Biology subjects

Terry, N.

Publications and source records attributed to Terry, N..

4 recordsLinked to original sources

bioRxiv2025

Accessing rare bacterial biosphere of soil through culturing: a comparative study of culture media effectiveness integrated with metataxonomics

Soil harbors a vast bacterial diversity, including a "rare biosphere" of low-abundance taxa increasingly recognized as crucial for ecosystem functioning. Traditional plate-based culturing can facilitate access to this fraction. Here, we investigated how culture medium type influences the recovery of rare soil bacteria. To do this, culture-independent bacterial diversity of agricultural, forest, and contaminated soils was compared with culture-dependent diversity on four media (TSA (tryptic soy agar), SEM (soil extract medium), R2A (Reasoners 2A), and 20-fold diluted R2A) using a high-throughput approach in which all colonies were collected and analyzed via 16S rRNA gene metabarcoding (metataxonomics). Across all media and soils, ~30% of the culture-independent taxa were recovered through culturing, of which ~40% were members of the rare community. Culturability of bacterial communities declined across soil types in the order: contaminated > agricultural > forest, but the community isolated from forest soil contained a higher proportion of rare taxa. SEM, characterized by its low nutrient content and chemical composition resembling that of soil, proved to be the most effective, yielding higher colony-forming unit counts, greater overall and rare richness, and recovering a more taxonomically diverse rare community. The rare community retrieved by SEM was dominated by non-spore-forming taxa, in contrast to the other media, including diluted R2A. Culturing revealed a unique fraction of culturable taxa, representing ~17% of the culture-independent community on average, likely members of the rare biosphere that escape detection in metabarcoding analyses. SEM was also the medium that best captured this fraction. Our study demonstrates that low-nutrient, soil-like media such as SEM are powerful tools for accessing and characterizing the rare soil biosphere, complementing metabarcoding and providing isolates to explore the ecological and functional significance of rare taxa.

microbiology↗

bioRxiv2022

Coupling of metataxonomics and culturing improves description of bacterial communities from a multi-contaminated waste sediment and identifies a novel Rhizorhapis sp. with metal resistance potential

Long-term contaminated environments have been recognized as potential hotspots for bacterial discovery in taxonomic and functional terms for bioremediation purposes. Here, bacterial diversity in waste sediment collected from a former industrial dumpsite and contaminated with petroleum hydrocarbon and heavy metals was investigated through the parallel application of culture-independent (16S rRNA gene amplicon sequencing) and -dependent (plate culturing followed by colony picking and identification of isolates by 16S rRNA gene Sanger sequencing) approaches. The bacterial diversities retrieved by both approaches greatly differed. Bacteroidetes and Proteobacteria were dominant in the culture-independent community, while Firmicutes and Actinobacteria were the main culturable groups. Only 2.7% of OTUs (operational taxonomic units) in the culture-independent dataset were cultured. Most of the culturable OTUs were absent or in very low abundances in the culture-independent dataset, revealing that culturing is a useful tool to study the rare bacterial biosphere. One culturable OTUs (comprising only the isolate SPR117) was identified as a potential new species in the genus Rhizorhapis (class Alphaproteobacteria) and was selected for further characterization. Phytopathogenicity tests showed that Rhizorhapis sp. strain SPR117 (ATCC TSD-228) is not pathogenic for lettuce, despite the only described species within this genus, Rhizorhapis suberifaciens, is causal agent of the lettuce corky root disease. The genome of the strain SPR117 was sequenced, assembled in 256 contigs, with a length of 4,419,522 bp and a GC content of 59.9%), and its further annotation revealed the presence of genes related to the resistance to arsenic, copper, iron, and mercury, among other metals. Therefore, the coupling of metataxonomics and culturing is a useful tool to obtain not only an improved description of bacterial communities in contaminated environments, but also to isolate microorganisms with bioremediation potential.

microbiology↗

bioRxiv2019

Conjugation-dependent \"gene drives\" harness indigenous bacteria for bioremediation

Engineering bacteria to clean-up oil spills is rapidly advancing but faces regulatory hurdles and environmental concerns. Here, we develop a new technology to harness indigenous soil microbial communities for bioremediation by flooding local populations with catabolic genes for petroleum hydrocarbon degradation. Overexpressing three enzymes (almA, xylE, p450cam) in E.coli led to degradation rates of 60-99% of target hydrocarbon substrates. Mating experiments, fluorescence microscopy and TEM revealed indigenous bacteria could obtain these vectors from E.coli through several mechanisms of horizontal gene transfer (HGT), including conjugation and cytoplasmic exchange through nanotubes. Inoculating petroleum-polluted sediments with E.coli carrying the vector pSF-OXB15-p450camfusion showed that the E.coli die after five days but a variety of bacteria received and carried the vector for over 60 days after inoculation. Within 60 days, the total petroleum hydrocarbon content of the polluted soil was reduced by 46%. Pilot experiments show that vectors only persist in indigenous populations when "useful," disappearing when this carbon source is removed. This approach to remediation could prime indigenous bacteria for degrading pollutants while providing minimal ecosystem disturbance.

synthetic biology↗

bioRxiv2018

A high-throughput fluorescence-based assay for the detection of petroleum hydrocarbon degrading bacteria

Over the past 100 years, oil spills and long-term waste deposition from oil refineries have significantly polluted the environment. These contaminants have widespread negative effects on human health and ecosystem functioning. Natural attenuation of long chain and polyaromatic hydrocarbons is slow and often incomplete. Bioaugmentation of polluted soils with indigenous bacteria that naturally consume petroleum hydrocarbons could speed up this process. However, the characterization of bacterial crude oil degradation efficiency--which often relies upon expensive, highly specialized gas-chromatography mass spectrometry analyses--can present a substantial bottleneck in developing and implementing these bioremediation strategies. Here, we develop a low-cost, rapid, high-throughput fluorescence-based assay for identifying wild-type bacteria that degrade crude oil using the dye Nile Red. We show that Nile Red fluoresces when in contact with crude oil and developed a robust linear model to calculate crude oil content in liquid cell cultures based on fluorescence intensity (FI). To test whether this assay could identify bacteria with enhanced metabolic capacities to break down crude oil, we screened bacteria isolated from a former Shell Oil refinery in Bay Point, CA and identified one strain (Cupriavidus sp. OPK) with superior crude oil depletion efficiencies (up to 83%) in only three days. We further illustrate that this assay can be combined with fluorescence microscopy to study how bacteria interact with crude oil and the strategies they use to degrade this complex substance. We show for the first time that bacteria use three key strategies for degrading crude oil: biofilm formation, direct adherence to oil droplets, and vesicle encapsulation of oil. We propose that the quantitative and qualitative data from this assay can be used to develop new bioremediation strategies based on bioaugmentation and/or biomimetic materials that imitate the natural ability of bacteria to degrade crude oil.

microbiology↗