Biology subjects

Voriskova, J.

Publications and source records attributed to Voriskova, J..

4 recordsLinked to original sources

bioRxiv2024

Climate History and Metabolic Trade-offs shape the Bacterial Response to Drought

Soil drying challenges microbial viability and survival, with bacteria employing various mechanisms to respond to shifts in osmolarity, including dormancy or metabolic upregulation of osmoprotectants. However, the extent to which these responses are shaped by an organisms phylogeny or the climate history of a given environment is poorly understood. This study examines the responses of phylogenetically similar bacteria from semi-arid and humid tropical forest soils to osmotic and matric stress using synchrotron radiation-based Fourier Transform Infrared spectromicroscopy. This non-destructive approach depicts the biochemical phenotype for whole cells under control and stress conditions. We observed that, under osmotic stress, bacteria upregulated cell-signaling pathways, rapidly turned over lipid-storage compounds, and increased osmolyte production. In contrast, matric stress induced a more muted response, typically elevating the production of carbohydrate stress compounds, such as glycine betaine and trehalose. While phylogenetically similar bacteria showed comparable biochemistry under control conditions, climate history played an important role in regulating responses to stress, whereby a stronger metabolic response was observed from semi-arid relative to tropical forest isolates. We conclude that bacterial stress response to drought can be more diverse than previously observed, and regulated by both phylogeny and climate history.

microbiology↗

bioRxiv2020

Culturing of "Unculturable" Subsurface Microbes: Natural Organic Carbon Source Fuels the Growth of Diverse and Distinct Bacteria from Groundwater

The recovery and cultivation of diverse field-related microorganisms from the terrestrial subsurface environment remains a challenge despite recent advances in modern molecular technology. Here we applied natural organic carbon (C), i.e., sediment-derived natural organic matter (NOM) and bacterial cell lysate, to groundwater microbial communities for a 30-day enrichment incubation, followed by conventional direct-plating for isolation. The groundwater was collected from a background well at the Oak Ridge Reservation Field Research Center, Tennessee. As a comparison, we also included enrichments amended with simple organic C sources, including glucose, acetate, benzoate, oleic acid, cellulose, and mixed vitamins. Our results demonstrate that complex natural organic C sources are more effective in enriching diverse bacterial species from groundwater than simple organic C sources. Microcosms amended with simple organic C (glucose, acetate, benzoate, or oleic acid) show significantly lower biodiversity than unamended control and are dominated by only few phyla such as Proteobacteria and Bacteroidetes. In contrast, microcosms amended with complex natural organic C (sediment NOM or bacterial cell lysate) display significantly higher biodiversity, and enrich distinct species from the phyla that are poorly represented in published culture collections (e.g., Verrucomicrobia, Planctomycetes, and Armatimonadetes). Our subsequent isolation efforts from natural organic C-amended enrichments led to 222 purified bacterial isolates representing 5 phyla, 16 orders, and 54 distinct species including candidate novel, rarely cultivated, and undescribed organisms. ImportanceInnovative strategies for recovering bacterial strains representing the true diversity of microbial communities in the terrestrial subsurface would significantly advance the understanding of ecologically critical taxa residing in these ecosystems. In this study, we demonstrate that complex natural organic C that mimic the naturally available resources for microbes encourages the growth of diverse bacteria much more robustly than traditional simplistic organic C sources. Results from this study will substantially advance and improve the design of strategies to effectively cultivate and isolate diverse and novel subsurface microorganisms in the laboratory. Obtaining axenic cultures of the once-unculturable microorganisms will greatly enhance our understanding of microbial physiology, function, and roles in different biogeochemical niches in terrestrial subsurface ecosystems.

microbiology↗

bioRxiv2020

GlobalFungi: Global database of fungal records from high-throughput-sequencing metabarcoding studies

Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultural and wild plants and pathogenicity. The high importance of fungi in the ecosystem processes contrasts with the incompleteness of understanding of the patterns of fungal biogeography and the environmental factors that drive it. To close this gap of knowledge, we have here collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at http://globalfungi.com. The GlobalFungi database contains over 650 million observations of fungal sequences across >20 000 samples with geographical locations and additional metadata contained in 207 original studies with millions of unique sequence variants of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. As it is, the study represents the most comprehensive atlas of fungal distribution on the global scale open to further additions.

ecology↗

bioRxiv2019

Capturing the Diversity of Subsurface Microbiota - Choice of Carbon Source for Microcosm Enrichment and Isolation of Groundwater Bacteria

Improved and innovative enrichment/isolation techniques that yield to relevant isolates representing the true diversity of environmental microbial communities would significantly advance exploring the physiology of ecologically important taxa in ecosystems. Traditionally, either simple organic carbon (C) or yeast extract is used as C source in culture medium for microbial enrichment/isolation in laboratory. In natural environment, however, microbial population and evolution are greatly influenced by the property and composition of natural organic C. In this study, 8 types of organic C sources were fed to intrinsic groundwater microbes collected at Oak Ridge Reservation Field Research Center (ORR-FRC) background site for a 30-day incubation period to investigate the response of indigenous bacterial communities to different C sources. The tested C sources included simple organic C (glucose, acetate, benzoate, oleic acid, and cellulose) that are either traditionally used as C source in bacterial culture medium or present in natural environments; naturally occurring undefined complex C (bacterial cell lysate and sediment-derived natural organic matter (NOM)); as well as vitamin mixture which is a commonly used ingredient in culture medium. Our results clearly indicate that natural complex C substrates served better in enriching diverse bacteria compared to other C sources. Microcosms amended with small organic C (glucose, acetate, benzoate, or oleic acid) showed significantly lower biodiversity than control groups, dominated by only a few phyla of bacteria such as Proteobacteria and Bacteroidetes which are commonly isolated and already have diverse representative isolates, while those amended with natural complex C (cell lysate or NOM) displayed significantly higher biodiversity than control groups, in which three phyla (Verrucomicrobia, Planctomycetes, and Armatimonadetes) that are poorly represented in published culture collections were abundantly enriched. Further isolation of pure bacterial strains from complex C-amended enrichments led to 51 species representing 4 phyla, 13 orders. Furthermore, 5 isolates with low similarities to published strains were considered to be novel. Results from this study will aid in the design of better cultivation and isolation strategy for maximize the diversity of organisms recovered from subsurface environment.

microbiology↗