Applied and Environmental Science
Research Article | Applied and Environmental ScienceMarine RNA Virus Quasispecies Are Distributed throughout the OceansVery little is known about aquatic RNA virus populations and genome evolution. This is the first study that analyzes marine environmental RNA viral assemblages in an evolutionary and broad geographical context. This study contributes the largest marine RNA virus metagenomic data set to date, substantially increasing the sequencing space for RNA viruses and also providing a baseline for comparisons of marine RNA virus diversity. The new...
Research Article | Applied and Environmental ScienceInterspecies Social Spreading: Interaction between Two Sessile Soil Bacteria Leads to Emergence of Surface MotilityThe wealth of studies on microbial communities has revealed the complexity and dynamics of the composition of communities in many ecological settings. Fewer studies probe the functional interactions of the community members. Function of the community as a whole may not be fully revealed by characterizing the individuals. In our two-species model community, we find an emergent trait resulting from the interaction of the soil bacteria...
Research Article | Applied and Environmental ScienceWood-Derived Dietary Fibers Promote Beneficial Human Gut MicrobiotaThe architecture of the gut bacterial ecosystem has a profound effect on the physiology and well-being of the host. Modulation of the gut microbiota and the intestinal microenvironment via administration of prebiotics represents a valuable strategy to promote host health. This work provides insights into the ability of two novel wood-derived preparations, AcGGM and AcAGX, to influence human gut microbiota composition and activity. These...
Opinion/Hypothesis | Applied and Environmental ScienceExtracellular Electron Transfer May Be an Overlooked Contribution to Pelagic Respiration in Humic-Rich Freshwater LakesHumic lakes and ponds receive large amounts of terrestrial carbon and are important components of the global carbon cycle, yet how their redox cycling influences the carbon budget is not fully understood. Here we compared metagenomes obtained from a humic bog and a clear-water eutrophic lake and found a much larger number of genes that might be involved in extracellular electron transfer (EET) for iron redox reactions and humic...
Research Article | Applied and Environmental ScienceDecreased Snow Cover Stimulates Under-Ice Primary Producers but Impairs Methanotrophic CapacitySmall lakes are an important source of greenhouse gases in the boreal zone. These lakes are severely impacted by the winter season, when ice and snow cover obstruct gas exchange between the lake and the atmosphere and diminish light availability in the water column. Currently, climate change is resulting in reduced spring snow cover. A short-term removal of the snow from the ice stimulated algal primary producers and subsequently...
Research Article | Applied and Environmental ScienceImage-Processing Software for High-Throughput Quantification of Colony LuminescenceLuminescent markers are widely used as reporters for various biologically interesting traits. In colony luminescence assays, the levels of luminescence around each colony can be used to compare the levels of traits of interest for different strains, treatments, etc., using quantitative measurements of the luminescence. However, automatic methods of obtaining this data are underdeveloped, making this a laborious manual process,...
Observation | Applied and Environmental ScienceGenetic Evidence for Two Carbon Fixation Pathways (the Calvin-Benson-Bassham Cycle and the Reverse Tricarboxylic Acid Cycle) in Symbiotic and Free-Living BacteriaPrimary production on Earth is dependent on autotrophic carbon fixation, which leads to the incorporation of carbon dioxide into biomass. Multiple metabolic pathways have been described for autotrophic carbon fixation, but most autotrophic organisms were assumed to have the genes for only one of these pathways. Our finding of a cultivable bacterium with two carbon fixation pathways in its genome, the rTCA and the CBB cycle, opens the...
Research Article | Applied and Environmental ScienceConjugative Selectivity of Plasmids Is Affected by Coexisting Recipient CandidatesMost previous studies on plasmid conjugal transfer employed experimental setups with two strains: one as a donor and the other as a recipient. However, the results obtained sometimes failed to agree with observations obtained under natural environmental conditions or in a model microcosm using natural soil and water samples. Therefore, we consider that there is a “gap” in our understanding of plasmid behavior in the context of bacterial...
Research Article | Applied and Environmental ScienceRegulation of Yeast-to-Hyphae Transition in Yarrowia lipolyticaMany yeasts undergo a morphological transition from yeast-to-hyphal growth in response to environmental conditions. We used forward and reverse genetic techniques to identify genes regulating this transition in Yarrowia lipolytica. We confirmed that the transcription factor Ylmsn2 is required for the transition to hyphal growth and found that signaling by the...
Research Article | Applied and Environmental ScienceModifying Saccharomyces cerevisiae Adhesion Properties Regulates Yeast Ecosystem DynamicsThe impact of direct (physical) versus indirect (metabolic) interactions between different yeast species has attracted significant research interest in recent years. This is due to the growing interest in the use of multispecies consortia in bioprocesses of industrial relevance and the relevance of interspecies interactions in establishing stable synthetic ecosystems. Compartment bioreactors have traditionally been used in this regard...