71. Liang T, Ji H, Lian L, Wu T, Gu W, et al. (2010) A rapid assay for simultaneous detection of Spiroplasma eriocheiris and white spot syndrome virus in Procambarus clarkii by multiplex PCR. Lett Appl Microbiol 51: 532–538. 72. Brown BV (1993) Taxonomy and Preliminary Phylogeny of the Parasitic Genus Apocephalus, Subgenus Mesophora (Diptera, Phoridae). Systematic Entomol- ogy 18: 191–230. 73. Core A, Runckel C, Ivers J, Quock C, DeNault S, et al. (2011) An emerging threat to honey bees from parasitic phorid flies. San FranciscoCA: San Francisco State University. 74. Otterstatter MC, Whidden TL, Owen RE (2002) Contrasting frequencies of parasitism and host mortality among phorid and conopid parasitoids of bumble-bees. Ecological Entomology 27: 229–237. 75. Johnson RM, Evans JD, Robinson GE, Berenbaum MR (2009) Changes in transcript abundance relating to colony collapse disorder in honey bees (Apis mellifera). P Natl Acad Sci Usa 106: 14790–14795. 76. Welch A, Drummond F, Tewari S, Averill A, Burand JP (2009) Presence and prevalence of viruses in local and migratory honeybees (Apis mellifera) in Massachusetts. Appl Environ Microbiol 75: 7862–7865. 77. Genersch E, von der Ohe W, Kaatz H, Schroeder A, Otten C, et al. (2010) The German bee monitoring project: a long term study to understand periodically high winter losses of honey bee colonies. Apidologie 41: 332–352. 78. Tentcheva D, Gauthier L, Zappulla N, Dainat B, Cousserans F, et al. (2004) Prevalence and seasonal variations of six bee viruses in Apis mellifera L. and Varroa destructor mite populations in France. Appl Environ Microbiol 70: 7185–7191. 79. Bourgeois AL, Rinderer TE, Beaman LD, Danka RG (2010) Genetic detection and quantification of Nosema apis and N. ceranae in the honey bee. J Invertebr Pathol 103: 53–58. 80. Gisder S, Hedtke K, Mo¨ckel N, Frielitz M-C, Linde A, et al. (2010) Five-year cohort study of Nosema spp. in Germany: does climate shape virulence and assertiveness of Nosema ceranae? Appl Environ Microbiol 76: 3032–3038. 81. Paxton RJ, Klee J, Korpela S, Fries I (2007) Nosema ceranae has infected Apis mellifera in Europe since at least 1998 and may be more virulent than Nosema apis. Apidologie 38: 558–565. 82. Hamiduzzaman MM, Guzman-Novoa E, Goodwin PH (2010) A multiplex PCR assay to diagnose and quantify Nosema infections in honey bees (Apis mellifera). J Invertebr Pathol. 83. Cameron SA, Lozier JD, Strange JP, Koch JB, Cordes N, et al. (2011) Patterns of widespread decline in North American bumble bees. P Natl Acad Sci Usa. 84. Foster LJ (2011) Interpretation of data underlying the link between CCD and an invertebrate iridescent virus. Mol Cell Proteomics. 85. Knudsen G, Chalkley RJ (2011) Commentary on Bromenshenk et al: The Effect of Using an Inappropriate Protein Database for Proteomic Data Analysis. submitted PLoS ONE. Temporal Analysis of the Honey Bee Microbiome 86. Bromenshenk JJ, Henderson CB, Wick CH, Stanford MF, Zulich AW, et al. (2010) Iridovirus and Microsporidian Linked to Honey Bee Colony Decline. Plos One 5: e13181. 87. Bailey L, Ball BV, Perry JN (1981) The Prevalence of Viruses of Honey Bees in Britain. Annals of Applied Biology 97: 109–118. 88. Singh R, Levitt AL, Rajotte EG, Holmes EC, Ostiguy N, et al. (2010) RNA Viruses in Hymenopteran Pollinators: Evidence of Inter-Taxa Virus Trans- mission via Pollen and Potential Impact on Non-Apis Hymenopteran Species. PLoS ONE 5: e14357. 89. DeGrandi-Hoffman G, Chen Y, Huang E, Huang MH (2010) The effect of diet on protein concentration, hypopharyngeal gland development and virus load in worker honey bees (Apis mellifera L.). J Insect Physiol 56: 1184–1191. 90. Maori E, Paldi N, Shafir S, Kalev H, Tsur E, et al. (2009) IAPV, a bee-affecting virus associated with Colony Collapse Disorder can be silenced by dsRNA ingestion. Insect Mol Biol 18: 55–60. 91. Chen Y, Evans JD (2007) Historical presence of Israeli acute paralysis virus in the United States. Am Bee J 147: 1027–1028. 92. Palacios G, Hui J, Quan PL, Kalkstein A, Honkavuori KS, et al. (2008) Genetic analysis of Israel acute paralysis virus: Distinct clusters are circulating in the United States. J Virol 82: 6209–6217. 93. Chen YP, Higgins JA, Feldlaufer MF (2005) Quantitative real-time reverse transcription-PCR analysis of deformed wing virus infection in the honeybee (Apis mellifera L.). Applied and Environmental Microbiology 71: 436–441. 94. Shen MQ, Yang XL, Cox-Foster D, Cui LW (2005) The role of varroa mites in infections of Kashmir bee virus (KBV) and deformed wing virus (DWV) in honey bees. Virology 342: 141–149. 95. Bailey L, Woods RD (1974) Three previously undescribed viruses from the honey bee. Journal of General Virology 25: 175–186. 96. Bailey L, Carpenter JM, Govier DA, Woods RD (1980) Bee Virus-Y. Journal of General Virology 51: 405–407. 97. Lommel SA, Morris TJ, Pinnock DE (1985) Characterization of nucleic acids associated with Arkansas bee virus. Intervirology 23: 199–207. 98. Harrap KA, Payne CC (1979) The structural properties and identification of insect viruses. Adv Virus Res 25: 273–355. 99. Yourth CP, Brown MJF, Schmid-Hempel P (2008) Effects of natal and novel Crithidia bombi (Trypanosomatidae) infections on Bombus terrestris hosts. Insect Soc 55: 86–90. 100. Eisen MB, Brown PO (1999) DNA arrays for analysis of gene expression. Meth Enzymol 303: 179–205. 101. Engel JC, Parodi AJ (1985) Trypanosoma cruzi cells undergo an alteration in protein N-glycosylation upon differentiation. J Biol Chem 260: 10105–10110. 102. Drummond AJ, Ashton B, Buxton SCM, Cooper A, Heled J, et al. (2010) Geneious v5.1, Available from http://www.geneious.com. 103. Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, et al. (2007) Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res 35: W71–74. PLoS ONE | www.plosone.org 18 June 2011 | Volume 6 | Issue 6 | e20656