Bioprospecting saline gradient of a Wildlife Sanctuary for bacterial diversity and antimicrobial activities
© The Author(s) 2017
Received: 15 June 2017
Accepted: 29 July 2017
Published: 11 August 2017
Antibiotic-resistant bacteria are becoming a global crisis, causing death of thousands of people and significant economic impact. The discovery of novel antibiotics is crucial to saving lives and reducing healthcare costs. To address the antibiotic-resistant crisis, in collaboration the Small World Initiative, which aims to crowdsource novel antibiotic discovery, this study aimed to identify antimicrobial producing bacteria and bacterial diversity in the soil of the Stimpson Wildlife Sanctuary, an inland area with a soil salt gradient.
Approximately 4500 bacterial colonies were screened for antimicrobial activity and roughly 100 bacteria were identified as antimicrobial producers, which belong to Entrococcaceae (74%), Yersiniaceae (19%), and unidentified families (7%). Several bacterial isolates showed production of broad spectrum inhibitory compounds, while others were more specific to certain pathogens. The data obtained from the current study provide a resource for further characterization of the soil bacteria with antimicrobial activity, with an aim to discover novel ones. The study showed no correlation between soil salt level and the presence of bacteria with antimicrobial activities. However, most of the identified antimicrobial producing bacteria do not belong to actinomycetes, the most common phyla of antibiotic producing bacteria and this could potentially lead to the discovery of novel antibiotics.
KeywordsAntimicrobial producing bacteria Bacterial diversity Saline soil
While the increasing use of antibiotics in medical and agricultural applications has been beneficial, in recent years overuse of broad-spectrum antibiotics combined with the evolution of bacteria has led to the evolution of deadly antibiotic-resistant bacteria [1–4]. The evolution of antibiotic-resistant bacteria is a global crisis causing the death of at least 23,000 people in the United States [5, 6]. Antibiotic-resistant bacteria have a negative economic impact and lead to increased costs associated with the health care of infected individuals. For example, Clostridium difficile is a microbe causing extreme gastrointestinal issues with acute infections resulting in death within thirty days of being infected for some 29,000 patients .
To combat the antibiotic-resistant bacteria crisis, there is a dire need for discovery and development of novel and effective antimicrobial compounds to treat these infections. Despite this need, major pharmaceutical companies are not investing in novel antibiotic development due to low profitability [8, 9] and other significant obstacles such as the instability of the global public health infrastructure and availability of funding and technology in underdeveloped countries. In addition, there is a need to limit the use of broad-spectrum antibiotics, thus minimizing the development of new superbugs .
To address the antibiotic-resistant bacteria crisis and as a part of the Small World Initiative (http://www.smallworldinitiative.org) course, two students aimed to explore the discovery of antimicrobial producing bacteria in the soil of the Stimpson Wildlife Sanctuary (SWS). The SWS has unique soil with many salt springs that allow for the formation of salt gradients ranging from fresh water to water with up to 50 Parts Per Thousand (PPT) Total Dissolved Salts (TDS). Bacteria that inhabit this area represent untapped sources of potentially new bioactive compounds, including antibiotics. This area provides an opportunity not only to discover antibiotic-producing bacteria but also to explore the bacterial diversity in response to salt stress. In this study, a culture-dependent approach was applied to isolate and discover bacteria with antimicrobial activities.
Materials and methods
Soil collection site
Samples were collected from the SWS located in Alabama, United States. A permission to collect samples was obtained from the Alabama Department of Conservation and Natural Resources. The SWS is characterized by the presence of a salt gradient, ranging from fresh water to water with up to 50 PPT TDS. Twenty soils and water samples were collected at various locations around SWS into sterilized 50 ml tubes and kept on ice during transportation to the laboratory. The water samples’ TDS was measured on site using HM Digital TDS meter.
One gram of soil was suspended into 10 ml 0.85% w/v NaCl, vortexed, spun down, and the supernatant was collected. A serial dilution was made, followed by spreading 100 µl onto Luria–Bertani (LB), tryptic soy, potato dextrose, terrific broth, yeast extract peptone dextrose media with 1.5% w/v agar. All plates were incubated overnight at 37 °C. The number of individual bacterial colonies and number of bacterial phenotypes were recorded. About 4500 bacterial colonies were picked into a 96-deep well plate containing 400 µl LB broth and incubated in 37 °C shaker set at 200 rpm for 24 h.
Screening of antimicrobial activity
Bacteria isolated from the soil were tested for antimicrobial activities against safe relatives of the ESKAPE pathogens, six pathogens with growing multidrug resistant virulence  and Salmonella Newport, a major cause of food poisoning . A liquid culture of a single colony of each ESKAPE relative was grown in 5 ml LB media for 12 h at 34 °C while shaking. Optical Density 600 was adjusted for all ESKAPE relatives to an average of 4 × 106 CFU/ml. To generate a bacterial lawn, 200 µl of liquid ESKAPE cultures were plated onto 150 mm Petri dishes with LB agar. Unknown bacterial strains were laid over ESKAPE plates using a 96-well pin replicator and incubated overnight at 26 °C. After 36 h, antimicrobial activity was assessed by the presence of inhibition zones of the ESKAPE relatives around the unknown bacterial strains.
Bacterial molecular identification
Antibiotic-producing bacteria were identified using 16S rRNA sequence. A small portion of every colony was used as a genomic DNA template in the PCR mix. The 16S rRNA gene primers (27 forward and 1492 reverse) were used to amplify and sequence a 1465 bp . PCR products were separated using 1% agarose gel, purified using 5 Prime GelElute Extraction Kit (Prime, Gaithersburg, MD), and then sequenced. DNA sequences were assembled using DNAStar and then searched against the non-redundant DNA sequence available in the NCBI database.
Number of single bacterial colony isolated from the SWS locations and number and percentage of bacteria with antimicrobial activities
No. of APB
% of APB
The specificity of the antimicrobial activities against known ESKAPE relatives was identified (Additional file 1: Table S1). Sample number D9 and H12 were effective in inhibiting four different ESKAPE (S. epidermidis, B. subtilis, E. coli and S. newport). We have observed that S. epidermidis and E. coli were killed by bacteria isolated from any of the sampling sites, which indicates that these bacteria are susceptible to a wide range of antimicrobial compounds. Two antimicrobial producing bacteria were effective only on E. coli, which indicates that the inhibitory compound produced by these bacteria has a very narrow effectiveness on various ESKAPE relatives.
Bacteria that inhabit the soil of environmentally stressed areas such as high salinity, represent a rich source of potential novel antimicrobial compounds producing bacteria. In addition, the diversity of soil bacteria under a stressed environment is usually lower compared to bacteria present in other soil. The Stimpson Wildlife Sanctuary is a unique soil habitat representing high and low salt levels within a relatively short distance. The physical state of this distinct habitat allowed the presence of bacterial strains to adapt to such environments. These bacterial strains most likely maintain specific metabolic pathways that are capable of producing secondary metabolites, including antimicrobial agents against other bacteria. In this study, we used a culture-dependent method to assess bacterial diversity and discover antimicrobial compounds producing bacteria present in the SWS’s soil and organic matter.
A Cypress knee is a distinctive structure formed above the roots of various tree species growing in swamps, which help in oxygenation to the tree’s roots or assist in anchoring the tree in the soft and muddy soil . Therefore, obtaining minimal bacterial diversity from the Cypress knee samples is not a surprise, as most of the associated bacteria are expected to be anaerobic while we focused on isolation of aerobic bacteria. Nutrient and carbon availability and soil moisture have been implicated as factors that may influence microbial community composition ; therefore, the number of bacteria obtained from the Tree Log, which is rich in nutrients, was much higher than the Cypress knees. Based on the rRNA sequencing data, Cypress knees’ bacterial community was more diverse and had more unique bacterial isolates compared to the Tree Log. Salinity is the major environmental element that affects soil microbial community, more than extremes of temperature, pH, or physical soil composition . Our data showed higher number of CFUs from soil nearby 50 PPT water; however, there were no specific trends of the number of bacteria and the changes in salt levels. Interestingly, the soil nearby with higher salt levels of 14 PPT and 50 PPT showed the most unique bacterial strains.
Antimicrobial activity testing against the safe relative of the ESKAPE relatives showed various levels of inhibition’s induction and specificity. It has been reported that the antimicrobial compounds are very diverse ; therefore it is an expected result to find variation on the level of inhibition and specificity. The identification of 54 bacterial isolates based on the 16S rRNA sequencing assigned them to two different phyla (Proteobacteria and Firmicutes). Interestingly, Actinomycetes, some of the most common soil bacteria that produce 60% of clinically important antibiotics , were not identified in our collection. Identification of antimicrobial compounds producing bacteria from phyla other than Actinomycetes is promising; some of these compounds may be novel. The mode of action and the nature of the identified antimicrobial compounds by these bacteria are unknown and its inhibitory effect could be due to production of antibiotics or other chemical production. Overall, most isolates in this study were identified as E. faecalis (Additional file 3: Table S3), which is part of the normal microbiota of animals and can cause disease as well . In addition, recovery of E. faecalis as the major bacteria could have been due to the methodology of using higher incubation temperature and aerobic conditions.
The Cypress Knee samples have two putative novel and unique bacterial species (sample 7G and 6A) with similarity to unknown bacteria in the Genbank database of less than 100%. Novel and/or known bacterial species represent a unique opportunity to possibly find novel metabolic pathways, including antibiotic production pathways. On the other hand, the Tree Log samples have all been previously identified bacteria, with some isolates having less than 100% match in the database which may indicate new bacterial strains.
Some of the bacterial strains with broad spectrum inhibitory compounds may be promising to identify the chemical nature of these compounds and can be used to treat infections of S. epidermidis, B. subtilis, E. coli and S. newport. Examples of these antibiotic-producing bacteria are Serratia sp. SH-AB-1 and S. marcescens . Recent studies have characterized and sequenced the genome of specific strain of S. marcescens, which is capable of producing multiple antibiotics [21, 22]. Interestingly, several Serratia sp. are also antibiotic-resistant bacteria . Overall, antibiotic-producing bacteria that are capable of inhibiting growth of both gram positive and negative bacteria (i.e. S. epidermidis and E. coli) were found in all sample sources. Antimicrobial compounds producing bacteria (isolated from Tree Log) were effective only on gram-negative (E. coli).
Strength and limitations
This is the first study that explored the bacterial diversity of an inland saline gradient (SWS) and identified antimicrobial producing bacteria. This study provided opportunities for undergraduates to perform authentic research and have a sense of ownership of their project. The major limitation of this study is the lack of comprehensive coverage of bacterial diversity in the soil, lack of physiological characterization of these bacteria, and the need for chemical characterization of the produced inhibitory compounds.
BMC Research Notes considers scientifically valid manuscripts irrespective of the interest of a study or its likely impact. In order to ensure submissions to BMC Research Notes are of maximum benefit to the research community, authors should clearly state the limitations of their work.
RK and MD conducted the research and drafted the manuscript. MM obtained funding for the study and edited the manuscript. RK, MD and MM contributed to the design of the study. All authors read and approved the final manuscript.
We would like to thank the University of West Alabama Honors Program and the Office of Sponsored Programs and Research for their support. We are grateful to the National Science Foundation Award Numbers 1354050, 1356248 and 1611829 for the financial support.
The authors declare that they have no competing interests.
Availability of data and materials
The Additional files 1, 2, 3 for this article are available in the figshare repository (https://figshare.com/s/b14316886f235361a605). Strains and other data will be provided by the corresponding author on reasonable request.
Consent to publish
Ethics approval and consent to participate
The National Science Foundation Award Numbers 1354050, 1356248 and 1611829.
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- Kuehn BM. CDC: hospital antibiotic use promotes resistance: checklist can improve practices. JAMA. 2014;311(15):1485–6.View ArticlePubMedGoogle Scholar
- Price LB, Koch BJ, Hungate BA. Ominous projections for global antibiotic use in food-animal production. Proc Natl Acad Sci. 2015;112(18):5554–5.View ArticlePubMedPubMed CentralGoogle Scholar
- Robinson TP, Wertheim HF, Kakkar M, Kariuki S, Bu D, Price LB. Animal production and antimicrobial resistance in the clinic. Lancet. 2016;387(10014):e1–3.View ArticlePubMedGoogle Scholar
- Silbergeld EK, Graham J, Price LB. Industrial food animal production, antimicrobial resistance, and human health. Annu Rev Public Health. 2008;29:151–69.View ArticlePubMedGoogle Scholar
- Health UDo, Services H. Antibiotic resistance threats in the United States. Atlanta: CDC; 2013.Google Scholar
- Frieden TR. CDC health disparities and inequalities report-United States, 2013. Foreword. MMWR Suppl. 2013;62(3):1–2.PubMedGoogle Scholar
- Hunter JC, Mu Y, Dumyati GK, Farley MM, Winston LG, Johnston HL, Meek JI, Perlmutter R, Holzbauer SM, Beldavs ZG. Burden of nursing home-onset clostridium difficile infection in the United States: estimates of incidence and patient outcomes. Open Forum Infect Dis. 2016;3(1):ofv196. doi:https://doi.org/10.1093/ofid/ofv196.View ArticlePubMedPubMed CentralGoogle Scholar
- Pammolli F, Magazzini L, Riccaboni M. The productivity crisis in pharmaceutical R&D. Nat Rev Drug Discov. 2011;10(6):428–38.View ArticlePubMedGoogle Scholar
- Scannell JW, Blanckley A, Boldon H, Warrington B. Diagnosing the decline in pharmaceutical R&D efficiency. Nat Rev Drug Discov. 2012;11(3):191–200.View ArticlePubMedGoogle Scholar
- Spellberg B, Guidos R, Gilbert D, Bradley J, Boucher HW, Scheld WM, Bartlett JG, Edwards J. America IDSo: the epidemic of antibiotic-resistant infections: a call to action for the medical community from the Infectious Diseases Society of America. Clin Infect Dis. 2008;46(2):155–64.View ArticlePubMedGoogle Scholar
- Boucher HW, Talbot GH, Bradley JS, Edwards JE, Gilbert D, Rice LB, Scheld M, Spellberg B, Bartlett J. Bad bugs, no drugs: no ESKAPE! An update from the Infectious Diseases Society of America. Clin Infect Dis. 2009;48(1):1–12.View ArticlePubMedGoogle Scholar
- Alpas H, Yeni F, Soyer Y, Fletcher J. Recent outbreaks of human pathogens on plants (HPOPs) on fresh produce–lessons learned from the practice. In: Gullino M, Stack J, Fletcher J, Mumford J, editors. Practical tools for plant and food biosecurity. Plant pathology in the 21st century, vol. 8. Cham: Springer; 2017. P. 77–96.View ArticleGoogle Scholar
- Marchesi JR, Sato T, Weightman AJ, Martin TA, Fry JC, Hiom SJ, Wade WG. Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol. 1998;64(2):795–9.PubMedPubMed CentralGoogle Scholar
- Pulliam W. Methane emissions from cypress knees in a southeastern floodplain swamp. Oecologia. 1992;91(1):126–8.View ArticlePubMedGoogle Scholar
- Staley JT, Reysenbach AL. Biodiversity of microbial life. Hoboken: Wiley; 2002.Google Scholar
- Lozupone CA, Knight R. Global patterns in bacterial diversity. Proc Natl Acad Sci. 2007;104(27):11436–40.View ArticlePubMedPubMed CentralGoogle Scholar
- Zasloff M. Antimicrobial peptides of multicellular organisms. Nature. 2002;415(6870):389–95.View ArticlePubMedGoogle Scholar
- Janardhan A, Kumar AP, Viswanath B, Saigopal D, Narasimha G. Production of bioactive compounds by actinomycetes and their antioxidant properties. Biotechnol Res Int. 2014;2014:8.View ArticleGoogle Scholar
- Penas PP, Mayer MP, Gomes BP, Endo M, Pignatari AC, Bauab KC, Pinheiro ET. Analysis of genetic lineages and their correlation with virulence genes in Enterococcus faecalis clinical isolates from root canal and systemic infections. J Endod. 2013;39(7):858–64.View ArticlePubMedGoogle Scholar
- Ito H, Arakawa Y, Ohsuka S, Wacharotayankun R, Kato N, Ohta M. Plasmid-mediated dissemination of the metallo-beta-lactamase gene blaIMP among clinically isolated strains of Serratia marcescens. Antimicrob Agents Chemother. 1995;39(4):824–9.View ArticlePubMedPubMed CentralGoogle Scholar
- Matilla M, Udaondo Z, Krell T, Salmond G. Genome Sequence of Serratia marcescens MSU97, a plant-associated bacterium that makes multiple antibiotics. Genome Announc. 2017;5(9):e01752–16.View ArticlePubMedPubMed CentralGoogle Scholar
- Bonnin RA, Didi J, Ergani A, Lima S, Naas T. Chromosome-encoded broad-spectrum Ambler class A β-lactamase RUB-1 from Serratia rubidaea. Antimicrob Agents Chemother. 2017;61(2):e01908–16.PubMedPubMed CentralGoogle Scholar
- Parente TMAL, de Lima Rebouças E, dos Santos VCV, Barbosa FCB, Zanin ICJ. Serratia marcescens resistance profile and its susceptibility to photodynamic antimicrobial chemotherapy. Photodiagn Photodyn Ther. 2016;14:185–90.View ArticleGoogle Scholar