Skip to main content
SpringerLink
Log in

Non-invasive bat species identification from mixed-species samples using a microarray

  • Methods and Resources Article
  • Published:
Conservation Genetics Resources Aims and scope Submit manuscript

Abstract

Identifying species from non-invasively collected, mixed species samples for biodiversity monitoring can be difficult and expensive using typical molecular methods because samples are often degraded. This is the case when identifying the species of bats present in roosts where guano may be the only means of assessment without disturbing the bats themselves. To aid in such studies, we developed species-specific DNA probes and a microarray capable of identifying most bat species in the United States and Canada using our existing database of 16S mitochondrial DNA sequences. The microarray was sensitive enough to detect DNA diluted 1:500 for several species combinations and was able to detect the presence of more species in mixed guano samples collected from roosts than did direct sequencing from individual fecal pellets. We suggest that these DNA probes and the microarray could be a valuable tool with which to non-invasively monitor bat populations and roost use.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  • Bonhomme CJ, Nappez C, Raoult D (2007) Microarray for serotyping of Bartonella species. BMC Microbiol 7:59

    Article  PubMed  PubMed Central  Google Scholar 

  • Bryant PA, Venter D, Robins-Browne R, Curtis N (2004) Chips with everything: DNA microarrays in infectious diseases. Lancet Infect Dis 4:100–111

    Article  CAS  PubMed  Google Scholar 

  • Carles M, Cheung MK, Moganti S, Dong TT, Tsim KW, Ip NY, Sucher NJ (2005) A DNA microarray for the authentication of toxic traditional Chinese medicinal plants. Planta Med 71:580–584

    Article  CAS  PubMed  Google Scholar 

  • Carstens BC, Dewey TA (2010) Species delimitation using a combined coalescent and information-theoretic approach: an example from north American Myotis bats. Syst Biol 59:400–414

    Article  PubMed  PubMed Central  Google Scholar 

  • Cleven BEE, Palka-Santini M, Gielen J, Meembor S, Kronke M, Krut o (2006) Identification and characterization of bacterial pathogens causing bloodstream infections by DNA microarray. J Clin Microbiol 44:2389–2397

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Forêt S, Kassahn KS, Grasso LC, Hayward DC, Iguchi A, Ball EE, Miller DJ (2007) Genomic and microarray approaches to coral reef conservation biology. Coral Reefs 26:475–486

    Article  Google Scholar 

  • Grattarola F, González S, Cosse M (2015) A novel primer set for mammal species identification from feces samples. Conserv Genet Resour 7:57–59

    Article  Google Scholar 

  • Hajibabaei M, Smith MA, Janzen DH, Rodriguez, J J, Whitfield JB, Herbert PDN (2006) A minimalist barcoade can identify a specimen whouse DNA is degraded. Mol Ecol Notes 6:959–964

    Article  CAS  Google Scholar 

  • Hajibabaei M, Singer GAC, Clare EL, Herbert PDN (2007) Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring. BMC Biol, 5, 24.

  • Hillis DM, Dixon MT (1991) Ribosomal DNA: molecular evolution and phylogenetic inference. Q Rev Biol 66:411–453

    Article  CAS  PubMed  Google Scholar 

  • Huang A, Li J-W, Shen Z-Q, Wang X-W, Jin M (2006) High-throughput identification of clinical pathogenic fungi by hybridization to an oligonucleotide microarray. J Clin Microbiol 44:3299–3305

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huang W, Yang Y, Zhang X, Zhao C, Yin A, Zhang X, He Z, Jiang Y, Zhang L (2013) An easy operating pathogen microarray (EOPM) platform for rapid screening of vertebrate pathogens. BMC Infect Dis 13:437

    Article  PubMed  PubMed Central  Google Scholar 

  • Kekkonen M, Hebert PDN (2014) DNA barcode-based delineation of putative species: efficient start for taxonomic workflows. Mol Ecol Resour 14:706–715

    Article  PubMed  PubMed Central  Google Scholar 

  • Kellogg CA, Piceno YM, Tom LM, DeSantis TZ, Zawada DG, Andersen GL (2012) PhyloChip™ microarray comparison of sampling methods used for coral microbial ecology. J Microbiol Methods 88:103–109

    Article  PubMed  Google Scholar 

  • Kochzius M, Nolte M, Weber H, Silkenbeumer N, Hjorleifsdottir S, Hreggvidsson GO, Marteinsson V, Kappel K, Planes S, Tinti F, Magoulas A, Garcia Vazquez E, Turan C, Hervet C, Campo Falgueras D, Antoniou A, Landi M, Blohm D (2008) DNA microarrays for identifying fishes. Mar Biotechnol 10:207–217

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kochzius M, Seidel C, Antoniou A, Botla SK, Campo D, Cariani A, Vazquez EG, Hauschild J, Hervet C, Hjörleifsdottir S, Hreggvidsson G, Kappel K, Landi M, Magoulas A, Marteinsson V, Nölte M, Planes S, Tinti F, Turan C, Venugopal MN, Weber H, Blohm D (2010) Identifying fishes through DNA barcodes and microarrays. PLoS ONE 5:e12620

    Article  PubMed  PubMed Central  Google Scholar 

  • Lin CC, Fung LL, Chan PK, Lee CM, Chow KF, Cheng SH (2014) A rapid low-cost high-density DNA-based multi-detection test for routine inspection of meat species. Meat Sci 96:922–929

    Article  CAS  PubMed  Google Scholar 

  • Lung O, Nadin-Davis S, Fisher M, Erickson A, Knowles M, Furukawa-Stoffer T, Ambagala A (2013) Microarray for identification of the chiropteran host species of rabies virus in Canada. Microarrays 2:153

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mayer F, Helversen Ov (2001) Cryptic diversity in European bats. Proc R Soc Lond B 268:1825–1832

    Article  CAS  Google Scholar 

  • Noyer C, Abot A, Trouilh L, Leberre VA, Dreanno C (2015) Phytochip: Development of a DNA-microarray for rapid and accurate identification of pseudo-Nitzschia spp and other harmful algal species. J Microbiol Methods 112:55–66

    Article  CAS  PubMed  Google Scholar 

  • Patro JN, Ramachandran P, Lewis JL, Mammel MK, Barnaba T, Pfeiler EA, Elkins CA (2015) Development and utility of the FDA ‘GutProbe’ DNA microarray for identification, genotyping and metagenomic analysis of commercially available probiotics. J Appl Microbiol 118:1478–1488

    Article  CAS  PubMed  Google Scholar 

  • Paulin LF, Soto-Del Río MdlD, Sánchez I, Hernández J, Gutiérrez-Ríos RM, López-Martínez I, Wong-Chew RM, Parissi-Crivelli A, Isa P, López S, Arias CF (2014) PhyloFlu, a DNA microarray for determining the phylogenetic origin of influenza A virus gene segments and the genomic fingerprint of viral strains. J Clin Microbiol 52:803–813

    Article  PubMed  PubMed Central  Google Scholar 

  • Peplies J, Lachmund C, Glöckner FO, Manz W (2006) A DNA microarray platform based on direct detection of rRNA for characterization of freshwater sediment-related prokaryotic communities. Appl Environ Microbiol 72:4829–4838

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pesole G, Gissi C, De Chirico A, Saccone C (1999) Nucleotide substitution rate of mammalian mitochondrial genomes. J Mol Evol 48:427–434

    Article  CAS  PubMed  Google Scholar 

  • Pfunder M, Holzgang O, Frey JE (2004) Development of microarray-based diagnostics of voles and shrews for use in biodiversity monitoring studies, and evaluation of mitochondrial cytochrome oxidase 1 vs. cytochrome b as genetic markers. Mol Ecol 13:1277–1286

    Article  CAS  PubMed  Google Scholar 

  • Rodriguez RM, Ammerman LK (2004) Mitochondrial DNA divergence does not reflect morphological difference between Myotis californicus and Myotis ciliolabrum. J Mammal 85:842–851

    Article  Google Scholar 

  • Rubenstein K (2003) Commercial aspects of microarray technology. Biotechniques 34:52–54

    Google Scholar 

  • Ruedi M, Mayer F (2001) Molecular systematics of bats of the genus Myotis (Vespertilionidae) suggests deterministic ecomorphological convergences. Mol Phylogenet Evol 21:436–448

    Article  CAS  PubMed  Google Scholar 

  • Salathia N, Lee HN, Sangster TA, Morneau K, Landry CR, Schellenberg K, Behere AS, Gunderson KL, Cavalieri D, Jander G, Queitsch C (2007) Technical Advance: Indel arrays: an affordable alternative for genotyping. Plant J 51:727–737

    Article  CAS  PubMed  Google Scholar 

  • Sarri C, Stamatis C, Sarafidou T, Galara I, Godosopoulos V, Kolovos M, Liakou C, Tastsoglou S, Mamuris Z (2014) A new set of 16S rRNA universal primers for identification of animal species. Food Control 43:35–41

    Article  CAS  Google Scholar 

  • Sherwin RE, Stricklan D, Rogers DS (2000) Roosting affinities of Townsend’s big-eared bat (Corynorhinus townsendii) in northern Utah. J Mammal 81:939–947

    Article  Google Scholar 

  • Stadelmann B, Lin LK, Kunz TH, Ruedi M (2007) Molecular phylogeny of New World Myotis (Chiroptera, Vespertilionidae) inferred from mitochondrial and nuclear DNA genes. Mol Phylogenet Evol 43:32–48

    Article  CAS  PubMed  Google Scholar 

  • Summerbell RC, Lévesque CA, Seifert KA, Bovers M, Fell JW, Diaz MR, Boekhout T, de Hoog GS, Stalpers J, Crous PW (2005) Microcoding: the second step in DNA barcoding. Philos Trans R Soc B 360:1897–1903

    Article  CAS  Google Scholar 

  • Taberlet P, Waits LP, Luikart G (1999) Noninvasive genetic sampling: look before you leap. Trends Ecol Evol 14:323–327

    Article  CAS  PubMed  Google Scholar 

  • Teletchea F, Bernillon J, Duffraisse M, Laudet V, Hänni C (2008) Molecular identification of vertebrate species by oligonucleotide microarray in food and forensic samples. J Appl Ecol 45:967–975

    Article  CAS  Google Scholar 

  • Volokhov D, Chizhikov V, Chumakov K, Rasooly A (2003) Microarray-based identification of thermophilic Campylobacter jejuni, C. coli, C. lari, and C. upsaliensis. J Clin Microbiol 41:4071–4080

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vonhof MJ, Russell AL, Miller-Butterworth CM (2015) Range-wide genetic analysis of little brown bat (Myotis lucifugus) populations: estimating the risk of spread of white-nose syndrome. PLoS One 10:e0128713

    Article  PubMed  PubMed Central  Google Scholar 

  • Wadley JJ, Austin JJ, Fordham DA (2014) Genetic inference as a method for modelling occurrence: a viable alternative to visual surveys. Austral Ecol 39:952–962

    Article  Google Scholar 

  • Waits LP, Paetkau D (2005) Noninvasive genetic sampling tools for wildlife biologists: a review of applications and recommendations for accurate data collection. J Wildl Manag 69:1419–1433

    Article  Google Scholar 

  • Wilhelm A (2012) Use of artificial roosts by bats in central Arizona. Thesis, Northern Arizona University

  • Yang DY, Eng B, Waye JS, Dudar JC, Saunders SR (1998) Technical note: improved DNA extraction from ancient bones using silica-based spin columns. Am J Phys Anthropol 105:539–543

    Article  CAS  PubMed  Google Scholar 

  • Zielinski WJ, Mazurek MJ, Zinck J (2007) Identifying the species of bats roosting in redwood basal hollows using genetic methods. Northwest Sci 81:155–162

    Article  Google Scholar 

  • Zinck JM, Duffield DA, Ormsbee PC (2004) Primers for identification and polymorphism assesment of vespertilionid bats in the Pacific Northwest. Mol Ecol Notes 4:239–242

    Article  CAS  Google Scholar 

Download references

Acknowledgments

Funding for this study was provided by the U.S. Army Corps of Engineers—Engineer Research and Development Center (Grants W9132T-05-C-0011 and W9132T-06-C-0010 through Portland State University). Laboratory work was conducted at Portland State University, and we wish to thank Dr. Deborah Duffield for lab space during this project. Matt Holman served as point of contact for the U.S. Army Corps of Engineers and we thank him for his logistical support and sample collection. Ammon Wilhelm also provided mixed species guano samples used in validation tests. Patricia Ormsbee and Aimee Hart provided samples and read previous versions of this manuscript. Caprice Rosato at Oregon State University offered invaluable advice and expertise developing and troubleshooting the array design.

Author information

Authors and Affiliations

  1. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA

    Lorelei E. Patrick

  2. Science and Engineering Division, Portland Community College, Portland, OR, 97280, USA

    Jan M. Just

  3. Department of Biological Sciences and Institute of the Environment and Sustainability, Western Michigan University, Kalamazoo, MI, 49008, USA

    Maarten J. Vonhof

Authors
  1. Lorelei E. Patrick
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jan M. Just
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Maarten J. Vonhof
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Lorelei E. Patrick.

Electronic supplementary material

Below is the link to the electronic supplementary material.

12686_2016_613_MOESM1_ESM.xls

Supplementary material 1. Table S1: Names, sequences, and information for probes tested in this study. FN= false negative; FP= false positive; TP = true positive; TP & FP = a probe that fluoresced for the target species and one or more additional species; NA= probes designed for species for which we did not have DNA. (XLS 53 KB)

12686_2016_613_MOESM2_ESM.xlsx

Supplementary material 2. Table S2: Probe specificity matrix indicating the species for which each probe fluoresces. (XLSX 17 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Patrick, L.E., Just, J.M. & Vonhof, M.J. Non-invasive bat species identification from mixed-species samples using a microarray. Conservation Genet Resour 9, 139–149 (2017). https://doi.org/10.1007/s12686-016-0613-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12686-016-0613-0

Keywords

Search

Navigation