Exploring Differences in Culturable Fungal Diversity Using Standard Freezing Incubation—A Case Study in the Limestones of Lemos Pantheon (Portugal)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Site Description and Sampling Strategy
2.2. Isolation, Morphological and Molecular Identification
2.3. Data Analysis
3. Results and Discussion
3.1. Frozen Diversity and Its Biodeteriorative Potential
3.2. Diversity vs. Isolation Method
3.3. Effect of Isolation Media
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A
Isolate | Sample | Medium | Isolate ID | GenBank Accession Numbers | Notes | ||||
---|---|---|---|---|---|---|---|---|---|
ITS | Translation Elongation Factor 1α (tef1) | β-Tubulin (benA) | Calmodulin (CaM) | Partial Actin (Act) | |||||
PL133 | L4 | MEA 10% | Parengyodontium album | OQ211122 | OQ330805 | – | – | – | a |
PL134 | L3 | RB | Cladosporium cladosporioides | OQ211118 | – | – | – | OQ330822 | a |
PL135 | L2 | PDA | Acremonium charticola | OQ211119 | OQ330803 | – | – | – | a |
PL136 | L2 | PDA | Acremonium charticola | OQ211123 | OQ330806 | – | – | – | a |
PL137 | L3 | MEA 10% | Cladosporium cladosporioides | – | – | – | – | – | b |
PL138 | L3 | PDA | Penicillium brevicompactum | OQ211120 | – | OQ330764 | – | – | a |
PL139 | L3 | CZA | Parengyodontium album | – | – | – | – | – | b |
PL140 | L1 | PDA | Cladosporium allicinum | OQ211114 | – | – | – | OQ330820 | a |
PL141 | L4 | HM 10% | Parengyodontium album | – | – | – | – | – | b |
PL142 | L4 | HM 10% | UnID Fi_1 | – | – | – | – | – | d |
PL143 | L4 | HM 10% | UnID Fi_1 | – | – | – | – | – | d |
PL144 | L3 | MEA 10% | Tapesia fusca | OQ211115 | OQ330802 | – | – | – | c |
PL145 | L2 | HM 10% | Penicillium jiangxiense | OQ211124 | – | OQ330765 | – | – | a |
PL146 | L2 | MEA 10% | Acremonium charticola | – | – | – | – | – | b |
PL147 | L1 | HM 10% | UnID Fi_1 | – | – | – | – | – | d |
PL148 | L1 | MEA 10% | Aspergillus protuberus | – | – | – | – | – | b |
PL149 | L2 | MEA 10% | Acremonium charticola | OQ211126 | OQ330807 | – | – | – | a |
PL150 | L3 | CZA | Penicillium brevicompactum | OQ211125 | – | OQ330766 | – | – | a |
PL151 | L3 | CZA | Coprinellus micaceus | OQ211121 | OQ330804 | – | – | – | c |
PL152 | L3 | MEA 10% | Stachybotrys chartarum | OQ211138 | OQ330811 | – | – | – | a |
PL153 | L3 | MEA 10% | Stachybotrys chartarum | – | – | – | – | – | b |
PL154 | L2 | MEA 10% | Cyphellophora olivacea | OQ211128 | OQ330808 | – | – | – | a |
PL155 | L2 | MEA 10% | Parengyodontium album | – | – | – | – | – | b |
PL156 | L2 | MEA 10% | Cyphellophora olivacea | OQ211135 | OQ330810 | – | – | – | a |
PL157 | L2 | HM 10% | Aspergillus protuberus | OQ211136 | – | OQ330771 | OQ330788 | – | a |
PL158 | L2 | HM 10% | Aspergillus penicillioides | OQ211141 | – | OQ330774 | OQ330798 | – | a |
PL159 | L2 | HM 10% | Penicillium crustosum | OQ211116 | – | OQ330763 | – | – | a |
PL160 | L2 | CZ | Penicillium crustosum | OQ211142 | – | OQ330775 | – | – | a |
PL161 | L2 | HM 10% | Penicillium crustosum | OQ211143 | – | – | – | – | a |
PL162 | L2 | HM 10% | Aspergillus penicillioides | OQ211131 | – | OQ330769 | – | – | a |
PL163 | L2 | HM 10% | Aspergillus penicillioides | – | – | – | – | – | b |
PL164 | L1 | MEA 10% | Cladosporium cladosporioides | OQ211117 | – | – | – | OQ330821 | a |
PL165 | L1 | CZA | Alternaria infectoria | OQ211140 | OQ330812 | – | – | – | a |
PL166 | L2 | RB | Aspergillus protuberus | OQ211148 | – | OQ330779 | OQ330789 | – | a |
PL167 | L2 | RB | Aspergillus protuberus | OQ211137 | – | OQ330772 | OQ330790 | – | a |
PL168 | L2 | RB | Aspergillus protuberus | OQ211145 | – | OQ330776 | OQ330791 | – | a |
PL169 | L1 | RB | Amycosphaerella africana | OQ211144 | OQ330814 | – | – | – | a |
PL170 | L2 | CZA | Aspergillus protuberus | OQ211139 | – | OQ330773 | OQ330792 | – | a |
PL171 | L2 | CZA | Aspergillus protuberus | OQ211147 | – | OQ330778 | OQ330793 | – | a |
PL172 | L2 | CZA | Streptomyces | – | – | – | – | – | e |
PL173 | L2 | CZA | Streptomyces | – | – | – | – | – | e |
PL174 | L2 | MEA 10% | Cyphellophora olivacea | OQ211156 | OQ330816 | – | – | – | a |
PL175 | L3 | PDA | Cladosporium halotolerans | OQ211149 | – | – | – | OQ330823 | a |
PL176 | L2 | PDA | Streptomyces | – | – | – | – | – | e |
PL177 | L2 | PDA | Penicillium crustosum | OQ211152 | – | OQ330781 | – | – | a |
PL178 | L2 | PDA | Streptomyces | – | – | – | – | – | e |
PL179 | L2 | RB | Aspergillus protuberus | – | – | – | – | – | b |
PL180 | L1 | RB | Amycosphaerella africana | – | – | – | – | – | b |
PL181 | L1 | HM 10% | UnID Fi_1 | – | – | – | – | – | d |
PL182 | L2 | HM 10% | Penicillium crustosum | OQ211151 | – | OQ330780 | – | – | a |
PL183 | L3 | RB | Cladosporium cladosporioides | OQ211150 | – | – | – | OQ330824 | a |
PL184 | L3 | RB | Cladosporium cladosporioides | – | – | – | – | – | b |
PL185 | L1 | RB | Amycosphaerella africana | OQ211154 | – | – | – | – | a |
PL186 | L1 | RB | Amycosphaerella africana | OQ211155 | OQ330815 | – | – | – | a |
PL187 | L3 | PDA | Penicillium brevicompactum | OQ211153 | – | OQ330782 | – | – | a |
PL188 | L3 | MEA 10% | Penicillium crustosum | OQ211162 | – | – | – | – | a |
PL189 | L3 | CZA | Parengyodontium album | OQ211129 | OQ330809 | – | – | – | a |
PL190 | L2 | MEA 10% | Cyphellophora olivacea | OQ211161 | OQ330818 | – | – | – | a |
PL191 | L2 | MEA 10% | Streptomyces | – | – | – | – | – | e |
PL192 | L2 | MEA 10% | Streptomyces | – | – | – | – | – | e |
PL193 | L3 | MEA 10% | Penicillium brevicompactum | OQ211163 | – | OQ330783 | – | a | |
PL194 | L2 | MEA 10% | Streptomyces | – | – | – | – | – | e |
PL195 | L2 | MEA 10% | Cyphellophora olivacea | OQ211165 | – | – | – | – | a |
PL196 | L1 | PDA | Cladosporium allicinum | OQ211166 | – | – | – | OQ330826 | a |
PL197 | L2 | CZA | Streptomyces | – | – | – | – | – | e |
PL198 | L2 | CZA | Cyphellophora olivacea | OQ211164 | OQ330819 | – | – | – | a |
PL199 | L2 | CZA | Streptomyces | – | – | – | – | – | e |
PL200 | L1 | PDA | UnID Fi_2 | – | – | – | – | – | d |
PL201 | L1 | MEA 10% | Aspergillus protuberus | OQ211127 | – | OQ330767 | OQ330794 | – | a |
PL202 | L1 | HM 10% | Aspergillus penicillioides | OQ211132 | – | OQ330770 | – | – | a |
PL203 | L2 | HM 10% | Aspergillus penicillioides | OQ211133 | – | – | – | – | a |
PL204 | L3 | MEA 10% | UnID Fi_3 | – | – | – | – | – | d |
PL205 | L4 | DG18 | UnID Fi_1 | – | – | – | – | – | d |
PL206 | L4 | DG18 | Cladosporium cladosporioides | OQ211168 | – | – | – | OQ330828 | a |
PL207 | L1 | HM 10% | Aspergillus penicillioides | OQ211130 | – | OQ330768 | – | – | a |
PL208 | L1 | PDA | Stereum hirsutum | OQ211160 | – | – | – | – | c |
PL209 | L3 | RB | Cladosporium cladosporioides | – | – | – | – | – | b |
PL210 | L1 | PDA | Stereum hirsutum | – | – | – | – | – | b |
PL211 | L2 | RB | Aspergillus protuberus | OQ211146 | – | OQ330777 | OQ330795 | – | a |
PL212 | L2 | MEA 10% | Stereum hirsutum | OQ211157 | OQ330817 | – | – | – | c |
PL213 | L2 | MEA 10% | Diaporthe foeniculina | OQ211158 | – | – | – | – | a |
PL214 | L3 | CZA | UnID Fi_4 | – | – | – | – | – | d |
PL215 | L1 | HM 10% | Cladosporium sinuosum | OQ211159 | – | – | – | OQ330825 | a |
PL216 | L3 | RB | UnID Fi_4 | – | – | – | – | d | |
PL217 | L1 | HM 10% | Cladosporium allicinum | OQ211167 | – | – | – | OQ330827 | a |
PL218 | L2 | CZA | Streptomyces | – | – | – | – | – | e |
PL219 | L1 | DG18 | Aspergillus penicillioides | OQ211169 | – | OQ330784 | OQ330799 | – | a |
PL220 | L1 | PDA | Aspergillus protuberus | OQ211170 | – | OQ330785 | OQ330796 | – | a |
PL221 | L4 | DG18 | UnID Fi_1 | – | – | – | – | – | d |
PL222 | L1 | PDA | Aspergillus protuberus | OQ211171 | – | OQ330786 | OQ330797 | – | a |
PL223 | L1 | DG18 | Aspergillus penicillioides | – | – | – | – | – | b |
PL224 | L1 | PDA | UnID Fi_2 | – | – | – | – | – | d |
PL225 | L1 | CZA | Talaromyces acaricola | OQ211172 | – | OQ330787 | OQ330800 | – | a |
PL226 | L1 | CZA | Talaromyces acaricola | OQ211173 | – | – | – | – | a |
PL227 | L1 | CZA | Talaromyces acaricola | OQ211174 | – | – | OQ330801 | – | a |
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Locus | Primers | Sequence (5′-3′) | Annealing (°C) | Amplification/Cycles | Length (bp) | Group | Reference |
---|---|---|---|---|---|---|---|
Internal transcribed spacer (ITS) | ITS1F ITS4 | ctt ggt cat tta gag gaa gta a tcc tcc gct tat tga tat gc | 52 | Standard 35 | ~600 | All Fungi | [49] |
Translation elongation factor 1α (Tef1) | EF1-1018F EF1-1620R | gay ttc atc aag aac atg at gac gtt gaa dcc rac rtt gtc | 56 | Touchdown 36 | ~600 | All Fungi * | [50] |
β-tubulin (BenA) | Bt2a Bt2b | ggt aac caa atc ggt gct gct ttc acc ctc agt gta gtg acc ctt ggc | 55 | Standard 35 | ~500 | Aspergillus, Penicillium and Talaromyces | [51,52] |
Calmodulin (CaM) | CMD5 CMD6 | ccg agt aca agg agg cct tc ccg ata gag gtc ata acg tgg | 55 | Standard 35 | ~580 | Aspergillus and Talaromyces | [52,53] |
Partial Actin (Act) | Act-512F Act-783R | atg tgc aag gcc ggt ttc gc tac gag tcc ttc tgg ccc at | 55 | Standard 35 | ~370 | Cladosporium | [54,55] |
Sample ID | Species Richness (S) | Shannon (H) | Evenness (e^H/S) | Dominance (D) |
---|---|---|---|---|
L1 | 11 | 1.77 | 0.53 | 0.22 |
L2 | 9 | 1.39 | 0.44 | 0.29 |
L3 | 10 | 1.27 | 0.35 | 0.37 |
L4 | 3 | 0.53 | 0.56 | 0.73 |
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Paiva, D.S.; Fernandes, L.; Pereira, E.; Trovão, J.; Mesquita, N.; Tiago, I.; Portugal, A. Exploring Differences in Culturable Fungal Diversity Using Standard Freezing Incubation—A Case Study in the Limestones of Lemos Pantheon (Portugal). J. Fungi 2023, 9, 501. https://doi.org/10.3390/jof9040501
Paiva DS, Fernandes L, Pereira E, Trovão J, Mesquita N, Tiago I, Portugal A. Exploring Differences in Culturable Fungal Diversity Using Standard Freezing Incubation—A Case Study in the Limestones of Lemos Pantheon (Portugal). Journal of Fungi. 2023; 9(4):501. https://doi.org/10.3390/jof9040501
Chicago/Turabian StylePaiva, Diana S., Luís Fernandes, Emília Pereira, João Trovão, Nuno Mesquita, Igor Tiago, and António Portugal. 2023. "Exploring Differences in Culturable Fungal Diversity Using Standard Freezing Incubation—A Case Study in the Limestones of Lemos Pantheon (Portugal)" Journal of Fungi 9, no. 4: 501. https://doi.org/10.3390/jof9040501
APA StylePaiva, D. S., Fernandes, L., Pereira, E., Trovão, J., Mesquita, N., Tiago, I., & Portugal, A. (2023). Exploring Differences in Culturable Fungal Diversity Using Standard Freezing Incubation—A Case Study in the Limestones of Lemos Pantheon (Portugal). Journal of Fungi, 9(4), 501. https://doi.org/10.3390/jof9040501