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New Insights into the Microbial Diversity of Polar Desert Soils: A Biotechnological Perspective

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Microbial Ecology of Extreme Environments

Abstract

Microorganisms represent the most abundant cold-adapted life-forms on earth. Far from just surviving, microorganisms appear to be thriving in cold climates, with microbial richness present in polar soils often in line with temperate soils. Recent advances in molecular techniques have allowed the true extent of global microbial diversity to be revealed. Antarctica in particular, has been found to harbour diverse and unique microbial populations comprise of high proportions of Chloroflexi, Actinobacteria, and unknown, previously uncultured taxa. Microorganisms have been the targets for bioprospecting for many years but efforts have thus far largely focused on easily obtainable temperate organisms, readily cultured within the laboratory. The extreme conditions that push the limits of life within cold environments leads to the evolution of unique physiologies and functional capabilities. Actinobacteria are well known to be prolific producers of useful natural products. Their high relative abundance along with the plethora of rare and previously unknown organisms highlights the potential for new biotechnological discoveries within cold adapted microorganisms. With limited to no higher organisms, Polar soils also provide ideal model ecosystems to examine the mechanisms driving microbial patterns of distribution. Thus far microbial communities have been found to be largely endemic and exhibit spatial patterns over meter, kilometre, regional and continental scales. While the mechanisms driving the patterns are not completely understood, a number of key biotic and abiotic factors, in particular pH, C/N ratio, NH4 and N concentrations, phosphorus and plant cover, have been identified as influencing polar microbial communities and their survival in these extreme environments. Identifying and understanding key environmental drivers of microbial populations through biogeochemical analysis, structural equation models, microbial co-occurrence models, or space for time substitution studies, are providing the first step towards identifying the distribution of populations with desirable genetic or functional capacity and likewise polar regions that may contain unique communities for protection. At the same time this research is improving our capacity to predict microbial responses to disturbance due to both a changing climate and anthropogenic contamination.

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References

  • AAD (2002) Antarctica environment and weather

    Google Scholar 

  • (AAD), A.A.D (2012) 25.09.15. Available from: http://www.antarctica.gov.au

  • ACIA (2005) Arctic climate impact assessment. In: Symon C, Arris L, Heal B (eds). Cambridge University Press, Cambridge

    Google Scholar 

  • Aislabie JM et al (2004) Hydrocarbon spills on Antarctic soils: effects and management. Environ Sci Technol 38(5):1265–1274

    Article  CAS  PubMed  Google Scholar 

  • AMAP (2011) Arctic Climate Issues 2011: changes in arctic snow, water, ice and permafrost. In: SWIPA 2011 overview report. 2012, arctic monitoring and assessment program (AMAP) Oslo, p 97

    Google Scholar 

  • Amato P (2013) Energy metabolism at low-temperature and frozen conditions in cold-adapted microorganisms. In: Yumoto I (ed). Cold-adapted microorganisms. Caister Academic Press, Norfolk, pp 1–12

    Google Scholar 

  • Arbel J et al (2015) Application of a Bayesian nonparametric model to derive toxicity estimates based on the response of Antarctic microbial communities to fuel-contaminated soil. Ecol Evol 5(13):2633–2645

    Article  PubMed  PubMed Central  Google Scholar 

  • Ayuso-Sacido A, Genilloud O (2004) New PCR primers for the screening of NRPS and PKS-I systems in actinomycetes: detection and distribution of these biosynthetic gene sequences in major taxonomic groups. Microb Ecol 49:10–24

    Article  PubMed  Google Scholar 

  • Babalola OO et al (2009) Phylogenetic analysis of actinobacterial populations associated with Antarctic Dry Valley mineral soils. Environ Microbiol 11(3):566–576

    Article  CAS  PubMed  Google Scholar 

  • Bargagli R (2008) Environmental contamination in Antarctic ecosystems. Sci Total Environ 400(1–3):212–226

    Article  CAS  PubMed  Google Scholar 

  • Benaud N (2014) Polar soil actinobacteria: a potential source of novel antibiotic secondary metabolites (Honours thesis) UNSW Australia

    Google Scholar 

  • Berdy J (2005) Bioactive microbial metabolites. J Antibiot (Tokyo) 58(1):1–26

    Article  CAS  Google Scholar 

  • Bissett A et al (2013) Microbial community responses to anthropogenically induced environmental change: towards a systems approach. Ecol Lett 16(suppl 1):128–139

    Google Scholar 

  • Blanc G et al (2012) The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation. Genome Biol 13(5):R39

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Blaud A, Phoenix GK, Osborn AM (2015) Variation in bacterial, archaeal and fungal community structure and abundance in high Arctic tundra soil. Polar Biol 38(7):1009–1024

    Article  Google Scholar 

  • Brage BH et al (2014) Warmer and wetter winters: characteristics and implications of an extreme weather event in the High Arctic. Environ Res Lett 9(11):114021

    Article  Google Scholar 

  • Braun C et al (2014) Environmental assessment and management challenges of the Fildes Peninsula region, in Antarctic futures. Springer, New York, pp 169–191

    Google Scholar 

  • Butler MS, Blaskovich MA, Cooper MA (2013) Antibiotics in the clinical pipeline in 2013. J Antibiot (Tokyo) 66(10):571–591

    Article  CAS  Google Scholar 

  • Carvajal F (1947) Screening tests for antibiotics. Mycologia 39(1):28–130

    Article  Google Scholar 

  • Cary SC et al (2010) On the rocks: the microbiology of Antarctic dry valley soils. Nat Rev Microbiol 8(2):129–138

    Article  CAS  PubMed  Google Scholar 

  • Casanueva A, Tuffin M, Cary C, Cowan DA (2010) Molecular adaptations to psychrophily: the impact of ‘omic’ technologies. Trends Microbiol 18:374–381

    Google Scholar 

  • Chan Y et al (2013) Functional ecology of an Antarctic dry valley. Proc Natl Acad Sci 110(22):8990–8995

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Charlop-Powers Z et al (2014) Chemical-biogeographic survey of secondary metabolism in soil. Proc Natl Acad Sci 111(10):3757–3762

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Charlop-Powers Z et al (2015) Global biogeographic sampling of bacterial secondary metabolism. eLife 4:e05048

    Google Scholar 

  • Chong CW et al (2011) Assessment of soil bacterial communities on Alexander Island (in the maritime and continental Antarctic transitional zone). Polar Biol 35(3):387–399

    Article  Google Scholar 

  • Chu H et al (2010) Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes. Environ Microbiol 12(11):2998–3006

    Article  CAS  PubMed  Google Scholar 

  • Chu H et al (2011) The influence of vegetation type on the dominant soil bacteria, archaea, and fungi in a low arctic tundra landscape. Soil Sci Soc Am J 75(5):1756–1765

    Article  CAS  Google Scholar 

  • Corsaro MM et al (2008) Highly phosphorylated core oligosaccaride structures from cold-adapted Psychromonas arctica. Chem Eur J 14(30):9368–9376

    Google Scholar 

  • Cowan DA et al (2011) Non-indigenous microorganisms in the Antarctic: assessing the risks. Trends Microbiol 19(11):540–548

    Article  CAS  PubMed  Google Scholar 

  • De Castro A, Fernandes G, Franco O (2014) Insights into novel antimicrobial compounds and antibiotic resistance genes from soil metagenomes. Front Microbiol 5

    Google Scholar 

  • de la Torre JR et al (2003) Microbial diversity of cryptoendolithic communities from the McMurdo dry valleys, Antarctica. Appl Environ Microbiol 69(7):3858–3867

    Article  PubMed  PubMed Central  Google Scholar 

  • Dobinski W (2011) Permafrost. Earth Sci Rev 108(3–4):158–169

    Article  Google Scholar 

  • Encheva-Malinova M et al (2014) Antibacterial potential of streptomycete strains from Antarctic soils. Biotechnol Biotechnol Equip 28(4):721–727

    Article  PubMed  PubMed Central  Google Scholar 

  • Ferrari BC et al (2008) Cultivating previously uncultured soil bacteria using a soil substrate membrane system. Nat Protoc 3(8):1261–1269

    Article  CAS  PubMed  Google Scholar 

  • Ferrari BC, Zhang C, van Dorst J (2011) Recovering greater fungal diversity from pristine and diesel fuel contaminated sub-antarctic soil through cultivation using both a high and a low nutrient media approach. Front Microbiol 2:217

    Article  PubMed  PubMed Central  Google Scholar 

  • Ferrari BC et al (2015) Geological connectivity drives microbial community structure and connectivity in polar, terrestrial ecosystems. Environ Microbiol 2015: p n/a-n/a

    Google Scholar 

  • Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 103(3):626–631

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Finlay BJ (2002) Global dispersal of free-living microbial eukaryote species. Science 296(5570):1061–1063

    Article  CAS  PubMed  Google Scholar 

  • Førland E, Hanssen-Bauer I (2001) Changes in temperature and precipitation in the Norwegian Arctic during the 20th century. In: Detecting and modelling regional climate change. Springer, New York, pp 153–161

    Google Scholar 

  • Frank-Fahle BA et al (2014) Microbial functional potential and community composition in permafrost-affected soils of the NW Canadian Arctic. PLoS ONE 9(1):e84761

    Article  PubMed  PubMed Central  Google Scholar 

  • Ganzert L et al (2011) The impact of different soil parameters on the community structure of dominant bacteria from nine different soils located on Livingston Island, South Shetland Archipelago, Antarctica. FEMS Microbiol Ecol 76(3):476–491

    Article  CAS  PubMed  Google Scholar 

  • Ganzert L, Bajerski F, Wagner D (2014) Bacterial community composition and diversity of five different permafrost-affected soils of Northeast Greenland. FEMS Microbiol Ecol 89(2):426–441

    Article  CAS  PubMed  Google Scholar 

  • Gesheva V (2010) Production of antibiotics and enzymes by soil microorganisms from the windmill islands region, Wilkes Land, East Antarctica. Polar Biol 33(10):1351–1357

    Article  Google Scholar 

  • Geyer KM et al (2013) Environmental controls over bacterial communities in polar desert soils. Ecosphere 4(10):1–17

    Article  Google Scholar 

  • Geyer KM et al (2014) Bacterial community composition of divergent soil habitats in a polar desert. FEMS Microbiol Ecol 89(2):490–494

    Article  CAS  PubMed  Google Scholar 

  • Gittel A et al (2014) Distinct microbial communities associated with buried soils in the siberian tundra. ISME J 8(4):841–853

    Article  CAS  PubMed  Google Scholar 

  • Gobet A, Boetius A, Ramette A (2014) Ecological coherence of diversity patterns derived from classical fingerprinting and next generation sequencing techniques. Environ Microbiol 16(9):2672–2681

    Article  CAS  PubMed  Google Scholar 

  • Grayston SJ et al (2004) Assessing shifts in microbial community structure across a range of grasslands of differing management intensity using CLPP, PLFA and community DNA techniques. Appl Soil Ecol 25(1):63–84

    Article  Google Scholar 

  • Guglielmin M (2012) Advances in permafrost and periglacial research in Antarctica: a review. Geomorphology 155–156:1–6

    Article  Google Scholar 

  • Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68(4):669–685

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Heal OW (1999) Looking North: current issues in arctic soil ecology. Appli Soil Ecol 11(2–3):107–109

    Article  Google Scholar 

  • Hemmings AD (2010) Does bioprospecting risk moral hazard for science in the Antarctic Treaty System?

    Google Scholar 

  • Hinsa-Leasure S, Bakermans C (2013) Diversity of bacteria in Permafrost, in cold-adapted microorganisms. In: Yumoto I (ed). Caister Academic Press, Norfolk, pp 1–12

    Google Scholar 

  • Hodkinson ID, Wookey PA (1999) Functional ecology of soil organisms in tundra ecosystems: towards the future. Appl Soil Ecol 11(2–3):111–126

    Article  Google Scholar 

  • Hoj L, Olsen RA, Torsvik VL (2005) Archaeal communities in high Arctic wetlands at Spitsbergen, Norway (78 degrees N) as characterized by 16S rRNA gene fingerprinting. FEMS Microbiol Ecol 53(1):89–101

    Article  CAS  PubMed  Google Scholar 

  • Høj L et al (2006) Effects of water regime on archaeal community composition in Arctic soils. Environ Microbiol 8(6):984–996

    Article  PubMed  Google Scholar 

  • Hopwood DA (2007) Streptomyces in nature and medicine. Oxford University Press, New York

    Google Scholar 

  • Hughes KA, Nobbs SJ (2004) Long-term survival of human faecal microorganisms on the Antarctic Peninsula. Antarct Sci 16(03):293–297

    Article  Google Scholar 

  • Hughes KA et al (2011) Untouched Antarctica: mapping a finite and diminishing environmental resource. Antarct Sci 23(06):537–548

    Article  Google Scholar 

  • Hughes KA, Cowan DA, Wilmotte A (2015) Protection of Antarctic microbial communities—‘out of sight, out of mind’. Front Microbiol 6:151

    Article  PubMed  PubMed Central  Google Scholar 

  • Jansson JK, Tas N (2014) The microbial ecology of permafrost. Nat Rev Microbiol 12(6):414–425

    Article  CAS  PubMed  Google Scholar 

  • Ji M et al (2015) Microbial diversity at Mitchell Peninsula, Eastern Antarctica: a potential biodiversity “hotspot”. Polar Biol 1–13

    Google Scholar 

  • Ji M (2016) Exploring microbial dark matter in east Antarctic soils (Doctoral dissertation). Available from: http://handle.unsw.edu.au/1959.4/51775

  • Kim HM et al (2014) Bacterial community structure and soil properties of a subarctic tundra soil in Council, Alaska. FEMS Microbiol Ecol 89(2):465–475

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lauber CL et al (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75(15):5111–5120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee LH et al (2012a) Molecular characterization of Antarctic actinobacteria and screening for antimicrobial metabolite production. World J Microbiol Biotechnol 28(5):2125–2137

    Article  CAS  PubMed  Google Scholar 

  • Lee CK et al (2012b) The inter-valley soil comparative survey: the ecology of dry valley edaphic microbial communities. ISME J 6(5):1046–1057

    Article  CAS  PubMed  Google Scholar 

  • Lipson DA et al (2013) Metagenomic insights into Anaerobic metabolism along an Arctic peat soil profile. PLoS ONE 8(5):e64659

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Madeleine G et al (2009) Forty years of weather data to understand recent climate change in the arctic (Svalbard, 79°N). IOP Conf Ser Earth Environ Sci 6(1):012009

    Article  Google Scholar 

  • Männistö MK, Tiirola M, Häggblom MM (2007) Bacterial communities in Arctic fjelds of Finnish Lapland are stable but highly pH-dependent. FEMS Microbiol Ecol 59(2):452–465

    Article  PubMed  Google Scholar 

  • Metsä-Ketelä M et al (1999) An efficient approach for screening minimal PKS genes from streptomyces. FEMS Microbiol Lett 180(1):1–6

    Article  PubMed  Google Scholar 

  • Metsä-Ketelä M et al (2002) Molecular evolution of aromatic polyketides and comparative sequence analysis of Polyketide Ketosynthase and 16S ribosomal DNA genes from various streptomyces species. Appl Environ Microbiol 68(9):4472–4474

    Article  PubMed  PubMed Central  Google Scholar 

  • Moyer CL, Morita RY (2001) Psychrophiles and Psychrotrophs. In: eLS. Wiley, New York

    Google Scholar 

  • Neufeld JD, Mohn WW (2005) Unexpectedly high bacterial diversity in arctic tundra relative to boreal forest soils, revealed by serial analysis of ribosomal sequence tags. Appl Environ Microbiol 71(10):5710–5718

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Newsham KK et al (2016) Relationship between soil fungal diversity and temperature in the maritime Antarctic. Nat Clim Change 6(2):182–186

    Google Scholar 

  • Nobu MK et al (2015) Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor. ISME J 9(8):1710–1722

    Article  PubMed  PubMed Central  Google Scholar 

  • Pearce DA et al (2012) Metagenomic analysis of a southern maritime antarctic soil. Front Microbiol 3:403

    Article  PubMed  PubMed Central  Google Scholar 

  • Peat HJ, Clarke A, Convey P (2007) Diversity and biogeography of the Antarctic flora. J Biogeogr 34(1):132–146

    Article  Google Scholar 

  • Peters GP et al (2011) Future emissions from shipping and petroleum activities in the Arctic. Atmos Chem Phys 11(11):5305–5320

    Article  CAS  Google Scholar 

  • Rice C et al (2015) Bacterial lipoteichoic acid enhances cryosurvival. Extremophiles Life Under Extreme Conditions 19(2):297–305

    Google Scholar 

  • Rinke C et al (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature 499(7459):431–437

    Article  CAS  PubMed  Google Scholar 

  • Roesch LFW et al (2012) Soil bacterial community abundance and diversity in ice-free areas of Keller Peninsula, Antarctica. Appl Soil Ecol 61:7–15

    Article  Google Scholar 

  • Rooney-Varga JN et al (2007) Links between archaeal community structure, vegetation type and methanogenic pathway in Alaskan peatlands. FEMS Microbiol Ecol 60(2):240–251

    Article  CAS  PubMed  Google Scholar 

  • Schuur EA et al (2008) Vulnerability of permafrost carbon to climate change: implications for the global carbon cycle. Bioscience 58(8):701–714

    Article  Google Scholar 

  • Schuur E et al (2015) Climate change and the permafrost carbon feedback. Nature 520(7546):171–179

    Article  CAS  PubMed  Google Scholar 

  • Shaw JD et al (2014) Antarctica’s protected areas are inadequate, unrepresentative, and at risk. PLoS Biol 12(6):e1001888

    Article  PubMed  PubMed Central  Google Scholar 

  • Shekh RM et al (2010) Antifungal activity of Arctic and Antarctic bacteria isolates. Polar Biol 34(1):139–143

    Article  Google Scholar 

  • Shi Y et al (2015) Vegetation-associated impacts on Arctic tundra bacterial and microeukaryotic communities. Appl Environ Microbiol 81(2):492–501

    Article  PubMed  PubMed Central  Google Scholar 

  • Siciliano SD et al (2014) Soil fertility is associated with fungal and bacterial richness, whereas pH is associated with community composition in polar soil microbial communities. Soil Biol Biochem 78:10–20

    Article  CAS  Google Scholar 

  • Siciliano SD et al (2014) Fertility controls richness but pH controls composition in polar microbial communities. Soil Biol Biochem

    Google Scholar 

  • Staddon WJ et al (1998) Soil microbial diversity and community structure across a climatic gradient in western Canada. Biodivers Conserv 7(8):1081–1092

    Google Scholar 

  • Stewart KJ, Snape I, Siciliano SD (2012) Physical, chemical and microbial soil properties of frost boils at browning Peninsula, Antarctica. Polar Biol 35(3):463–468

    Article  Google Scholar 

  • Terauds A et al (2012) Conservation biogeography of the Antarctic. Divers Distrib 18(7):726–741

    Article  Google Scholar 

  • Tin T, Fleming ZL, Hughes KA, Ainley DG, Convey P, Moreno CA, Pfeiffer S, Scott J, Snape I (2009) Impacts of local human activities in the Antarctic environment. Antarct Sci 21:3–33

    Article  Google Scholar 

  • Turner J et al (2005) Antarctic climate change during the last 50 years. Int J Climatol 25(3):279–294

    Article  Google Scholar 

  • Tytgat B et al (2014) Bacterial diversity assessment in Antarctic terrestrial and aquatic microbial mats: a comparison between bidirectional pyrosequencing and cultivation. PLoS ONE 9(6):e97564

    Article  PubMed  PubMed Central  Google Scholar 

  • van Dorst J et al (2014) Bacterial targets as potential indicators of diesel fuel toxicity in subantarctic soils. Appl Environ Microbiol 80(13):4021–4033

    Article  PubMed  PubMed Central  Google Scholar 

  • Van Horn DJ et al (2014) Soil microbial responses to increased moisture and organic resources along a salinity gradient in a polar desert. Appl Environ Microbiol 80(10):3034–3043

    Article  PubMed  PubMed Central  Google Scholar 

  • Willig MR, Kaufman DM, Stevens RD (2003) latitudinal gradients of biodiversity: pattern, process, scale, and synthesis. Annu Rev Ecol Evol Syst 34(1):273–309

    Article  Google Scholar 

  • Woodhouse JN, Fan L, Brown MV, Thomas T, Neilan BA (2013) Deep sequencing of non-ribosomal peptide synthetases and polyketide synthases from the microbiomes of Australian marine sponges. The ISME J 7:1842–1851

    Google Scholar 

  • Yergeau E et al (2007) Size and structure of bacterial, fungal and nematode communities along an Antarctic environmental gradient. FEMS Microbiol Ecol 59(2):436–451

    Article  CAS  PubMed  Google Scholar 

  • Yergeau E et al (2010) The functional potential of high Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses. ISME J 4(9):1206–1214

    Article  CAS  PubMed  Google Scholar 

  • Yi Pan S (2013) Diversity and bioactivity of actinomycetes from Signy Island terrestrial soils, maritime Antarctic. Adv Polar Sci 24(4):208–212

    Article  Google Scholar 

  • Zeglin LH et al (2009) Landscape distribution of microbial activity in the McMurdo dry valleys: linked biotic processes, hydrology, and geochemistry in a cold desert ecosystem. Ecosystems 12(4):562–573

    Article  CAS  Google Scholar 

  • Zhao J, Yang N, Zeng R (2008) Phylogenetic analysis of type I polyketide synthase and nonribosomal peptide synthetase genes in Antarctic sediment. Extremophiles 12(1):97–105

    Article  CAS  PubMed  Google Scholar 

  • Zhao J et al (2011) Phylogenetic diversity of Type I polyketide synthase genes from sediments of Ardley Island in Antarctica. Acta Oceanol Sinica 30(6):104–111

    Article  Google Scholar 

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van Dorst, J., Benaud, N., Ferrari, B. (2017). New Insights into the Microbial Diversity of Polar Desert Soils: A Biotechnological Perspective. In: Chénard, C., Lauro, F. (eds) Microbial Ecology of Extreme Environments. Springer, Cham. https://doi.org/10.1007/978-3-319-51686-8_7

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