Biology subjects

Franz, O.

Publications and source records attributed to Franz, O..

3 recordsLinked to original sources

bioRxiv2023

NIRis: A low-cost, versatile imaging system for NIR fluorescence detection of phototrophic cell colonies used in science and education

A variety of costly research-grade imaging devices are available for the detection of spectroscopic features. Here we present an affordable, open-source and versatile device, suitable for a range of applications. We provide the files to print the imaging chamber with commonly available 3D printers and instructions to assemble it with easily available hardware. The imager is suitable for rapid sample screening in research, as well as for educational purposes. We provide details and results for an already proven set-up which suits the needs of a research group and students interested in UV-induced near-infrared fluorescence detection of microbial colonies grown on Petri dishes. The fluorescence signal confirms the presence of bacteriochlorophyll a in aerobic anoxygenic phototrophic bacteria (AAPB). The imager allows for the rapid detection and subsequent isolation of AAPB colonies on Petri dishes with diverse environmental samples. To this date, 15 devices have been build and more than 7000 Petri dishes have been analyzed for AAPB, leading to over 1000 new AAPB isolates. Parts can be modified depending on needs and budget. The latest version with automated switches and double band pass filters costs around 350{euro} in materials and resolves bacterial colonies with diameters of 0.5 mm and larger. The low cost and modular build allow for the integration in high school classes to educate students on light properties, fluorescence and microbiology. Computer-aided design of 3D-printed parts and programming of the employed Raspberry Pi computer could be incorporated in computer sciences classes. Students have been also inspired to do agar art with microbes. The device is currently used in seven different high schools in Finland. Additionally, a science education network of Finnish universities has incorporated it in its program for high school students. Video guides have been produced to facilitate easy operation and accessibility of the device. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=62 SRC="FIGDIR/small/543100v2_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@6dfcb7org.highwire.dtl.DTLVardef@ea7fbcorg.highwire.dtl.DTLVardef@1681e78org.highwire.dtl.DTLVardef@a88d51_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

Aerobic anoxygenic phototrophic bacteria are ubiquitous in phyllo- and endosphere microbiomes of boreal and subarctic plants

In addition to oxygenic photosynthetic systems, solar radiation is utilized for energy by diverse anoxygenic photosynthetic systems. Aerobic anoxygenic phototrophic bacteria (AAPB) perform photosynthesis without producing oxygen but still live in aerobic conditions. Typically they have been reported from aquatic ecosystems, but they can also be found from polar and desert soil ecosystems and primary succession communities like soil crusts. Recently, AAPB have been discovered in the metagenomic data of several plant phyllospheres. By utilizing citizen science, we screened plant foliar samples from eleven different locations in Finland for AAPB by near infrared fluorescence imaging of culturable phyllosphere and endosphere bacteria. Near infrared fluorescence reports the presence of AAPB which contain Bacteriochlorophyll a molecules, embedded in Light Harvesting 1 - Reaction Center complex. We found that AAPB were ubiquotous in phyllosphere communities of diverse plant species in all sampling locations. They were also consistently present in the endosphere of plant species with perennial leaves. Most of the AAPB isolated represent alphaproteobacterial genera Sphingomonas and Methylobacterium, but several isolates from genus Lichenihabitans as well as putative novel alphaproteobacterial taxa were also identified. Methylobacterial isolates were mostly detected in the phyllosphere with weak host specificity, while Sphingomonas AAPB were detected also in the endosphere of several plant species, with clear host specific taxa. We studied also the fluorescence spectral properties of several AAPBs. All the observed spectra resemble typical fluorescence spectral properties of Light Harvesting complex 1. Still, slight variation among each spectra could be obtained, revealing some physical difference among the complexes. Our results demonstrate for the first time, that AAPB are common in cold climate plant endophytic as well as epiphytic microbiomes and they build up substantial amounts of Bacteriochlorophyll a containing Light Harvesting complexes. Their putative role in plant adaptation to strong seasonality in light and temperature or tolerance of abiotic stressors remains to be investigated in future studies.

microbiology↗

bioRxiv2022

Single-cell resolution genetic association analysis of heterogeneous bacterial communities by utilizing droplet digital PCR

Microbial communities often respond to environmental challenges, such as the presence of antibiotics, as a whole. Dissecting these community-level effects into separate acting entities requires the identification of organisms that carry functional genes for the observed feature. However, unculturable microbes are abundant in various environments, hence making the identification challenging. Moreover, while at present the development and application of single-cell tools for eukaryotic cells are enhancing, the comparable methodologies applicable for prokaryotic cells are still scarce and have not gained broad and solid status as tools for investigating microbial populations. Here, we present a cultivation-free technique that can be utilized to link functional genes with the carrying bacterial species at single-cell resolution. The developed protocol is relatively simple to use, utilizes commercially available droplet microfluidics devices, does not require toxic reagents, and eliminates invalid signals emerging from extracellular DNA. We validate the methodology by studying the conjugative transfer of antibiotic resistance plasmids in an environment challenged by antibiotics. Furthermore, the method can be customized for any given genetic trait to accurately identify its hosting subpopulation from a heterogeneous and potentially uncultivable bacterial community. ImportanceBacterial systems usually contain numerous different species that may harbor highly similar or identical genes that confer same phenotypic qualities for the community. To decipher the functions of these systems, we report the development of a novel methodology that enables investigating microbial communities at single-cell level. This user-friendly method utilizes droplet digital PCR (ddPCR) to find and identify carriers of specific genes potentially from various microbial sample types. By pinpointing gene carriers, such as those responsible for antibiotic resistance, this method can provide insights to the behavior of microbial communities and gene transfer therein. By strategically combining the use of common methods (ddPCR and amplicon sequencing), the workflow is highly accessible. Thus, it allows also the researchers without a background in single-cell techniques or access to special equipment to adopt the method for producing single-cell data to serve their own research, enabling new research avenues in microbial genetics and ecology.

microbiology↗