Abstract
The McMurdo Dry Valleys of Antarctica support extensive yet cryptic microbial communities but little evidence for ‘top-down’ herbivory control. A question therefore arises as to how standing microbial biomass is regulated. Here, we present results from a survey of soil and rock microbial community metagenomes using the GeoChip microarray that demonstrate antibiotic resistance and phage infection are widespread. We interrogated a range of dry valley locations from maritime to extreme inland sites. Antibiotic resistance genes were identified in three categories: beta-lactamases, tetracycline and vanomycin plus a range of transporter genes. Frequency of recovery generally reflected microbial diversity, with greatest abundance among Halobacteria, Proteobacteria and the photosynthetic bacteria (Chlorobi, Chloroflexi and Cyanobacteria). However, no clear differences between locations and soil/rock communities were apparent. Phage signals were also recovered from all locations in soil and rock communities. The Leviviridae, Myoviridae, Podoviridae and Siphoviridae were ubiquitous . The Corticoviridae occurred only in moisture-sufficient hyporheic soils, the Microviridae occurred only in maritime and hyporheic sites and an unidentified group within the order Caudovirales occurred only at dry inland sites. We postulate that widespread antibiotic resistance indicates potential inter-specific interaction and that phage signals indicate possible ‘bottom-up’ trophic regulation in the dry valleys.
References
Adriaenssens EM, Van Zyl L, De Maayer P et al (2014) Metagenomic analysis of the viral community in Namib Desert hypoliths. Environ Microbiol. doi:10.1111/1462-2920.12528
Arenz BE, Blanchette RA (2011) Distribution and abundance of soil fungi in Antarctica at sites on the Peninsula, Ross Sea Region and McMurdo Dry Valleys. Soil Biol Biochem 43:308–315. doi:10.1016/j.soilbio.2010.10.016
Bahl J, Lau MCY, Smith GJD et al (2011) Ancient origins determine global biogeography of hot and cold desert cyanobacteria. Nat Commun 2:163. doi:10.1038/ncomms1167
Breitbart M, Rohwer F (2005) Here a virus, there a virus, everywhere the same virus? Trends Microbiol 13:278–284. doi:10.1016/j.tim.2005.04.003
Breitbart M, Wegley L, Leeds S et al (2004) Phage community dynamics in hot springs. Appl Environ Microbiol 70:1633–1640. doi:10.1128/AEM.70.3.1633
Broady PA (2005) The distribution of terrestrial and hydro-terrestrial algal associations at three contrasting locations in southern Victoria Land, Antarctica. Algol Stud für Hydrobiol Suppl 118:95–112. doi:10.1127/1864-1318/2006/0118-0095
Caruso T, Chan Y, Lacap DC et al (2011) Stochastic and deterministic processes interact in the assembly of desert microbial communities on a global scale. ISME J 5:1406–1413. doi:10.1038/ismej.2011.21
Cary SC, McDonald IR, Barrett JE, Cowan DA (2010) On the rocks: the microbiology of Antarctic Dry Valley soils. Nat Rev Microbiol 8:129–138. doi:10.1038/nrmicro2281
Chan Y, Van Nostrand JD, Zhou J et al (2013) Functional ecology of an Antarctic Dry Valley. Proc Natl Acad Sci USA 110:8990–8995. doi:10.1073/pnas.1300643110
Cowan DA, Tow LA (2004) Endangered antarctic environments. Annu Rev Microbiol 58:649–690. doi:10.1146/annurev.micro.57.030502.090811
Cowan DA, Pointing SB, Stevens MI et al (2010) Distribution and abiotic influences on hypolithic microbial communities in an Antarctic Dry Valley. Polar Biol 34:307–311. doi:10.1007/s00300-010-0872-2
Cowan DA, Khan N, Pointing SB, Cary SC (2012) Diverse hypolithic refuge communities in the McMurdo Dry Valleys. Antarct Sci 22:714–720. doi:10.1017/S0954102010000507
De La Torre JR, Goebel BM, Friedmann EI, Pace NR (2003) Microbial diversity of cryptoendolithic communities from the McMurdo Dry Valleys, Antarctica. Appl Environ Microbiol 69:3858–3867. doi:10.1128/AEM.69.7.3858-3867.2003
De Los Ríos A, Grube M, Sancho LG et al (2007) Ultrastructural and genetic characteristics of endolithic cyanobacterial biofilms colonizing Antarctic granite rocks. FEMS Microbiol Ecol 59:386–395. doi:10.1111/j.1574-6941.2006.00256.x
De Los Ríos A, Wierzchos J, Ascaso C (2014) The lithic microbial ecosystems of Antarctica’s McMurdo Dry Valleys. Antarct Sci 26:459–477. doi:10.1017/S0954102014000194
Fierer N, Leff JW, Adams BJ et al (2012) Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci USA 109:21390–21395. doi:10.1073/pnas.1215210110
Fraser CI, Terauds A, Smellie J et al (2014) Geothermal activity helps life survive glacial cycles. Proc Natl Acad Sci USA 111:5634–5639. doi:10.1073/pnas.1321437111
Friedmann EI (1982) Endolithic microorganisms in the Antarctic cold desert. Science 215:1045–1053. doi:10.1126/science.215.4536.1045
Golubic S, Friedmann EI, Schneider J (1981) The lithobiontic ecological niche, with special reference to microorganisms. J Sediment Res 51:475–478. doi:10.1306/212f7cb6-2b24-11d7-8648000102c1865d
Hibbing ME, Fuqua C, Parsek MR, Peterson SB (2010) Bacterial competition: surviving and thriving in the microbial jungle. Nat Rev Microbiol 8:15–25. doi:10.1038/nrmicro2259
Hulo C, de Castro E, Masson P et al (2011) ViralZone: a knowledge resource to understand virus diversity. Nucleic Acids Res 39:D576–D582. doi:10.1093/nar/gkq901
Koskella B, Brockhurst MA (2014) Bacteria-phage coevolution as a driver of ecological and evolutionary processes in microbial communities. FEMS Microbiol Rev. doi:10.1111/1574-6976.12072
López-Bueno A, Tamames J, Velázquez D et al (2009) High diversity of the viral community from an Antarctic lake. Science 326:858–861. doi:10.1126/science.1179287
Pointing SB, Belnap J (2012) Microbial colonization and controls in dryland systems. Nat Rev Microbiol 10:551–562. doi:10.1038/nrmicro2831
Pointing SB, Warren-Rhodes KA, Lacap DC, Rhodes KL, McKay CP (2007) Hypolithic community shifts occur as a result of liquid water availability along environmental gradients in China’s hot and cold hyperarid deserts. Environ Microbiol 9:414–424
Pointing SB, Chan Y, Lacap DC et al (2009) Highly specialized microbial diversity in hyper-arid polar desert. Proc Natl Acad Sci USA 106:19964–19969. doi:10.1073/pnas.0908274106
Pointing SB, Bollard-Breen B, Gillman LN (2014) Diverse cryptic refuges for life during glaciation. Proc Natl Acad Sci USA 111:5452–5453. doi:10.1073/pnas.1403594111
Rao S, Chan Y, Lacap DC et al (2011) Low-diversity fungal assemblage in an Antarctic Dry Valleys soil. Polar Biol 35:567–574. doi:10.1007/s00300-011-1102-2
Richter I, Herbold CW, Lee CK et al (2014) Influence of soil properties on archaeal diversity and distribution in the McMurdo Dry Valleys, Antarctica. FEMS Microbiol Ecol 89:347–359. doi:10.1111/1574-6941.12322
Roossinck MJ (2011) The good viruses: viral mutualistic symbioses. Nat Rev Microbiol 9:99–108. doi:10.1038/nrmicro2491
Siebert J, Hirsch P, Hoffmann B et al (1996) Cryptoendolithic microorganisms from Antarctic sandstone of Linnaeus Terrace (Asgard Range): diversity, properties and interactions. Biodivers Conserv 5:1337–1363. doi:10.1007/BF00051982
Wall DH, Virginia RA (1999) Controls on soil biodiversity: insights from extreme environments. Appl Soil Ecol 13:137–150. doi:10.1016/S0929-1393(99)00029-3
Wierzchos J, Ríos ADL, Ascaso C (2012) Microorganisms in desert rocks: the edge of life on Earth. Int Microbiol 15:173–183. doi:10.2436/20.1501.01.170
Wood SA, Rueckert A, Cowan DA, Cary SC (2008) Sources of edaphic cyanobacterial diversity in the Dry Valleys of Eastern Antarctica. ISME J 2:308–320. doi:10.1038/ismej.2007.104
Wynn-Williams DD (1990) Ecological aspects of Antarctic microbiology. Advances in microbial ecology. Springer, New York, pp 71–146
Yergeau E, Kowalchuk GA (2008) Responses of Antarctic soil microbial communities and associated functions to temperature and freeze-thaw cycle frequency. Environ Microbiol 10:2223–2235. doi:10.1111/j.1462-2920.2008.01644.x
Yung CCM, Chan Y, Lacap DC et al (2014) Characterization of Chasmoendolithic Community in Miers Valley, McMurdo Dry Valleys, Antarctica. Microb Ecol 68:351–359. doi:10.1007/s00248-014-0412-7
Zablocki O, van Zyl L, Adriaenssens EM et al (2014) High diversity of tailed phages, eukaryotic viruses and virophage-like elements in the metaviromes of Antarctic soils. Appl Environ Microbiol. doi:10.1128/AEM.01525-14
Acknowledgments
The authors gratefully acknowledge Roberta Farrell and Craig Cary (University for Waikato) for enabling access to field sites. Logistical support was provided by Antarctica New Zealand and the US Antarctic Program.
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Wei, S.T.S., Higgins, C.M., Adriaenssens, E.M. et al. Genetic signatures indicate widespread antibiotic resistance and phage infection in microbial communities of the McMurdo Dry Valleys, East Antarctica. Polar Biol 38, 919–925 (2015). https://doi.org/10.1007/s00300-015-1649-4
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00300-015-1649-4