Fungal metabolic profile dataset was not influenced by long-term in vitro preservation of strains

Abstract

Comparative ecophysiology is highly valuable approach to reveal adaptive traits linked with specific ecological niches. Although long-term in vitro preserved fungal isolates are often used for analyses, only sparse data is available about the effect of such handling on fungal physiology. The purpose of our data is to show the effect of long-term in vitro preservation of fungal strains on their metabolic profiles. This data is related to research paper “Adaptive traits of bark and ambrosia beetle-associated fungi” (Veselská et al., 2019). Biolog MicroPlates™ for Filamentous fungi were used to compare metabolic profiles between freshly isolated and long-term in vitro preserved strains of two Geosmithia species. Additionally, carbon utilization profiles of 35 Geosmithia species were assessed, including plant pathogen G. morbida and three ambrosia species. Data also shows differences in carbon utilization profiles among diverse ecology types presented in the genus Geosmithia.

Specifications Table

Subject area	Microbiology
More specific subject area	Fungal physiology
Type of data	Table, graph
How data was acquired	Biolog MicroPlateTMfor Filamentous fungi, plate reader INFINITE M200 TECAN (Tecan Instrument, Austria) with MAGELLAN software, PAST program
Data format	Analyzed data, Raw data in supplementary material
Experimental factors	Species ecology and time of preservation, i.e. short vs. long-term.
Experimental features	Fungal conidia were inoculated into Biolog MicroPlatesTMfor Filamentous fungi and the absorbance at 750 nm was recorded to assess fungal growth. Comparative ecophysiology and comparison of freshly isolated and long-term in vitro preserved fungal strains were assessed using statistical program PAST.
Data source location	Collection location, plant and beetle hosts are in Table 1
Data accessibility	Data is with this article.
Related research article	Veselská, T., Skelton, J., Kostovčík, M., Hulcr, J., Baldrian, P., Chudíčková, M., Cajthaml, T., Vojtová, T., Garcia-Fraile, P. and Kolařík, M., 2019. Adaptive traits of bark and ambrosia beetle-associated fungi. Fungal Ecology. 41, 165–176.https://doi.org/10.1016/j.funeco.2019.06.005.

Value of the Data •Comparative ecophysiology is valuable tool for tracing of species adaptive traits and identification of potential virulence factors in plant, animal and human pathogenic fungi. Usually, long-term in vitro preserved isolates are used for physiological analysis, but little is known about the effect of such handling on fungal physiology. Presented data investigate the reliability of using the long-term preserved fungal cultures for physiological analysis. •Data disproves negative effect of long-term preservation on fungal metabolic profile, which enables researchers to use such strains for physiological studies. •Data shows metabolic profiles of carbon utilization for most of Geosmithia species which includes also ambrosia fungi and severe phytopathogen G. morbida. •Raw data provides growth values on each carbon source. This is helpful for further identification of adaptive traits of these important species.

1. Data

Biolog MicroPlate™ for Filamentous fungi was used to assess carbon sources utilization profiles of Geosmithia fungi living in symbiosis with bark beetles [1]. Their ecology spans from facultative to obligatory ambrosia symbiosis and from saprotrophic to pathogenic nourishment of severe phytopathogen G. morbida (Table 1). The aims were to test whether metabolic profiles of Geosmithia species are modified by their ecology and whether long-term preservation of strains has effect on their metabolic profiles. The distinct metabolic profiles belonging to particular ecology types are pictured in Fig. 1 and Table S1. The similarity in metabolic profiles of freshly isolated and long-term preserved strains of Geosmithia sp. 5 and G. langdonii is shown in Fig. 1 and Table S1. Raw data containing growth value of individual strains on each carbon source is presented in Table S1. Raw data is helpful for further identification of adaptive traits of important ambrosia and pathogenic species.

Table 1.

List of Geosmithia species.

Species	Ecology type	Strain code	Culture collection	Strain code in Fig. 1	Substrate (mostly as insect vector/plant hosts)	Locality	Year of isolation	Reference
G. sp. 1	PF, G	1_1790	CCF4529	1	Hypoborus ficus/Ficus carica	Azerbaijan, Shaki Rayonu	2006	[6]
G. sp. 2	PF, G	2_1510	CCF4270	2	Scolytus kirschii/Ulmus minor	Italy, Termoli	2004	[6]
G. sp. 4	PF, G	4_1722	CCF4278	4	Pteleobius vittatus F./Ulmus laevis	Czech R., Břeclav	2004	[7]
G. putterillii	PF, G	6_103	CCF3342	6	Scolytus rugulosus/Prunus sp.	Czech R., Velemín	2000	[8]
G. flava	PF, G	7_264	CCF3354	7	Hylesinus fraxini/Fraxinus excelsior	Slovakia, Muráň castle	2002	[8]
G. sp. 8	PF, HWS	8_124	CCF3350	8a	Scolytus intricatus/Quercus sp.	Czech R., Prague	2001	[7]
		8_1712a	CCF4277	8b	Scolytus intricatus/Quercus cerris	Bulgaria, Kardzaly	2005	[7]
		37_1806	CCF4207	8c	Scolytid beatle/Acacia smithii	Australia, Eungella, Credition Hall	2006	[6]
G. sp. 11	PF, G	11_551	CCF3555	11	Scolytus intricatus/Quercus pubescens	Hungary, Vilányi hegy Mts.	2003	[7]
G. sp. 12	PF, HWS	12_284	CCF4300	12a	Ernoporicus fagi/Fagus silvatica	Slovakia, Pieniny National Park	2002	[7]
		12_1632	CCF4274	12b	Hylesinus varius/Fraxinus excelsior	Czech R., Pacov	2005	[7]
G. ulmacea	PF, HWS	13_924	CCF4601	13	Scolytus multistriatus/Ulmus minor	Czech R., Hodonín, Bulhary	2004	[7]
G. obscura	PF, G	17_391	CCF3424	17	Taphrorychus bicolor/Fagus sylvatica	Czech R., Louny, Hřivice	2003	[7]
G. lavendula	PF, G	18_1219	CCF4268	18a	Hypoborus ficus/Ficus carica	Croatia, Dalmatia, Sibenik	2005	[6]
		18_1781	CCF4285	18b	Hypoborus ficus/Ficus carica	Azerbaijan, Baki Sahari, Baku	2006	[6]
G. sp. 19	PF, G	19_1085a	CCF3658	19	Hypoborus ficus/Ficus carica	Italy, Molise, Termoli	2004	[6]
G. sp. 20	PF, G	20_764	CCF4527	20	Phloetribus scarabeoides/Olea europea	Syria, Krak des Chevaliers	2004	[6]
G. sp. 21	PF, G	21_1665	CCF4530	21	Hypoborus ficus/Ficus carica	Spain, Rosal de la Frontera	2005	[6]
G. sp. 22	PF, G	22_739	CCF3645	22	Phloetribus scarabeoides/Olea europea	Jordan, Wadi al Mujib	2004	[6]
G. morbida	HWS, P	41_1218	CCF3879 (CBS 124664)	41a	Pityophthorus juglandis/J. nigra	USA, Colorado, Boulder	2007	[9]
		41_U173	CCF4576	41b	Pityophthorus juglandis/J. nigra	USA, California, Rio Oso	2009	[9]
		41_U1259.55	–	41c	Pityophthorus juglandis/Juglans sp.	USA, Oregon	2008	[9]
		41_U1259.59	–	41d	Pityophthorus juglandis/Juglans sp.	USA, Oregon	2008	[9]
G. sp. 9	PF, SP	9_1210	CCF3703	9	Cryphalus piceae/Abies alba	Poland, Myślenice	2005	[10]
G. sp. 16	PF, SP	16_08 m	CCF4201	16	Pityophthorus pityographus/Picea abies	Poland, Czajowice	2007	[11]
G. sp. 24	PF, SP	24_RJ06ka	CCF4525	24	Pityogenes bidentatus/Pinus sylvestris	Poland, Zaborze	2007	[11]
G. sp. 26	PF, SP	26_1796	CCF4223	26	Pityophthorus pityographus/Pinus silvestris	Czech R., Seník	2006	[11]
G. sp. 27	PF, SP	27_0919	CCF4206	27	Pityogenes bidentatus/Pinus silvestris	Poland, Żurada	2006	[11]
G. sp. 28	PF, SP	28_279	CCF4210	28	Polygraphus poligraphus/Picea abies	Poland, Chyszówki	2007	[11]
G. sp. 30	PF, SP	30_09 m	CCF4209	30	Pityophthorus pityographus/Picea abies	Poland, Czajowice	2007	[11]
G. sp. 31	PF, SP	31_21k	CCF4526	31	Pityophthorus pityographus/Pinus sylivestris	Poland, Czajowice	2007	[11]
G. sp. 29	PF, SP	33_1827b	CCF4221	33	Pityophthorus pityographus + Cryphalus piceae/Abies alba	Czech R., Boubín hill	2008	[11]
G. sp. 30	PF, SP	34_1833	CCF4208	34	Cryphalus abietis/Abies alba	Czech R., Jílové u Prahy	2008	[11]
G. sp. 25	PF, SP	35_1835	CCF4205	25	C. piceae + P. pityographus/Abies alba	Czech R., Plešné jezero lake	2008	[11]
G. sp. 5	PF, G	5_U1.2c.25	CNR28	5a	Scolytus multistriatus/Ulmus minor	Czech R., Středokluky	2009	[2]
		5_U6.3e.35	CNR48	5b	Scolytus multistriatus/Ulmus minor	Czech R., Velký Osek	2009	[2]
		5_U7.8b	CNR30	5c	Scolytus multistriatus/Ulmus laevis	Czech R., Velký Osek	2009	[2]
		5_U8.1a	CNR49	5d	Scolytus multistriatus/Ulmus minor	Czech R., Maršovice	2009	[2]
		5_U8.1b	–	5e	Scolytus multistriatus/Ulmus minor	Czech R., Maršovice	2009	[2]
		5_U8.12b	–	5f	Scolytus multistriatus/Ulmus minor	Czech R., Maršovice	2009	[2]
		5_580	–	5g	Hypoborus ficus/Ficus carica	France, Biaritz, Ondres	2003	[6]
		5_1550	CCF4271	5h	Scolytus intricatus/Quercus petraea	Czech R., Mlynářův luh, 1997	1997	[7]
		5_137 m	CCF4215	5i	Pityophthorus pityographus galleries/Picea abies	Poland, Szydłowiec	2007	[11]
G. omnicola	PF, G	10_989	CCF3560	10a	Scolytus pygmaeus/Ulmus minor	Czech R., Břeclav	2004	[7]
		10_1788	CCF4286	10b	Hypoborus ficus/Ficus carica	Azerbaijan, Suvalan	2006	[6]
		10_U2.6a	CNR5	10c	Scolytus multistriatus/Ulmus minor	Czech R., Středokluky	2009	[2]
		10_U7.5a	CNR8	10d	Scolytus multistriatus/Ulmus laevis	Czech R., Velký Osek	2009	[2]
		10_942	–	10e	Hypoborus ficus/Ficus carica	Croatia, Brač Island	2004	[6]
G. langdonii	PF, G	15_U5.3a	CNR11	15a	Scolytus multistriatus/Ulmus minor	Czech R., Velký Osek	2009	[2]
		15_U7.9a	CNR6	15b	Scolytus multistriatus/Ulmus laevis	Czech R., Velký Osek	2009	[2]
		15_U8.6c	CNR117	15c	Scolytus multistriatus/Ulmus minor	Czech R., Maršovice	2009	[2]
		15_U8.12a	–	15d	Scolytus multistriatus/Ulmus minor	Czech R., Maršovice	2009	[2]
		15_1645	–	15e	Scolytus multistriatus/Ulmus laevis	Czech R., Neratovice	2005	[12]
		15_1683	CCF4276	15f	Ernoporus tiliae/Tilia sp.	Czech R., Nové Hrady	2005	[7]
		15_1603c	CCF3562	15g	Phloeosinus thujae/Thuja occidentalis	Czech R., Poříčí nad Sázavou	2005	[7]
		15_1619	CCF4272	15h	bostrichid beetle/Pistacia lentiscus	Portugal, Sesimbra	2005	[6]
G. cnesini	AF	29_1820	CCF4292	29	Cnesinus lecontei/Croton draco	Costa Rica, Heredia	2007	[13]
G. microcorthyli	AF	38_A2	CCF3861	38	Microcorthylus sp./Cassia grandis	Costa Rica, Heredia	2006	[14]
G. eupagioceri	AF	39_A1	CCF3754	39	Eupagiocerus dentipes/Paullinia renesii	Costa Rica, Heredia	2006	[14]
G. rufescencs	AAF	42_1821	CCF4524	42	Cnesinus lecontei/Croton draco	Costa Rica, Heredia	2007	[14]

Ecology: PF – association with phloem feeding beetles, G – generalist, SF – specialists to Fagus, SP – specialist to Pinaceae, HWS – hardwood specialists, P – pathogen, AF –ambrosia fungi, AAF – auxiliary ambrosia fungi.

Fig. 1.

Principal component analysis (PCA) plot of the metabolic profiles of 60 Geosmithia strains and comparison of “new” and “old” strains of G. sp. 5 and G. langdonii. Different ecology types as follow: diamond – long-term co-evolved specialists, dot, triangle, star – facultative symbionts, cross – obligatory symbiont, inverted triangle – auxiliary ambrosial fungi, polygon, square – hardwood specialists, square – pathogen, triangle – new (5a-f) and old (5g-i) strains of G. sp. 5, star – new (15a-d) and old (15e-h) strains of G. langdonii. Based on one-way NPMANOVA, facultative generalists were significantly (p < 0.005) different from long-term co-evolved specialists and phytopathogen.

2. Experimental design, materials and methods

2.1. Fungal strains

The metabolic profiles of 60 strains belonging to 35 Geosmithia species (Table 1) were analyzed. These strains are deposited in the Culture Collection of Fungi (CCF) or at Institute of Microbiology of the Czech Academy of Sciences for several years. Then, two species, G. sp. 5 and G. langdonii, were chosen and the effect of long-term in vitro preservation (0–10 years) on fungal carbon assimilation profiles was observed. Fresh strains of these species were isolated from active beetle galleries in 2009 and identified as it is described in Pepori et al. [2]. These strains were analyzed within a 2 months on Biolog MicroPlates™ for Filamentous fungi. Altogether, three “old” and six “new” strains of G. sp. 5 and four “old” and four “new” strains of G. langdonii were compared. The species classification follows Kolařík et al. [3].

2.2. Biolog MicroPlate™ for Filamentous fungi

Biolog MicroPlate™ for Filamentous fungi contains 95 different dried carbon sources and one negative control. Fungal conidia from grown cultures were transferred into the inoculating fluid (0.25% Phytagel, 0.03% Tween 40) by rolling a swab across sporulating areas to get the final transmittance of 75 ± 2%. The inoculated plates (200 μl per well) were then incubated in the dark at 25 °C and absorbance at 750 nm was used to measure mycelial growth at 24, 48, 72, 96 and 168 h. An absorbance reading taken 96 h after the inoculation was included in the analysis, because sporulation occurred in some strains after that time. Two technical replicates per strain were prepared.

2.3. Statistical analysis

The absorbance of the negative control was subtracted from all substrates within one plate and negative values were assigned a value of zero [4]. Biolog™ data were visualized on PCA (Principal Component Analysis) in PAST program [5]. The statistical significance of the type of ecology was evaluated by one-way NPMANOVA with Bonferroni-corrected p values using Bray-Curtis distance and 9999 permutations.

Conflict of Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Appendix A. Supplementary data

The following is the Supplementary data to this article: