The potential benefits from the study of the unique abilities of Bacteria to everyday Human life is ever more obvious. Bacteria are used industrially in food preparation, drug production, waste treatment and many other roles. Advances in biotechnology techniques have facilitated the use of known Bacterial species and their enzymes, proteins and pathways. For example, it is now possible, and indeed not very difficult, to identify genes of interest in a bacterial species, clip those genes out of that species and insert them into another work horse species of Bacteria to allow the products of those genes to be produced industrially. Ironically, as our ability to harness the power of Bacteria becomes ever more sophisticated, one of the key challenges is still finding the useful Bacteria in the first place. In a world with as many as a trillion Bacterial species, how does one speed the discovery of Bacterial species with a particular use or even simply strains of a particular bacterial taxon with sequences of interest? One approach is to engage citizen scientists. In as much as the first step in the discovery of novel, useful microbes is often collection from nature, collections made by the public have the potential to speed up this key and often rate-limiting first step. What is more, in a rapidly interconnected digital era, the potential for truly global projects that rely on hundreds, thousands, or even hundreds of thousands of individuals is ever greater.
In a paper published in the journal PeerJ on 14 April 2020, Noah Riley of the Department of Biological Sciences at North Carolina State University, Carlos Goller, also of the Department of Biological Sciences and of the Biotechnology Program at North Carolina State University, Zakiya Leggett of the Department of Forestry and Environmental Resources at North Carolina State University, Danica Lewis and Karen Ciccone of North Carolina State University Libraries, and Robert Dunn of the Department of Applied Ecology at North Carolina State University, the Natural History Museum of Denmark at the University of Copenhagen, and the German Centre for Integrative Biodiversity Research, describe the results of a study using a citizen science approach to to detect new species of the gold-precipitating Bacterium Delftia, on a university campus.
Citizen scientists contribute data to many publicly-accessible projects, from birdwatchers helping conservation efforts with the e-Bird project, game enthusiasts folding proteins for the FoldIt project, to homeowners exploring the microbial diversity in their houses through the Wild Life of Our Homes project. Additionally, projects like the Science Education Alliance - Phage Hunters Advancing Genomics and Evolutionary Science and Tiny Earth engage students in large research projects as part of course-based undergraduate research experiences. Citizen scientists, Riley et al. argue, can also help discover bacteria with novel, useful traits.
Delftia is a genus of Betaproteobacteria first discovered in the city Delft, where bacteria themselves were discovered by Leeuwenhoek. Delftia has genes capable of precipitating gold by excreting a metabolite called delftibactin. Gold in solution as gold chloride is toxic to bacteria, so Delftia has evolved this novel mechanism for precipitating aqueous gold out of solution to nontoxic solid gold nanoparticles. This mechanism has obvious potential uses in gold recycling in used electronics, gold mining, and urban waste, but to date, the existing genetic diversity of Delftia in strain collections is modest. There are only six known species of Delftia. Full genome assemblies exist for four of these species within the National Center for Biotechnology Information database. Discovery of novel Delftia species and their relatives has the potential to better elucidate variations in Delftia genetic sequences, especially within the gold precipitation gene cluster and other industrially and human health related sequences. The more information about these gold precipitation genes, for example, the greater potential for using Delftia or its genetic potential to recycle our electronics and make mining more sustainable.
A colony of Delftia acidovorans. Khalifa et al. (2019).
The Wolfpack Citizen Science Challenge for Spring 2018 was a collaborative project to document the presence and genetic diversity of Delftia spp. across the North Carolina State University campus and create a scalable and interdisciplinary model to continue learning about this and other organisms. In addition to involving students in two introductory courses in the initial data collection, we also involved students in two upper-level courses in the downstream study of the microbes detected during
the Challenge.
the Challenge.
Participants were primarily recruited from two courses, ES 100: Introduction to Environmental Sciences (176 students) and LSC 170: First Year Seminar in the Life Sciences: Meet Your Microbes (20 students). However, anyone interested was able to obtain a sampling kit and participate. A post-event survey indicated that 96% of the participants were required to participate as part of a course and that 48% were currently enrolled as Science, Technology, Engineering and Mathematics majors.
Three events were held to create excitement and share results from the challenge. In January, the Challenge was launched with a public event attended by 19 people, in which Goller and Riley shared information about Delftia acidovorans found in sinks, drains and soil and encouraged members of the campus to think critically about the microbial communities around us. In March, the sequencing data were shared with the campus community at an event at which participants used the National Center for Biotechnology Information Basic Local Alignment Search Tool to find regions of similarity between the discovered sequences and those deposited in the National Center for Biotechnology Information database. This Basic Local Alignment Search Tool workshop was attended by 55 people. In April, results of the project were shared at a closing event open to the campus and general public, attended by 30 people.
Participants registered as teams of up to five members and were provided kits with instructions and materials to collect samples: three swabs and two 50 millilitre conical tubes for soil samples along with gloves, plastic spoons for scooping soil, alcohol swabs to sanitise the soil collection spoons and labels for samples. Approximately 40 kits were distributed and over 150 swab and soil samples were received between 30 January and 14 February 2018. Samples were delivered in person to either the Biotechnology Program teaching laboratories or the North Carolina State University Libraries front desk. Samples were stored in −20°C freezer until ready for metagenomic DNA extraction. Along with physical samples, metadata including location descriptors and latitude–longitude data were submitted online through a customized SciStarter citizen science website. Students’identifying information was removed from samples and a numerical identity was assigned.
Participants were provided with detailed instructions on how to sample environments around the campus and use the sampling kit. Participants were instructed to use the swab to sample a safe location and immediately place the swab in the transport container. Students collected soil samples with the provided tube and spoon while wearing disposable gloves. For processing of samples, students in molecular biology courses were trained in lab safety procedures and given a document detailing the potential hazards and safety procedures used in the teaching laboratory. For all extractions and qPCR reactions, students wore provided disposable lab coats, safety glasses and gloves, and disinfected all surfaces before and after use.
Metagenomic DNA was extracted from samples using the Invitrogen PureLink Microbiome DNA Purification Kit according to the corresponding protocol for swab and soil samples.Soil was transferred from collection tubes to bead tubes with alcohol-sterilised metal scoops. Swab tips were cut off into bead tubes with alcohol-sterilised metal scissors. Samples were lysed and homogenized by heat, bead beating and lysis buffer. After purification, samples were eluted in 50 μl of elution buffer. DNA concentration was determined spectrophotometrically using a ThermoFisher NanoDrop 2000c instrument and normalized to five ng/μl. Samples were matched with descriptive location data in an online spreadsheet using information submitted on the SciStarter website. Isolations were performed by Noah Riley in batches of 12–24 samples.
An Eppendorf epMotion 5075 TC liquid handler was used to set up quantitative real-time polymerase chain reaction DNA amplification reactions with New England BioLabs Luna Universal Probe qPCR reagents, primers and double-quenched probes. Quantitative polymerase chain reactions were run on a Bio-Rad CFX Connect instrument and data were exported as spreadsheets with cycle threshold values for each reaction. Samples were screened for the quantity of Delftia present using double-quenched, Delftia-specific primers and probe for a portion of the unique gold biomineralisation metabolite production system (the 'gold gene'). Presence and abundance of Delftia were then confirmed with a second set of primers and probe for a putative Delftia-specific toxin–antitoxin sequence unique to Delftia spp.. Reactions were set up in duplicate along with an 8-point, ten-fold dilution standard curve with 'gold gene' standard beginning at 40 pg/μl and toxin–antitoxin sequence standard at 30 pg/μl.
Undergraduate juniors and seniors and first- and second-year graduate students enrolled in an upper-level High-throughput Discovery 8-week lab module programed an epMotion 5075 TC liquid handler with the quantitative polymerase chain reaction script, prepared metagenomic samples for quantitative polymerase chain reaction and calculated Delftia copy numbers using the quantitative polymerase chain reaction cycle threshold data. Students were provided a spreadsheet template with detailed explanations and information on the use of a standard curve for calculation of absolute copy numbers of target sequences. Data were shared with students and groups of three to four were tasked with determining copy numbers for one 96-well polymerase chain reaction plate containing: 23 genomic DNA samples tested in duplicate along with an 8-point standard curve and negative buffer only controls. Multiple groups analysed the same samples to confirm the results and copy number trends were further supported by analysing quantitative polymerase chain reaction data for the same samples with a primer set for the single-copy Delftia-specific toxin–antitoxin sequence. Data were then analysed as a class and shared with Danica Lewis for visualisation and dissemination of the results to participants and the public. Samples with the highest Delftia copy number using both primer sets were selected for further analysis of the unique gold gene sequence.
For 20 samples with high Delftia counts, a portion of the gold gene sequence was amplified using primers Seq7 and Seq8 and the New England Biolabs Q5(R) High-Fidelity 2X Master Mix. The amplified portion of the gold gene was selected because it is highly specific to Delftia and based on current sequence database information, varies slightly between known species and strains, allowing for identification from metagenomic samples. The target Delftia sequence is 1045 base pairs in length. Of the 20 tested samples, 17 produced sufficient PCR product for sequencing and were sent to the North Carolina State University Genomic Sciences Laboratory for Sanger DNA sequencing using primers Seq7 and Seq8. Amplicons (pieces of DNA or RNA that are the source and/or product of amplification or replication events) were sequenced from both directions and sequences were trimmed based on stringent quality settings to match existing sequences in the National Center for Biotechnology Information database. The sequencing data were shared with the campus community at an event at which participants used the National Center for Biotechnology Information Basic Local Alignment Search Tool to find regions of local similarity between the discovered sequences and those deposited in the National Center for Biotechnology Information database. This allowed participants to identify which Delftia species and strains best matched the samples that were sequenced.
The Google Maps Fusion Tables extension was used to create a heatmap of Delftia presence and abundance across campus and Tableau Public software was used to create an interactive map. Participants were invited to explore the data and evaluate which samples had the highest amount of Delftia. Students in the courses involved in sampling and analysis were shown the results and asked to discuss future research questions.
Map showing the sites at which Delftia spp. was sampled on the North Carolina State University Campus. Danica Lewis/Tableau Public.
Over 150 samples were received from participants. Of these, 135 were labeled correctly and matched with the online SciStarter database containing sampling location descriptions and latitude–longitude coordinates. Through quantitative polymerase chain reaction analysis using primers and probe Seq1, Seq2, and Seq3, 125 samples (92.6%) had detectable quantities of the target Delftia 'gold gene' DNA sequence. Quantities of Delftia within samples were confirmed using the toxin–antitoxin sequence quantitative polymerase chain reaction primers and probe Seq4, Seq5 and Seq6. The 20 samples with highest Delftia counts were primarily swabs from sinks and drains. In contrast, the samples with the least Delftia DNA tended to be those from soil samples and outdoor locations. However, it is worth reiterating that nearly all of the samples contained some Delftia, a relatively understudied genus of Bacteria.
Riley et al. next compared the Delftia gold gene sequences in the samples to those of sequenced strains. Collectively, the sequences from their samples were most similar to those of Delftia tsuruhatensis strain CM13, Delftia acidovorans strains ANG1 and SPH-1, or Delftia acidovorans strain RAY209. Differentiation between Delftia acidovorans strains ANG1 and SPH-1 was not possible as each matched query had the same identity, query coverage and E value results for both strains. However, for strains of Delftia tsuruhatensis CM13 and Delftia acidovorans RAY209, the sequences matched with highest probability to each, respectively. None of the samples were close matches for the other sequenced Delftia species of Delftia deserti, D. lacustris, Delftia litopenaei, Delftia rhizosphaerae, or other strains of Delftia acidovorans and Delftia tsuruhatensis. A total of 14 out of the 17 sequences had less than 97% sequence identity with the Delftia strains they most closely matched.
Riley et al. sought to simultaneously test whether they could engage students campus-wide in a citizen science style microbial research project and in doing so, understand the distribution and diversity of strains of one particular Bacterial genus, Delftia. They were indeed able to engage students from diverse majors across campus. In doing so, they discovered that some sampling sites had many more Delftia counts than did others, that Delftia was relatively ubiquitous and that some of the strains we identified had gold genes that appeared relatively divergent from those known from the literature. Although they were unable to accurately determine the diversity of Delftia strains present, this unanswered question presents a new challenge and opportunity for our citizen science and Delftia research efforts.
Collectively, the quantitative polymerase chain reaction, Sanger DNA sequencing and Basic Local Alignment Search Tool comparison results showed that strains of Delftia are diverse, abundant and frequent (found at many sites) in environments in and around the college campus. Based on available genomic sequences deposited in the National Center for Biotechnology Information database and partial sequencing of the highly conserved gold gene, the strains students discovered best matched the reference strains Delftia tsuruhatensis CM13 and Delftia acidovorans ANG1 and SPH-1. However, 14 of 17 samples contained strains that were a 97% or lower match to strains in the National Center for Biotechnology Information database. Riley et al.'s suspicion is that these strains represent uncharacterised genetic diversity among strains in Delftia’s gold gene. However, because Riley et al. sequenced from complex environmental samples they can’t preclude the possibility that some of this variation is due to cases in which the forward and reverse sequences obtained were from different Delftia species or strains in the sample.
The sequenced Delftia gold gene from many of the participant samples matched well to known Delftia species, but some samples matched two different existing strains equally well. For example, samples from 7-1 to 24-1 were equally similar to the strains Delftia acidovorans ANG1 and SPH-1. Clearly further work can be done to sequence additional portions or the entire genomes of these samples to identify what known strain is present or discover a new lineage of Delftia. More extensive community analyses of the samples using both targeted (16S rRNA gene) and whole genome shotgun sequencing would aid in the identification of which microbes associate with the presence of Delftia and the identity of the gold sequences in the environment, respectively. Additionally, high-throughput sequencing approaches such as Hi-C from Phase Genomics or Nanopore single-molecule long-read sequencing can be employed to attempt to sequence and assemble the entire Delftia genome in metagenomic samples positive for Delftia by quantitative polymerase chain reaction. Ultimately, selective media capable of isolating and identifying Delftia would allow us to increase our collection of Delftia strains for basic functional studies and genome sequencing.
Riley et al.'s sequencing results best matched the species Delftia acidovorans and Delftia tsuruhatensis, both of which have been found in environments similar to those they studied. Delftia acidovorans was originally discovered in soil and has been found in drains, waterspouts and showerheads in the built environment. Delftia tsuruhatensis was first discovered in a wastewater treatment plant and has been found in similar locations along with Delftia acidovorans. The Delftia species Riley et al. did not encounter in their study are species that have so far been associated with more restricted habitats. Delftia deserti has been found to inhabit desert environments, Delftia lacustris in lake water, Delftia litopenaei in pond water, and Delftia rhizosphaerae in the rhizosphere of the Gum Rockrose, Cistus ladanifer, a Plant native to the Mediterranean region. The apparent ubiquity of the genus Delftia hides the reality that individual species appear to show considerable habitat restriction. In the future, it would be interesting to understand which traits and genes of individual Delftia species confer the ability to survive in particular habitats.
It is unclear the extent to which the life history of Delftia in the above habitats is the same as that of Delftia in the built environment of a college campus. Nor is it well understood whether the presence of Delftia in water systems is problematic or potentially beneficial. Like many Bacterial taxa, Delftia species are recorded as opportunistic pathogens that can infect hospitalised or immunocompromised patients. However, there is no indication that Human bodies are a common habitat for this genus. Instead, in buildings such as those we sampled it appears to be much more common in water systems; in drains, showerheads and downspouts. In as much as the ecological conditions of water systems differ greatly, it is possible that a comparative study of water systems, such as those that are or are not chlorinated, might reveal more about the built environment natural history of this organism.
Riley et al.'s approach kindled campus-wide student interest in microbial diversity and molecular biology techniques through the excitement of discovering this unique microbe in places that students frequent on campus. Groups of students from various academic disciplines and courses produced and analyzed samples that contributed to a large public dataset. The findings helped teach the student community about Delftia and also reinforced the importance of the collaborative nature of scientific discovery. The success of this project, in terms of the documentation of Delftia’s distribution helps to validate Riley et al.'s general approach. In addition, this approach has the potential to encourage future students to participate. Riley et al. aim to continue the challenge of accurately identifying new Delftia lineages and engage others by expanding the sampling opportunity to a multi-section first-year English class that is required for all undergraduate students on the campus. Using a similar approach and incorporating the expertise of faculty in the English department, they will engage students in writing tasks related to the project. Additionally, an upper-level metagenomics course will tie into this endeavor by processing, sequencing and analysing the microbial communities in samples with high numbers of Delftia sequences. With relatively minor changes to the course schedules and curricula, 100 more students per semester can participate, learn and contribute to the project. Riley et al. are creating resources that are accessible for other faculty and campuses to implement this project and share findings. For this, students participating in the project are writing The Delftia Book, and Riley et al. have created a group for instructor resources on the QUBES web portal. Liquid handlers can be cost-prohibitive, but less expensive models such as the Opentrons OT-2 are available, and Riley et al. are developing scripts for this instrument. Student groups in lab-based courses can always set up quantitative polymerase chain reactions manually to participate in this project.
As the future plans for integrating this project into courses indicate, enthusiasm for the project was high among Riley et al.'s colleagues and grew as the project proceeded. However, if they are to continue the project it is key that it continues to yield new scientific insights. Fortunately, this seems very likely to be the case. For example, although Delftia abundance was very patchy on campus, Riley et al. have yet to explain what factors account for such patchiness. Additional samples will help to have sufficient coverage across sample types to allow spatial models of Delftia diversity and abundance. In addition, Riley et al.'s results suggest that new variants of the Delftia gold gene and even new Delftia strains remain to be discovered. Conversely, there is a lack of genomic diversity represented in the National Center for Biotechnology Information database. By leveraging the enthusiasm of university students and staff, interconnecting courses and researchers, and using Riley et al.'s model pipeline, new lineages of Delftia can be rapidly identified and studied (e.g., groups of students cloning novel gold gene cluster into a host such as Escherichia coli or Yeast for functional characterisation). This will yield a better understanding of the ecological and environmental significance of these organisms and simultaneously help to connect students and faculty across campus in a common scientific project. Finally, it is of note that Delftia species, while little known, are of potentially great applied importance. In addition, they contain genes that allow many strains to precipitate gold. Given the many waste streams in which gold is present but hard to concentrate, this ability has the potential to be very useful moving forward.
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