Cyanobacteria drive community composition and functionality in rock-soil interface communities

Molecular Ecology

Volumn 24, Issue 4, 2015, Pages 812-821

  Valverde, Angel ^a   Makhalanyane, Thulani P ^a   Seely, Mary ^b   Cowan, Don A ^a  

^a UNIVERSITY OF PRETORIA   (South Africa)

^b DESERT RESEARCH FOUNDATION OF NAMIBIA   (Namibia)

Author keywords

cyanobacteria; heterotrophic bacteria; hypoliths; metazoa; network analysis; protozoa

Indexed keywords

BACTERIA (MICROORGANISMS); CYANOBACTERIA; METAZOA; PROTISTA; PROTOZOA;

BACTERIAL DNA; RNA 16S;

BACTERIUM; CLASSIFICATION; CYANOBACTERIUM; DESERT CLIMATE; ECOSYSTEM; FOOD CHAIN; GENETICS; HETEROTROPHY; MICROBIOLOGY; NAMIBIA; RESTRICTION FRAGMENT LENGTH POLYMORPHISM;

BACTERIA; CYANOBACTERIA; DESERT CLIMATE; DNA, BACTERIAL; ECOSYSTEM; FOOD CHAIN; HETEROTROPHIC PROCESSES; NAMIBIA; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RNA, RIBOSOMAL, 16S; SOIL MICROBIOLOGY;

EID: 84923087940     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.13068     Document Type: Article

References (51)

1. Bader GD, Hogue CW (2003) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics, 4, 2.
2. Baho DL, Peter H, Tranvik LJ (2012) Resistance and resilience of microbial communities-temporal and spatial insurance against perturbations. Environmental Microbiology, 14, 2283-2292.
3. Barberan A, Bates ST, Casamayor EO, Fierer N (2011) Using network analysis to explore co-occurrence patterns in soil microbial communities. The ISME Journal, 6, 343-351.
4. Bates ST, Clemente JC, Flores GE et al. (2013) Global biogeography of highly diverse protistan communities in soil. The ISME Journal, 7, 652-659.
5. Berry D, Widder S (2014) Deciphering microbial interactions and detecting keystone species with co-occurrence networks. Frontiers in Microbiology, 5, 219.
6. Bissett A, Brown MV, Siciliano SD, Thrall PH (2013) Microbial community responses to anthropogenically induced environmental change: towards a systems approach. Ecology Letters, 16, 128-139.
7. ter Braak CJF, Schaffers AP (2004) Co-correspondence analysis: a new ordination method to relate two community compositions. Ecology, 85, 834-846.
8. Cardinale BJ, Matulich KL, Hooper DU et al. (2011) The functional role of producer diversity in ecosystems. American Journal of Botany, 98, 572-592.
9. Cardinale BJ, Duffy JE, Gonzalez A et al. (2012) Biodiversity loss and its impact on humanity. Nature, 486, 59-67.
10. Caruso T, Chan Y, Lacap DC, Lau MCY, McKay CP, Pointing SB (2011) Stochastic and deterministic processes interact in the assembly of desert microbial communities on a global scale. The ISME Journal, 5, 1406-1413.
11. Cary SC, McDonald IR, Barrett JE, Cowan DA (2010) On the rocks: the microbiology of Antarctic Dry Valley soils. Nature Reviews Microbiology, 8, 129-138.
12. Chaffron S, Rehrauer H, Pernthaler J, von Mering C (2010) A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Research, 20, 947-959.
13. Chan Y, Lacap DC, Lau MCY et al. (2012) Hypolithic microbial communities: between a rock and a hard place. Environmental Microbiology, 14, 2272-2282.
14. Chan Y, Van Nostrand JD, Zhou J, Pointing SB, Farrell RL (2013) Functional ecology of an Antarctic Dry Valley. Proceedings of the National Academy of Sciences of the United States of America, 110, 8990-8995.
15. Chow CET, Kim DY, Sachdeva R, Caron DA, Fuhrman JA (2014) Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists. The ISME Journal, 8, 816-829.
16. Clarke KR (1993) Non-parametric multivariate analyses of changes in community structure. Australian Journal of Ecology, 18, 117-143.
17. Cowan DA, Sohm JA, Makhalanyane TP et al. (2011) Hypolithic communities: important nitrogen sources in Antarctic desert soils. Environmental Microbiology Reports, 3, 581-586.
18. Csárdi G, Nepusz T (2006) The igraph software package for complex network research. International Journal Complex Systems, 1695, 1-9.
19. Eckardt FD, Soderberg K, Coop LJ et al. (2013) The nature of moisture at Gobabeb, in the central Namib Desert. Journal of Arid Environments, 93, 7-19.
20. Euringer K, Lueders T (2008) An optimised PCR/T-RFLP fingerprinting approach for the investigation of protistan communities in groundwater environments. Journal Microbiology Methods, 75, 262-268.
21. Faust K, Raes J (2012) Microbial interactions: from networks to models. Nature Reviews Microbiology, 10, 538-550.
22. Faust K, Sathirapongsasuti JF, Izard J et al. (2012) Microbial co-occurrence relationships in the human microbiome. PloS Computational Biology, 8, e1002606.
23. Fierer N, Leff JW, Adams BJ et al. (2012) Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proceedings of the National Academy of Sciences of the United States of America, 109, 21390-21395.
24. Fonseca VG, Carvalho GR, Sung W et al. (2010) Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nature Communications, 1, 98.
25. Garcia-Pichel F, Loza V, Marusenko Y, Mateo P, Potrafka RM (2013) Temperature drives the continental-scale distribution of key microbes in topsoil communities. Science, 340, 1574-1577.
26. Garland JL, Mills AL, Young JS (2001) Relative effectiveness of kinetic analysis vs single point readings for classifying environmental samples based on community-level physiological profiles (CLPP). Soil Biology & Biochemistry, 33, 1059-1066.
27. Jones CG, Lawton JH, Shachak M (1994) Organisms as ecosystem engineers. Oikos, 69, 373-386.
28. Lewinsohn TM, Prado PI, Jordano P, Bascompte J, Olesen JM (2006) Structure in plant-animal interaction assemblages. Oikos, 113, 174-184.
29. Lozupone CA, Knight R (2007) Global patterns in bacterial diversity. Proceedings of the National Academy of Sciences of the United States of America, 104, 11436-11440.
30. Maechler M, Rousseeuw P, Struyf A, Hubert M, Hornik K (2014) cluster: cluster analysis basics and extensions, R package version 1.15.1, http://CRAN.R-project.org/package=cluster edn.
31. Makhalanyane TP, Valverde A, Birkeland N et al. (2013a) Evidence for successional development in Antarctic hypolithic bacterial communities. The ISME Journal, 7, 2080-2090.
32. Makhalanyane TP, Valverde A, Lacap DC et al. (2013b) Evidence of species recruitment and development of hot desert hypolithic communities. Environmental Microbiology Reports, 5, 219-224.
33. Oksanen J, Blanchet FG, Kindt R et al. (2013) Vegan: Community Ecology Package, R package version 2.0-2, http://CRAN.R-project.org/package=vegan edn.
34. Olesen JM, Bascompte J, Dupont YL, Jordano P (2007) The modularity of pollination networks. Proceedings of the National Academy of Sciences of the United States of America, 104, 19891-19896.
35. Pointing SB, Belnap J (2012) Microbial colonization and controls in dryland systems. Nature Reviews Microbiology, 10, 551-562.
36. Pointing SB, Chan Y, Lacap DC et al. (2009) Highly specialized microbial diversity in hyper-arid polar desert. Proceedings of the National Academy of Sciences of the United States of America, 106, 19964-19969.
37. Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics, 12, 38.
38. Rooney N, McCann KS (2012) Integrating food-web diversity, structure and stability. Trends in Ecology & Evolution, 27, 40-46.
39. Saavedra S, Stouffer DB, Uzzi B, Bascompte J (2011) Strong contributors to network persistence are the most vulnerable to extinction. Nature, 478, 233-235.
40. Saito R, Smoot ME, Ono K et al. (2012) A travel guide to Cytoscape plugins. Nature Methods, 9, 1069-1076.
41. Schaffers AP, Raemakers IP, Sykora KV, Ter Braak CJF (2008) Arthropod assemblages are best predicted by plant species composition. Ecology, 89, 782-794.
42. Scherber C, Eisenhauer N, Weisser WW et al. (2010) Bottom-up effects of plant diversity on multitrophic interactions in a biodiversity experiment. Nature, 468, 553-556.
43. Schloss PD, Westcott SL, Ryabin T et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology, 75, 7537-7541.
44. Schloss PD, Gevers D, Westcott SL (2011) Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE, 6, e27310.
45. Simpson GL (2009) cocorresp: Co-correspondence analysis ordination methods (R package version 0.1-9) http://cran.r-project.org/package=cocorresp. edn.
46. Steele JA, Countway PD, Xia L et al. (2011) Marine bacterial, archaeal and protistan association networks reveal ecological linkages. The ISME Journal, 5, 1414-1425.
47. Stomeo F, Valverde A, Pointing SB et al. (2013) Hypolithic and soil microbial community assembly along an aridity gradient in the Namib Desert. Extremophiles, 17, 329-337.
48. Tracy CR, Streten-Joyce C, Dalton R et al. (2010) Microclimate and limits to photosynthesis in a diverse community of hypolithic cyanobacteria in northern Australia. Environmental Microbiology, 12, 592-607.
49. Valverde A, Tuffin M, Cowan DA (2012) Biogeography of bacterial communities in hot springs: A focus on the actinobacteria. Extremophiles, 16, 669-679.
50. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology, 73, 5261-5267.
51. Wang J, Shen J, Wu Y et al. (2013) Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes. The ISME Journal, 7, 1310-1321.