics"]
doi:10.7287/peerj.preprints.2685v1
70 downloads
346 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
108 downloads
896 views

Press disturbances are stressors that are extended or ongoing relative to the generation times of community members, and, due to their longevity, have the potential to alter communities beyond the possibility of recovery. They also provide key opportunities to...

["Biodiversity","Ecology","Environmental Sciences","Microbiology","Soil Science"]
doi:10.7287/peerj.preprints.2446v2
43 downloads
201 views

Cascaded performance and compartments of constructed wetlands may harbor the internal eco-environmental gradients and further differentiate the niche and community structure of ammonia-oxidizing archaea (AOA). Here, we used quantitative PCR and 454 pyrosequencing...

["Biodiversity","Ecology","Microbiology"]
doi:10.7287/peerj.preprints.2629v1
124 downloads
358 views

It is generally accepted that diverse, poorly characterized microorganisms reside deep within Earth’s crust. One such lineage of deep subsurface-dwelling Bacteria is an uncultivated member of the Firmicutes phylum that can dominate molecular surveys from both marine...

["Ecology","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.2592v1
586 downloads
1,689 views

Microorganisms are the most abundant, diverse, and functionally important organisms on Earth. Over the past decade, microbial ecologists have produced the largest ever community datasets. However, these data are rarely used to uncover law-like patterns of commonness...

["Biodiversity","Ecology","Microbiology"]
doi:10.7287/peerj.preprints.1450v4
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