Wpływ zanieczyszczenia gleby na występowanie i różnorodność przedstawicieli Mucoromycota oraz ich bakteryjnych endosymbiontów

@article{Ciach24,

title = {The interkingdom horizontal gene transfer in 44 early diverging fungi boosted their metabolic, adaptive, and immune capabilities},

author = {Ciach, Michał Aleksander and Pawłowska, Julia and Górecki, Paweł and Muszewska, Anna},

url = {https://doi.org/10.1093/evlett/qrae009},

doi = {10.1093/evlett/qrae009},

issn = {2056-3744},

year  = {2024},

date = {2024-03-05},

urldate = {2024-03-05},

journal = {Evolution Letters},

volume = {03},

pages = {qrae009},

abstract = {Numerous studies have been devoted to individual cases of horizontally acquired genes in fungi. It has been shown that such genes expand the hosts’ metabolic capabilities and contribute to their adaptations as parasites or symbionts. Some studies have provided an extensive characterization of the horizontal gene transfer (HGT) in Dikarya. However, in the early diverging fungi (EDF), a similar characterization is still missing. In order to fill this gap, we have designed a computational pipeline to obtain a statistical sample of reliable HGT events with a low false discovery rate. We have analyzed 44 EDF proteomes and identified 829 xenologs in fungi ranging from Chytridiomycota to Mucoromycota. We have identified several patterns and statistical properties of EDF HGT. We show that HGT is driven by bursts of gene exchange and duplication, resulting in highly divergent numbers and molecular properties of xenologs between fungal lineages. Ancestrally aquatic fungi are generally more likely to acquire foreign genetic material than terrestrial ones. Endosymbiotic bacteria can be a source of useful xenologs, as exemplified by NOD-like receptors transferred to Mortierellomycota. Closely related fungi have similar rates of intronization of xenologs. Posttransfer gene fusions and losses of protein domains are common and may influence the encoded proteins’ functions. We argue that there is no universal approach for HGT identification and inter- and intra-kingdom transfers require tailored identification methods. Our results help to better understand how and to what extent HGT has shaped the metabolic, adaptive, and immune capabilities of fungi.Horizontal gene transfer is a transmission of genes between organisms, distinct from vertical inheritance from parents to offspring. HGT seems to occur among all living forms. Our study focuses on horizontally transferred genes present in early diverging fungi (EDF). EDF is a relatively understudied group of organisms with vastly diverse lifestyles and tremendous ecological importance. They include arbuscular mycorrhizal Glomeromycota, the gut-dwelling symbionts of herbivores Neocallimastigomycota, or the parasitic Batrachochytrium. HGT has been reported to contribute to this diversity by facilitating niche adaptations in certain lineages. In our work, we have analyzed horizontally acquired genes in 44 fungal genomes, focusing on cases with clear phylogenetic evidence. We have designed a computational pipeline that detects a statistical sample of reliable HGTs. The pipeline is published alongside the article. We have analyzed the donors, acceptors, and properties of the transferred genes. We found transfers of genes that can expand the metabolic, adaptive, and immune capabilities of fungi.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1111/1462-2920.16007,

title = {Marginal lands and fungi – linking the type of soil contamination with fungal community composition},

author = {Alicja Okrasińska and Przemyslaw Decewicz and Maria Majchrowska and Lukasz Dziewit and Anna Muszewska and Somayeh Dolatabadi and Łukasz Kruszewski and Zuzanna Błocka and Julia Pawłowska},

url = {https://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.16007},

doi = {https://doi.org/10.1111/1462-2920.16007},

year  = {2022},

date = {2022-05-31},

urldate = {2022-05-31},

journal = {Environmental Microbiology},

abstract = {Summary Fungi can be found in almost all ecosystems. Some of them can even survive in harsh, anthropogenically transformed environments, such as post-industrial soils. In order to verify how the soil fungal diversity may be changed by pollution, two soil samples from each of the 28 post-industrial sites were collected. Each soil sample was characterized in terms of concentration of heavy metals and petroleum derivatives. To identify soil fungal communities, fungal internal transcribed spacer 2 (ITS2) amplicon was sequenced for each sample using Illumina MiSeq platform. There were significant differences in the community structure and taxonomic diversity among the analysed samples. The highest taxon richness and evenness were observed in the non-polluted sites, and lower numbers of taxa were identified in multi-polluted soils. The presence of monocyclic aromatic hydrocarbons, gasoline and mineral oil was determined as the factors driving the differences in the mycobiome. Furthermore, in the culture-based selection experiment, two main groups of fungi growing on polluted media were identified – generalists able to live in the presence of pollution, and specialists adapted to the usage of BTEX as a sole source of energy. Our selection experiment proved that it is long-term soil contamination that shapes the community, rather than temporary addition of pollutant.

},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Trovão2021,

title = {Fungal Planet description sheets: 1284–1382},

author = {Crous Pedro and Osieck, E.R and (...) Pawłowska, Julia and Portugal, A and (...) and Trovão, João and (...) Groenewald, J.Z.},

url = {https://www.ingentaconnect.com/contentone/nhn/pimj/2021/00000047/00000001/art00006},

doi = {https://doi.org/10.3767/persoonia.2021.47.06},

issn = {1878-9080},

year  = {2021},

date = {2021-12-24},

journal = {Persoonia},

volume = {47},

pages = {309},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{muszewska2021,

title = {Metabolic Potential, Ecology and Presence of Associated Bacteria Is Reflected in Genomic Diversity of Mucoromycotina},

author = {Anna Muszewska and Alicja Okrasińska and Kamil Steczkiewicz and Olga Drgas and Małgorzata Orłowska and Urszula Perlińska-Lenart and Tamara Aleksandrzak-Piekarczyk and Katarzyna Szatraj and Urszula Zielenkiewicz and Sebastian Piłsyk and Ewa Malc and Piotr Mieczkowski and Joanna S. Kruszewska and Przemysław Bernat and Julia Pawłowska},

url = {https://www.frontiersin.org/article/10.3389/fmicb.2021.636986},

doi = {10.3389/fmicb.2021.636986},

year  = {2021},

date = {2021-02-15},

journal = {Frontiers in Microbiology},

volume = {12},

pages = {239},

abstract = {Mucoromycotina are often considered mainly in pathogenic context but their biology remains understudied. We describe the genomes of six Mucoromycotina fungi representing distant saprotrophic lineages within the subphylum (i.e., Umbelopsidales and Mucorales). We selected two Umbelopsis isolates from soil (i.e., U. isabellina, U. vinacea), two soil-derived Mucor isolates (i.e., M. circinatus, M. plumbeus), and two Mucorales representatives with extended proteolytic activity (i.e., Thamnidium elegans and Mucor saturninus). We complement computational genome annotation with experimental characteristics of their digestive capabilities, cell wall carbohydrate composition, and extensive total lipid profiles. These traits inferred from genome composition, e.g., in terms of identified encoded enzymes, are in accordance with experimental results. Finally, we link the presence of associated bacteria with observed characteristics. Thamnidium elegans genome harbors an additional, complete genome of an associated bacterium classified to Paenibacillus sp. This fungus displays multiple altered traits compared to the remaining isolates, regardless of their evolutionary distance. For instance, it has expanded carbon assimilation capabilities, e.g., efficiently degrades carboxylic acids, and has a higher diacylglycerol:triacylglycerol ratio and skewed phospholipid composition which suggests a more rigid cellular membrane. The bacterium can complement the host enzymatic capabilities, alter the fungal metabolism, cell membrane composition but does not change the composition of the cell wall of the fungus. Comparison of early-diverging Umbelopsidales with evolutionary younger Mucorales points at several subtle differences particularly in their carbon source preferences and encoded carbohydrate repertoire. Nevertheless, all tested Mucoromycotina share features including the ability to produce 18:3 gamma-linoleic acid, use TAG as the storage lipid and have fucose as a cell wall component.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Okrasińskae02707-20,

title = {New Endohyphal Relationships between Mucoromycota and Burkholderiaceae Representatives},

author = {Alicja Okrasińska and Aleksandra Bokus and Katarzyna Duk and Aleksandra Gęsiorska and Blanka Sokołowska and Aleksandra Miłobędzka and Marta Wrzosek and Julia Pawłowska},

editor = {Maia Kivisaar},

url = {https://aem.asm.org/content/87/7/e02707-20},

doi = {10.1128/AEM.02707-20},

issn = {0099-2240},

year  = {2021},

date = {2021-01-01},

journal = {Applied and Environmental Microbiology},

volume = {87},

number = {7},

publisher = {American Society for Microbiology Journals},

abstract = {Mucoromycota representatives are known to harbor two types of endohyphal bacteria (EHB)—Burkholderia-related endobacteria (BRE) and Mycoplasma-related endobacteria (MRE). While both BRE and MRE occur in fungi representing all subphyla of Mucoromycota, their distribution is not well studied. Therefore, it is difficult to resolve the evolutionary history of these associations in favor of one of the following two alternative hypotheses explaining their origin: textquotedblleftearly invasiontextquotedblright and textquotedblleftlate invasion.textquotedblright Our main goal was to fill this knowledge gap by surveying Mucoromycota fungi for the presence of EHB. We screened 196 fungal strains from 16 genera using a PCR-based approach to detect bacterial 16S rRNA genes, complemented with fluorescence in situ hybridization (FISH) imaging to confirm the presence of bacteria within the hyphae. We detected Burkholderiaceae in ca. 20% of fungal strains. Some of these bacteria clustered phylogenetically with previously described BRE clades, whereas others grouped with free-living Paraburkholderia. Importantly, the latter were detected in Umbelopsidales, which previously were not known to harbor endobacteria. Our results suggest that this group of EHB is recruited from the environment, supporting the late invasion scenario. This pattern complements the early invasion scenario apparent in the BRE clade of EHB.IMPORTANCE Bacteria living within fungal hyphae present an example of one of the most intimate relationships between fungi and bacteria. Even though there are several well-described examples of such partnerships, their prevalence within the fungal kingdom remains unknown. Our study focused on early divergent terrestrial fungi in the phylum Mucoromycota. We found that ca. 20% of the strains tested harbored bacteria from the family Burkholderiaceae. Not only did we confirm the presence of bacteria from previously described endosymbiont clades, we also identified a new group of endohyphal Burkholderiaceae representing the genus Paraburkholderia. We established that more than half of the screened Umbelopsis strains were positive for bacteria from this new group. We also determined that, while previously described BRE codiverged with their fungal hosts, Paraburkholderia symbionts did not.},

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pubstate = {published},

tppubtype = {article}

}

@article{8660838,

title = {Outline of Fungi and fungus-like taxa},

author = {N N Wijayawardene and K D Hyde and L K T Al-Ani and L Tedersoo and Danny Haelewaters and K C Rajeshkumar and R L Zhao and A Aptroot and V Leontyev D. and R K Saxena and Y S Tokarev and D Q Dai and P M Letcher and S L Stephenson and D Ertz and H T Lumbsch and M Kukwa and V Issi I. and H Madrid and A J L Phillips and L Selbmann and W P Pfliegler and E Horvath and K Bensch and P M Kirk and K Kolarikova and H A Raja and R Radek and V Papp and B Dima and J Ma and E Malosso and S Takamatsu and G Rambold and P B Gannibal and D Triebel and A K Gautam and S Avasthi and S Suetrong and E Timdal and S C Fryar and G Delgado and M Reblova and M Doilom and S Dolatabadi and Julia Z. Pawłowska and R A Humber and R Kodsueb and I Sanchez-Castro and B T Goto and D K A Silva and F A de Souza and F R Oehl and G A da Silva and I R Silva and J Blaszkowski and K Jobim and L C Maia and F R Barbosa and P O Fiuza and P K Divakar and B D Shenoy and R F Castaneda-Ruiz and S Somrithipol and A A Lateef and S C Karunarathna and S Tibpromma and P E Mortimer and D N Wanasinghe and R Phookamsak and J Xu and Y Wang and F Tian and P Alvarado and D W Li and I Kusan and N Matocec and A Masic and Z Tkalcec and S S N Maharachchikumbura and M Papizadeh and G Heredia and F Wartchow and M Bakhshi and E Boehm and N Youssef and V P Hustad and J D Lawrey and A L C M A Santiago and J D P Bezerra and C M Souza-Motta and A L Firmino and Q Tian and J Houbraken and S Hongsanan and K Tanaka and A J Dissanayake and J S Monteiro and H P Grossart and A Suija and G Weerakoon and J Etayo and A Tsurykau and V Vazquez and P Mungai and U Damm and Q R Li and H Zhang and S Boonmee and Y Z Lu and A G Becerra and B Kendrick and F Q Brearley and J Motiejunaite and B Sharma and R Khare and S Gaikwad and D S A Wijesundara and L Z Tang and M Q He and A Flakus and P Rodriguez-Flakus and M P Zhurbenko and E H C McKenzie and M Stadler and D J Bhat and J K Liu and M Raza and R Jeewon and E S Nassonova and M Prieto and R G U Jayalal and M Erdogdu and A Yurkov and M Schnittler and O N Shchepin and Y K Novozhilov and A G S Silva-Filho and E Gentekaki and P Liu and J C Cavender and Y Kang and S Mohammad and L F Zhang and R F Xu and Y M Li and M C Dayarathne and A H Ekanayaka and T C Wen and C Y Deng and O L Pereira and S Navathe and D L Hawksworth and X L Fan and L S Dissanayake and E Kuhnert and M Thines},

url = {http://dx.doi.org/10.5943/mycosphere/11/1/8},

doi = {http://dx.doi.org/10.5943/mycosphere/11/1/8},

issn = {2077-7000},

year  = {2020},

date = {2020-01-01},

journal = {Mycosphere},

volume = {11},

number = {1},

pages = {1060--1456},

publisher = {Mycosphere Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pawlowska2019,

title = {Carbon assimilation profiles of mucoralean fungi show their metabolic versatility},

author = {Julia Pawłowska and Alicja Okrasińska and Kamil Kisło and Tamara Aleksandrzak-Piekarczyk and Katarzyna Szatraj and Somayeh Dolatabadi and Anna Muszewska },

url = {https://www.nature.com/articles/s41598-019-48296-w#citeas},

doi = {https://doi.org/10.1038/s41598-019-48296-w},

year  = {2019},

date = {2019-08-14},

journal = {Scientific Reports},

volume = {9},

pages = {11864},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Crous2019Jun,

title = {Fungal Planet description sheets: 868-950},

author = {Crous PW and Carnegie AJ and Wingfield MJ and Sharma R and Mughini G and Noordeloos ME and Santini A and Shouche YS and Bezerra JDP and Dima B and Guarnaccia V and Imrefi I and Jurjević Ž and Knapp DG and Kovács GM and Magistà D and Perrone G and Rämä T and Rebriev YA and Shivas RG and Singh SM and Souza-Motta CM and Thangavel R and Adhapure NN and Alexandrova AV and Alfenas AC and Alfenas RF and Alvarado P and Alves AL and Andrade DA and Andrade JP and Barbosa RN and Barili A and Barnes CW and Baseia IG and Bellanger JM and Berlanas C and Bessette AE and Bessette AR and Biketova AY and Bomfim FS and Brandrud TE and Bransgrove K and Brito ACQ and Cano-Lira JF and Cantillo T and Cavalcanti AD and Cheewangkoon R and Chikowski RS and Conforto C and Cordeiro TRL and Craine JD and Cruz R and Damm U and Oliveira de RJV and Souza de JT and Souza de HG and Dearnaley JDW and Dimitrov RA and Dovana F and Erhard A and Esteve-Raventós F and Félix CR and Ferisin G and Fernandes RA and Ferreira RJ and Ferro LO and Figueiredo CN and Frank JL and Freire KTLS and García D and Gené J and Gêsiorska A and Gibertoni TB and Gondra RAG and Gouliamova DE and Gramaje D and Guard F and Gusmão LFP and Haitook S and Hirooka Y and Houbraken J and Hubka V and Inamdar A and Iturriaga T and Iturrieta-González I and Jadan M and Jiang N and Justo A and Kachalkin AV and Kapitonov VI and Karadelev M and Karakehian J and Kasuya T and Kautmanová I and Kruse J and Kušan I and Kuznetsova TA and Landell MF and Larsson KH and Lee HB and Lima DX and Lira CRS and Machado AR and Madrid H and Magalhães OMC and Majerova H and Malysheva EF and Mapperson RR and Marbach PAS and Martín MP and Martín-Sanz A and Matočec N and McTaggart AR and Mello JF and Melo RFR and Mešić A and Michereff SJ and Miller AN and Minoshima A and Molinero-Ruiz L and Morozova OV and Mosoh D and Nabe M and Naik R and Nara K and Nascimento SS and Neves RP and Olariaga I and Oliveira RL and Oliveira TGL and Ono T and Ordoñez ME and Ottoni AM and Paiva LM and Pancorbo F and Pant B and Pawłowska J and Peterson SW and Raudabaugh DB and Rodríguez-Andrade E and Rubio E and Rusevska K and Santiago ALCMA and Santos ACS and Santos C and Sazanova NA and Shah S and Sharma J and Silva BDB and Siquier JL and Sonawane MS and Stchigel AM and Svetasheva T and Tamakeaw N and Telleria MT and Tiago PV and Tian CM and Tkalčec Z and Tomashevskaya MA and Truong HH and Vecherskii MV and Visagie CM and Vizzini A and Yilmaz N and Zmitrovich IV and Zvyagina EA and Boekhout T and Kehlet T and Læssøe T and Groenewald JZ.},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6712538/},

doi = {10.3767/persoonia.2019.42.11},

year  = {2019},

date = {2019-06-01},

journal = {Persoonia},

volume = {42},

pages = {291},

publisher = {Westerdijk Fungal Biodiversity Institute},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{4ed53db950814a7ebd07f50586eb547b,

title = {Notes for genera: basal clades of Fungi (including Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota)},

author = {Nalin N. Wijayawardene and Julia Pawłowska and Peter M. Letcher and Paul M. Kirk and Richard A. Humber and Arthur Schüßer and Marta Wrzosek and Anna Muszewska and Alicja Okrasińska and Łukasz Istel and Aleksandra Gęsiorska and Paul Mungai and Adebola Azeez Lateef and Kunhiraman C. Rajeshkumar and Rajshree V. Singh and Renate Radek and Grit Walther and Lysett Wagner and Christopher Walker and Siril D. A. Wijesundara and Moslem Papizadeh and Somayeh Dolatabadi and Belle D. Shenoy and Yuri S. Tokarev and Saisamorn Lumyong and Kevin D. Hyde},

doi = {10.1007/s13225-018-0409-5},

issn = {1560-2745},

year  = {2018},

date = {2018-01-01},

journal = {Fungal Diversity},

volume = {92},

number = {1},

pages = {43--129},

publisher = {Springer},

keywords = {},

pubstate = {published},

tppubtype = {article}

}