Academic literature on the topic 'Rock fungi'

The endolithic environment, the tiny pores and cracks in rocks, buffer microbial communities from a number of physical stresses, such as desiccation, rapid temperature variations, and UV radiation. Considerable knowledge has been acquired about the diversity of microorganisms in these ecosystems, but few culture-independent studies have been carried out on the diversity of fungi to date. Scanning electron microscopy of carbonate rock fragments has revealed that the rock samples contain certain kinds of filamentous fungi. We evaluated endolithic fungal communities from bare dolomite and limestone rocks collected from Nanjiang Canyon (a typical karst canyon in China) using culture-independent methods. Results showed that Ascomycota was absolutely dominant both in the dolomite and limestone fungal clone libraries. Basidiomycota and other eukaryotic groups (Bryophyta and Chlorophyta) were only detected occasionally or at low frequencies. The most common genus in the investigated carbonate rocks was Verrucaria. Some other lichen-forming fungi (e.g., Caloplaca , Exophiala , and Botryolepraria ), Aspergillus , and Penicillium were also identified from the rock samples. The results provide a cross-section of the endolithic fungal communities in carbonate rocks and help us understand more about the role of microbes (fungi and other rock-inhabiting microorganisms) in rock weathering and pedogenesis.

Rock-inhabiting fungi (RIF) are usually extremely tolerant or extremophilic, as they can survive on natural and artificial rocks despite being exposed to stressful conditions. RIF have serious negative effects on the appearance and cohesion of rocky substrates, causing the alteration and decomposition of building materials, but also on human and animal health, as they can act as opportunistic pathogens. Their identification is therefore of great importance, especially in urban areas. In the present study, culturing techniques for isolating fungi, and a polyphasic taxonomic approach to their identification, were used to assess the diversity of micromycetes that darken the surfaces of buildings in various villages and cities in Tarragona Province (Spain). Sixty-four species of RIF belonging to forty-one genera were identified, including a new genus (Coccodomyces) and the following six new fungal species: Coccodomyces pleiosporus, Exophiala caementiphila, Exophiala multiformis, Neocatenulostroma spinulosum, Neodevriesia longicatenispora, and Paradevriesia holothallica. Thus, we have established that building materials are ecological niches where a high biodiversity of RIF can develop.

Intensive agricultural cultivation on Cilembu’s Inceptisols has become several soil properties problem for crop production. Nanoparticle phosphate rock and phosphate solubilizing fungi have ability to increase some soil properties content. The research aimed to observe the effect of nanoparticle phosphate rock and phosphate solubilizing fungi on soil P-potential, P-retention, C-organic and base saturation on Cilembu’s Inceptisols. The experiment arranged in Completely Randomized Design. The nanoparticle phosphate rock consisted of 4 levels. The phosphate solubilizing fungi consisted of 2 levels, and 2 replication. Soil P-Potential, P-Retention, C-organic, and Base Saturation were observed. The factors was observed after one month incubation on soil. Results showed that there were an interaction between nanoparticle phosphate rock and phosphate solubilizing fungi on the C-organic after one month incubation. Nanoparticle phosphate rock had affected on C-organic, P-potential and base saturation significantly, but had not affected on P-retention. Utilization of phosphate solubilizing fungi as soil ameliorant had affected significantly on P-potential and C-organic, but had not affected on P-retention and base saturation. Nanoparticle phosphate rock with a dose of 6% had the best effect on increase P-potential and base saturation

Microbial N2-fixer and P-solubilizer were innoculated in a mixture of fresh manure and phosphate rock formulated as an Organonitrophos fertilizer. The population dynamics of bacteria and fungi growing during the composting process were observed. The inoculation treatments consisted of: K = mixture of 20% phosphate rock and 80% of fresh manure + decomposers (control), N = mixture of 20% phosphate rock and 80% of fresh manure + decomposers + N2-fixer (Azotobacter and Azospirillum sp.) , P = mixture of 20% phosphate rock and 80% of fresh manure + decomposers + P-solubilizer (A. niger and P. fluorescens), and NP = mixture of 20% phosphate rock and 80% of fresh manure + decomposers + N2-fixer + P-solubilizer. The results showed that inoculation of microbial N2-fixer and combination inoculation of N2-fixer and P-solubilizer increased the total bacterial population compared to that of the control as well as the only inoculation of microbial P-solubilizer on the 14th day of observation in which the bacteria reached the highest population. On all the observation days, the population of fungi in the inoculation of microbial P-solubilizer treatment increased significantly compared to that of the control. However, there was no difference between the populations of fungi in the inoculation of N2-fixer and combination inoculation of N2-fixer and Psolubilizer. The genus of fungy identified in the compost of the mixture of fresh manure and phosphate rock were Chytridium sp., Aspergillus sp., Rhizopus sp., and Fusarium sp.[How to Cite : Nugroho SG, Dermiyati, J Lumbanraja, S Triyono, H Ismono. 2013. Inoculation Effect of N2-Fixer and P-Solubilizer into a Mixture of Fresh Manure and Phosphate Rock Formulated as Organonitrofos Fertilizer on Bacterial and Fungal Populations. J Trop Soils, 18 (1): 75-80. doi: 10.5400/jts.2013.18.1.75][Permalink/DOI: www.dx.doi.org/10.5400/jts.2013.18.1.75]

The endolithic environment is a ubiquitous habitat for microorganisms and a critical interface between biology and geology. In this study, a culture-based method and the phylogenetic analysis based on 16S rRNA and internal transcribed spacer (ITS) sequences were used to investigate the diversity of endolithic bacteria and fungi in two main types of carbonate rocks (namely dolomite and limestone) from Nanjiang Canyon in Guizhou karst area, China. The results of bacterial diversity indicated that all bacteria isolated from dolomite and limestone rocks were divided into 4 bacterial groups, including Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. For these two kinds of rocks, Proteobacteria was the first dominant group, and Gammaproteobacteria occupied the greatest proportion which might be closely related to Pseudomonas in phylogeny to be the most dominant genera after isolation. Actinobacteria and Bacillus bacteria were also widespread in these two kinds of rock environments. There were only 9 and 8 strains of fungi isolated from dolomite and limestone respectively, which all belonged to Ascomycota. To the best of our knowledge, this is the first report on diversity of endolithic culturable bacteria and fungi in carbonate rocks in Guizhou karst region. These microorganisms may play an important and unprecedented role in the carbonate rock weathering during the long history of geological evolution.

Micromycetes are an integral part of the microbial community of cave ecosystems, they play the role of decomposers or lead a parasitic lifestyle. Microscopic fungi, including yeast, in caves are isolated from soil, air, water, mineral formations, rock surfaces and even troglobionts. By the ratio of fungi of different temperature regimes and the succession of species, one can inference the relationship between the underground cavity and the surface and the intensity of nutrient intake. Representatives of Chrysosporium, Mucor, Mortierella, Peniciliium, Trihoderma, Aspergillus, Geomyces predominate among microscopic fungi in caves. Micromycetes are actively involved in geochemical transformations of the environment, causing corrosion of rocks, which can pose a danger to the preservation of rock paintings in decorated cavities. Anthropogenic load leads to changes in the composition of microscopic fungi due to an increase in the trophic status of cave ecosystems, as well as due to the possible active transboundary transfer of microorganisms by visitors. The use of underground cavities as tourist sites dictates the need to develop criteria for standardizing the content of micromycetes in the air, taking into account the specifics of caves to ensure the safety of people. This review is aimed at summarizing the accumulated data on the diversity and distribution of microscopic fungi in karst caves.

Kakao (Theobroma cacao L.) merupakan salah satu komoditas ekspor yang mampu memberikan kontribusi dalam upaya peningkatan devisa negara. Pertumbuhan bibit kakao pada media ditentukan oleh berbagai faktor di antaranya adalah pemupukan. Penelitian ini bertujuan untuk menguji pengaruh berbagai dosis pemberian rock phosphate dan Fungi Mikoriza Arbuskular (FMA) terhadap pertumbuhan bibit kakao dan juga menguji interaksi antara dosis rock phosphate dan dosis Fungi Mikoriza Arbuskular (FMA) yang tepat terhadap pertumbuhan bibit kakao. Penelitian dilaksanakan di Desa Suli, Kecamatan Salahutu, Kabupaten Maluku Tengah pada bulan November 2021- Febuari 2022. Penelitian menggunakan metode eksperimen berbentuk Rancangan Acak Kelompok (RAK ) 2 faktor dengan 3 ulangan. Faktor pertama yaitu dosis rock phosphate yang terdiri atas 5 taraf yaitu 0 g/tanaman, 4 g/tanaman, 8 g/tanaman, 12 g/tanaman, dan 16 g/tanaman. Faktor kedua adalah dosis Fungi Mikoriza Arbuskular (FMA) yang terdiri atas 4 taraf yaitu 0 spora/tanaman (0 g/tanaman), 100 spora/tanaman (4 g/tanaman), 200 spora/tanaman (8 g/tanaman), 300 spora/tanaman (12 g/tanaman). Hasil penelitian didapatkan informasi bahwa pemberian dosis rock Phosphate berpengaruh signifikan terhadap jumlah daun dan luas daun, sedangkan pemberian dosis Fungi Mikoriza Arbuskukar (FMA) berpengaruh signifikan terhadap luas daun. Interaksi antara pemberian rock Phosphate dan Fungi Mikoriza Arbuskular (FMA) dalam penelitian tidak memperlihatkan adanya pengaruh yang signifikan terhadap semua peubah pengamatan.

Arid and semi-arid desert areas characterized by extreme conditions, including northern Mexico, have rocks with micrometric coatings. These coatings are known as desert varnish, an often dark-red microlayer deposited over millennia and developed on different rock types. These microlaminations, rich in clay minerals and Fe- /Mn-oxides, can serve as habitats for various microorganisms, mainly fungi and bacteria. However, the role of microorganisms in these varnish formations is still under debate. In the Chihuahuan desert (Mexico), particularly in the Samalayuca ridge, extensive areas are covered by rocks with desert varnish Here we present a research effort focused on isolating Fe- and Mn-oxidising microorganisms in different culture media, along with directed sequencing. Using a benzidine spot test to detect oxidant species revealed the presence of bacteria and fungi inhabiting these layers. Likewise, we contribute to a better understanding of the formation of desert varnish, representing the first report of specific microorganisms isolated from rock vanish of the Chihuahuan desert.

Fungi with dark-coloured mycelia - also known as black fungi - form a ubiquitous fraction of microbial communities on rock surfaces all over the world. These organisms show a high capacity to adapt to a wide range of ecological conditions, including those peculiar of extreme environments. Their high tolerance to multiple abiotic stresses, such as solar radiation and osmotic stress is assured by the production of melanin pigments and osmoprotective compounds. The cosmopolitan genera Lichenothelia and Saxomyces were taken as iconic representatives of polyextremotolerant rock-inhabiting black fungi. I investigated their phylogenetic relationships with an extended taxon sampling within the class Dothideomycetes, the most diverse and life-style rich fungal class in Ascomycota. The three loci phylogenetic inference I set up, considering both environmental samples and culture isolates, highlighted the paraphyly of the two genera. The integrative taxonomy approach based on morphological as well as phylogenetic evidences allowed the taxonomical revision of the genera and the description of three new taxa. Rock inhabiting fungi often share substrata with green algae and cyanobacteria and some of them are associated with lichen thalli. Lichenothelia is of a particular interest because it includes lichen parasites and species which are loosely associated with algae or which grow independently on rock. Given their life style plasticity, we chose it for an in vitro culture experiment, studying the development of three Lichenothelia species when co-cultured with two different subaerial algae isolated from lichens (i.e., lichen photobionts). The results showed that the presence of algae neither influence the growth rate of fungi nor the formation of any lichen-like structure. However, this standardized approach proved suitable for future investigations on fungal-algal interactions in other systems. Previous multi-locus phylogenies of Dothideomycetes have investigated evolutionary relationships at order and family level within the class but they often failed to resolve the early diverging nodes, which were generating inconsistent placements of some clades. Here, I applied a phylogenomic approach to resolve relationships in Dothideomycetes, adding the newly sequenced Lichenothelia and Saxomyces genomes, to a wide dataset comprised of 238 individuals. I explored the influence of tree inference methods, supermatrix vs. coalescent-based species tree, and the impact of varying amounts of genomic data. The phylogenomic reconstructions, based on up to three thousand genes, provide well-supported topologies for Dothideomycetes, recovering Lichenothelia and Saxomyces among the earliest diverging lineages in the class together with other rock inhabiting fungi and lichens and thus, suggesting the rock-inhabiting life style as ancestral in the class. Further studies will be necessary to shed light on the molecular bases of stress tolerance and latent capacity of establishing symbiosis of these fungi.

The weathering of silicate rocks and minerals plays a foundational role in soil formation, provides essential nutrient elements required by terrestrial and marine ecosystems, and regulates atmospheric CO2 concentrations over geological time through transfer of calcium from continental silicates into marine carbonate sediments. Increasing evidence from experimental and modelling studies implicate evolutionary advances in plants and their mycorrhizal fungal symbionts in enhancing weathering rates over the past 400 million years. The rise of angiosperms to ecological dominance over gymnosperms during the Cretaceous (145.5-65.5 Ma) coincided with the first appearance of ectomycorrhizal fungi, which are more aggressive weathering agents than the ancestral arbuscular mycorrhizal fungi. However, the relative importance of the plant and fungal components of biotic weathering to the long-term decline of C02 from the Cretaceous onwards has not been fully resolved. To address these issues, this thesis reports axenic microcosm experiments that are used to investigate for the first time the influences of angiosperm and gymnosperm host type and atmospheric CO2 concentration on ectomycorrhizal fungal colonisation of silicate rock grains. Using a representative gymnosperm species, Pinus sylvestris and angiosperm species, Betula pendula in symbiosis with the common generalist EM fungi Paxillus involutus, carbon fluxes from ectomycorrhizal seedlings to fungal hyphae colonising weathering arenas were quantified. 14C02 pulse labelling studies and biomass quantification techniques elucidate temporal and spatial carbon dynamics of fungal hyphae colonising grains of basalt, apatite, granite and quartz. Fungal alteration of silicate mineral surfaces was investigated by vertical scanning interferometry and the formation of new biogenic minerals studied by scanning electron microscopy. Additional experiments investigated the effects of the generalist fungus Thelephora terrestris and the suilloid group specialists of the pinaceae. EM fungal proliferation and carbon allocation is shown to respond to elevated CO2 growth conditions, and to seedling host type. Furthermore, preferential fungal colonisation of the Ca and Mg rich silicate rock basalt and evidence of accelerated Ca weathering indicates a need to reassess the current paradigm of plant weathering which overlooks the eo-evolution of roots with their mycorrhizal symbionts.

Verrucariaceae are a family including mostly lichenized species (Verrucariales, Ascomycota). Its current generic classification, which mainly relies on three morphological characters (spore septation, thallus structure, and hymenial algae), has never been subjected to molecular data. Because these characters were suspected to be homoplastic, the monophyly of the genera as currently delimited based on morphology need to be assessed. A three-gene phylogenetic analysis was carried out using three methods (Maximum Parsimony, Maximum Likelihood, and a Bayesian approach) on 83 taxa, selected from 15 genera in Verrucariaceae. Ancestral state reconstructions were undertaken for four characters (spore septation, thallus structure, hymenial algae, and upper cortex structure). The results confirmed that most of the genera were not monophyletic, and that the most recent common ancestor of Verrucariaceae was most likely crustose, lacking hymenial algae, and with simple spores and a pseudocortex. The use of symplesiomorphic traits to define Verrucaria, the largest and type genus for the Verrucariaceae, as well as the non monophyly of the genera Polyblastia, Staurothele and Thelidium, explain most of the discrepancies between the current classification and a classification using monophyly as a grouping criterion. In order to accommodate newly inferred monophyletic groups, existing genera were re-delimited and three new genera were proposed. Recent broad-scale phylogenetic analyses have shown that Verrucariales was sister to Chaetothyriales, an order first known as including mostly saprophytes and opportunistic animal and human parasites. Investigations of fungal communities colonizing rocks in extreme environments have shown that some slow-growing melanized fungi inhabiting bare rock surfaces belonged to the Chaetothyriales. Multigene phylogenetic analyses were carried out using Maximum Likelihood and a Bayesian approach in order to confirm the affiliation of 25 of these rock isolates. Ancestral state reconstructions were then undertaken on two different datasets to look at the evolutionary history of lichenization within Pezizomycotina, and the rock-inhabiting habit within Eurotiomycetes. Results suggest that the ancestor of the lineage including Verrucariales and Chaetothyriales was likely to be an extremotolerant non-lichenized, rock-inhabiting fungus. Virulence factors of opportunistic parasites within Chaetothyriales, such as melanization and meristematic growth, might have primary been adaptations for life in extreme habitats.<br>Dissertation

Tese no âmbito do Doutoramento em Biociências, especialização em Biologia Celular e Molecular, orientada pelo Professor Doutor António Manuel Santos Carriço Portugal, Professor Doutor Francisco Paulo de Sá Campos Gil, Doutor Igor Clemente Tiago e apresentada ao Departamento de Ciências da Vida da Faculdade de Ciências e Tecnologia da Universidade de Coimbra.<br>Among the distinct microbial populations able to grow in stone monuments, colonization by fungi often results in severe aesthetic, physical and chemical biodeterioration of the substrate. This multidisciplinary thesis attempts to understand the biodeteriorative role of fungal communities thriving in stone monuments present within the UNESCO World heritage site of “University of Coimbra- Alta and Sofia”. Accordingly, this work aims were: (1) to produce a detailed inventory characterizing fungal communities using both classical and -omics approaches in key monuments in this area; (2) to describe novel fungal taxa colonizing these supports; (3) to link the detected fungal species, environmental and stone petrochemical characteristics with the observed deterioration processes; (4) to assess fungal biodeteriorative potential and the studied limestone bioreceptivity; and (5) to evaluate and develop control procedures targeting specific harmful biodeteriorating fungal species. This comprehensive research is started with a set of studies aiming to identify the fungal species and their deteriorative action, in various biodeterioration outlines present in the dolomitic limestone walls of the Old Cathedral of Coimbra. The combined approach using traditional cultivation methodologies coupled with modern Next Generation Sequencing techniques, allowed to identify the fungal communities present in this monument, while also allowing to verify that in similar studies their joined application is advised. During this survey, isolates from an unknown microcolonial black fungal species were retrieved. In order to understand this species taxonomic status, a polyphasic study was conducted, allowing the description of a new family, Aeminiaceae fam. nov., a new genus Aeminium gen. nov., and a new species, Aeminium ludgeri sp. nov. Moreover, considering the significance of this finding and in order to explore gene content and genomic traits, the species genome was also sequenced and thoroughly studied. Several distinctive traits that putatively contribute to the organism extremotolerance and biodeteriorative profile were thus highlighted. In order to further understand fungal dolomitic limestone bioreceptivity and biodeterioration, an extensive analysis aiming to identify biodeteriorative abilities and limestone bioreceptivity to fungi thriving in this site was then conducted. The results showed that a significant number of the tested species contributed to dolomitic limestone biodeterioration and that fungal proliferation was slightly superior in oligotrophic rather than copiotrophic conditions. In the ensuing section, attention is given to a series of studies focusing in the biodeteriorative effects of the proliferation of fungal communities in the relieves adorning the Ançã limestone tomb of the First Portuguese King. A multi-disciplinary approach to fully characterize these phenomena allowed to verify a massive fungal diversity and abundance in this monument, while also pinpointing that the establishment of differential fungal populations coupled with the deposition of environmental particles contributed to the development of the distinct phenomena by various mechanisms. In order to further study Ançã limestone fungal bioreceptivity and biodeterioration, an experimental laboratorial analysis was also carried out. The results revealed that all tested species contributed to the substratum biodeterioration and that Penicillia growth was favored in rich micro-nutrient environments, while Aspergilli and Aeminium ludgeri denoted a slightly more accentuated growth under depleted nutrient conditions. Subsequently, focus is then given to the fungal communities thriving in the Coimbra Roman cryptoporticus and in particular to the presence of whitish mold-like propagations in some areas of this site. Fearing that a putative fungal outbreak could be taking place, the fungal communities in these sites were deeply characterized. The results revealed that these propagations are a result of Lecanicillium psalliotae proliferations and that possible outbreaks by this species are putatively occurring through animal vectored dispersion. In the penultimate section of this thesis, the main advantages of cultivation approaches are highlighted, with the description and biodeteriorative profiling of several unknown filamentous fungal taxa retrieved from the studied monuments. Moreover, one of the species described, exhibited a very high ability to induce the formation of calcium oxalates in vitro, a deteriorative profile that would never be noted, if solely the use of Next-generation sequencing methodologies was considered. Lastly, considering the ongoing efforts to restore and preserve various monuments in this UNESCO area, the final focus in then given to test the in vitro efficiency of chemical biocides previously used in the University tower against various fungal species retrieved during the course of this thesis. Moreover, they were also compared with an increasing attractive green option, Ocimum basilicum essential oil. Altogether, the scientific information developed and gathered during the course of this thesis provides a massive update concerning the current knowledge on fungal limestone interactions and biodeterioration, while also providing a strong evaluation of the current methodologies applied to study them in similar contexts.<br>Entre as distintas populações microbianas capazes de crescer em monumentos rochosos, a colonização por fungos frequentemente resulta numa severa biodeterioração estética, física e química do substrato. Esta tese multidisciplinar procura compreender o papel biodeteriorativo das comunidades de fungos que prosperam em monumentos de pedra presentes no património mundial da UNESCO da “Universidade de Coimbra-Alta e Sofia”. Assim, os objetivos deste trabalho foram: (1) produzir um inventário detalhado caracterizando as comunidades de fungos, usando para isso abordagens clássicas e -ómicas em monumentos-chave nesta área; (2) descrever novos taxa de fungos que colonizam estes suportes; (3) relacionar as espécies de fungos detectadas, as características ambientais e petroquímicas da rocha com os processos de deterioração observados; (4) avaliar o potencial biodeteriorativo dos fungos e a sua bioreceptividade nos calcários estudados; e (5) avaliar e desenvolver procedimentos de controlo visando espécies específicas de fungos biodeterioradores prejudiciais. Esta abrangente investigação inicia-se com um conjunto de estudos que visam identificar as espécies fúngicas e a sua ação deterioradora nos diversos perfis de biodeterioração presentes nas paredes calcárias dolomíticas da Sé Velha de Coimbra. A abordagem combinada utilizando metodologias de cultivo tradicionais aliadas a modernas técnicas de Sequenciamento de Próxima Geração, permitiu identificar as comunidades fúngicas presentes neste monumento, permitindo também verificar que em estudos semelhantes é aconselhável a sua aplicação conjunta. Durante esta pesquisa, isolados de uma espécie desconhecida de fungo microcolonial negro foram recuperados. Com o objetivo de compreender o status taxonómico desta espécie, foi realizado um estudo polifásico, permitindo a descrição de uma nova família, Aeminiaceae fam. nov., um novo género Aeminium gen. nov., e uma nova espécie, Aeminium ludgeri sp. nov. Além disso, considerando a importância desta descoberta e com o fim de explorar o conteúdo genético e as suas características genómicas, o genoma da espécie foi também sequenciado e estudado exaustivamente. Vários traços distintivos que putativamente contribuem para a extremotolerância do organismo e o seu perfil biodeteriorativo foram assim destacados. A fim de compreender melhor a bioreceptividade e a biodeterioração do calcário dolomítico por espécies fúngicas, foi realizada uma extensa análise com o objetivo de identificar as suas habilidades biodeteriorativas e a bioreceptividade do calcário a fungos que prosperam neste local. Os resultados mostraram que um número significativo das espécies testadas contribuiram para a biodeterioração do calcário dolomítico e que a proliferação de fungos foi ligeiramente superior em condições oligotróficas do que copiotróficas. Na secção seguinte, é dada atenção a um conjunto de estudos que incidem sobre os efeitos biodeteriorativos da proliferação de comunidades fúngicas nos relevos que adornam o túmulo de calcário de Ançã do Primeiro Rei Português. Uma abordagem multidisciplinar para caracterizar completamente esses fenómenos permitiu verificar uma enorme diversidade e abundância de fungos neste monumento, ao mesmo tempo que apontou que o estabelecimento de populações diferenciais de fungos, juntamente com a deposição de partículas ambientais, contribuíram para o desenvolvimento dos distintos fenómenos por vários mecanismos. Com o objetivo de aprofundar o estudo da bioreceptividade e biodeterioração fúngica do calcário de Ançã, foi realizada uma análise laboratorial experimental. Os resultados revelaram que todas as espécies testadas contribuíram para a biodeterioração do substrato e que o crescimento de Penicillia foi favorecido em ambientes ricos em micronutrientes, enquanto Aspergilli e Aeminium ludgeri denotaram um crescimento ligeiramente mais acentuado em condições de depleção de nutrientes. Posteriormente, o enfoque é dado às comunidades de fungos que prosperam no criptopórtico Romano de Coimbra e, em particular, à presença de propagações esbranquiçadas semelhantes a fungos em algumas áreas deste local. Temendo que um possível surto fúngico pudesse estar a ocorrer, as comunidades de fungos nesses locais foram profundamente caracterizadas. Os resultados revelaram que essas propagações são resultado da proliferação de Lecanicillium psalliotae e que possíveis surtos por esta espécie estão a ocorrer putativamente por meio de dispersão vetorial animal. Na penúltima seção desta tese, as principais vantagens das abordagens de cultivo são destacadas, com a descrição e a caracterização do perfil biodeteriorativo de vários taxa de fungos filamentosos desconhecidos e recuperados dos monumentos estudados. Além disso, uma das espécies descritas, exibiu uma capacidade muito elevada de induzir a formação de oxalatos de cálcio in vitro, um perfil de deterioração que nunca seria notado se apenas o uso de metodologias de sequenciamento de próxima geração fosse considerado. Por último, considerando os esforços em curso para restaurar e preservar vários monumentos nesta área da UNESCO, o enfoque final é então dado na testagem da eficácia in vitro de biocidas químicos anteriormente utilizados na torre da Universidade contra várias espécies de fungos recuperadas no decorrer desta tese. Além disso, eles também foram comparados com uma opção verde cada vez mais atraente, o óleo essencial de Ocimum basilicum. No seu conjunto, a informação científica desenvolvida e recolhida ao longo desta tese, fornece uma atualização maciça sobre o conhecimento atual sobre as interações e biodeterioração do calcário fúngico, ao mesmo tempo que fornece uma forte avaliação das metodologias atuais aplicadas para estudá-los em contextos semelhantes.

AbstractThe world cultural heritage sites face new challenges for an effective protection and management because of destruction and damage initiated by both natural and anthropogenic causes. Fresh rock and sandstone surfaces of buildings are quickly colonized and covered by a layer of microorganisms, including phototrophs, lithotrophs, and heterotrophs to form a biofilm that alters the local conditions of the stone surfaces, especially under the favorable tropical climate conditions for autotrophic microorganisms and plants. Biofilms had been studied with indigenous or pure cultures of isolated microorganisms, but the selective ones that contribute to deterioration of the cultural heritage cannot be confirmed easily. Currently, high-throughput sequencing and metegenomics analyses are capable of obtaining microbial community and composition in great depth, but they also suffer from similar weakness unable to identify the culprits in the community. With these as background, this article presents a different approach by focusing on the biochemical processes and the responsible microorganisms involved to reveal the destruction processes for management and protection. Among these different functional groups of microorganisms, lichens are known as pioneering rock-decomposing microorganisms, and both sulfur-oxidizing bacteria and fungi participate in the decomposition of sandstone via sulfur cycling and initiation of salt attack of the stone afterward, resulting in defoliation and cracking of stone. Other microorganisms including ammonia-oxidizing bacteria and archaea, especially the latter, have been recently detected on sandstone monuments providing evidence on the new organisms involved in the deterioration of cultural heritage and buildings. In addition, fungi can colonize the surfaces of the matured biofilms and play a new role in the removal of them, which has a potential biotechnological application in conservation of cultural heritage. The new proposed approach by focusing the microorganisms with identified biochemical function is more productive than a description of the community composition and assembly when assessing cultural heritage biodeterioration, and this provides basic and useful information for effective protection strategies and management.

Abstract Soil, ranking third in importance after air and water for supporting life on land, provides habitat, nutrients, water, and a physical foundation for plants, animals, fungi, and microorganisms. Thus, forest ecosystems, like all land-based ecosystems, are entirely dependent on soil for their existence. Consequently, soil health is critical to ecosystem connectivity, since without healthy soils, there are no healthy ecosystems or species to connect with one another. Therefore, a foundational knowledge of soil properties, its formation, and its role in shaping forest ecosystems is essential to comprehending the concept of forest ecosystem connectivity. Soil is formed by the weathering of Earth’s rocky surface and reflects past climates, geology, and vegetation. By studying soil, we can learn about previous environmental conditions and predict which plants may grow on it now and in the future. Soil not only supports plants but is teeming with complex assemblages of diverse and abundant life. A handful of healthy forest soil can contain as many individual organisms as all the people on Earth. Plants play three pivotal roles in impacting soil properties, by shaping its physical structure, chemical composition, and the habitats it provides for other organisms. However, not only plants but all terrestrial organisms, from tiny microbes to larger animals, influence soil structure and function. Through burrowing, bioturbation, and microbial activity, soil organisms help shape the complex structure of soil, optimising it for their own needs. This chapter aims to describe the most important properties, services, and interactions of soil within forest ecosystems, underscoring its importance in maintaining forest health and connectivity.

Abstract Algal production is utilized in two ways: herbivores eat the living plants, while detritivores eat the dead remains. The distinction is, however, diffcult to make on rocky shores because most animals have a wide range of food sources. The gastropods that rasp bioIlms off rock surfaces take in microalgae, germlings of macroalgae, fungi, and probably algal detritus. Similarly, sea urchins may ingest both live and dead macroalgae and even some invertebrates. Here, therefore, we consider all these categories under the title ‘grazer’.

Endophytic filamentous fungi from three genera, Trichoderma, Aspergillus and Penicillium, isolated from saffron corms, were tested in vitro for their ability to solubilize phosphorus from tricalcium phosphate and rock phosphate. When fungal strain filtrates were transferred into NBRIP medium amended with Ca3(PO4)2, Penicillium aeris showed the highest soluble phosphorus concentration, reaching 39.66 μg/ml after 5 days of incubation at 28°C, while the concentrations of soluble phosphorus in Trichoderma filtrates ranged from 18.33 to 29.4µg/ml, and those in Aspergillus filtrates ranged from 32,33 to 35,66µg/ml. The pH values decreased over time, reaching their lowest points of 3.38 and 3.57 after 196 hours of incubation in the culture filtrates of Aspergillus niger and Penicillium aeris, respectively. For rock phosphate solubilization, Trichoderma isolates, along with Aspergillus nomius, A. ochraceus, A. niger, Penicillium sp. and P. aeris, are among the most effective. This study highlights endophytic fungi's role in enhancing soil fertility and plant growth by solubilizing phosphates.

Plants and animals require water, energy sources, and nutrients to make tissues and perform vital functions. The primary source of energy is the sun. Green plants use solar energy to manufacture organic compounds that are later oxidized to produce energy for both plants and animals. Many microorganisms produce energy by inorganic chemical reactions, but that source of energy is minor compared to the very large amounts of solar energy used by green plants. The major source of water and nutrients (other than CO2) for green plants is soil. Barren rocks, including ultramafic rock outcrop and talus, are colonized by lichens, which are symbiotic alliances of fungi and either cyanobacteria or green algae. These and other small organisms promote weathering and contribute to soil formation. Once soils are deep enough to support vascular plants (plants with roots), plants are the primary users of soils and producers of ecosystem biomass. Vascular plants send roots into soils and exploit both a high soil particle surface area and soil solutions, neither of which are available to lichens growing on rock surfaces. The surface area of particles in a soil 10 cm deep is about a thousand times greater than a planar bedrock surface if the soil is coarse sand, or about a billion times greater if the soil is clayey. With these dramatic increases in surface area accompanying soil formation, and lack of water retained on rock surfaces, it is easy to understand that ecosystem productivity is relatively low on rock surfaces and increases greatly with soil depth in very shallow soils. Annual plants approach maximum productivity in moderately deep soils and trees in deep or very deep soils. Ecosystems with serpentine soils are generally less productive than ecosystems with other kinds of soils, and they have unique plant species distributions. Therefore, serpentine soils attract attention from botanists who are interested in the profound effects that serpentine soils have on plant distributions and growth. These effects include those that affect the supply of water (section 8.1) and those that affect the supply of nutrients (section 8.2) to plants. These in turn affect plant growth and productivity (section 8.3).

This proposal is focused on examination of two plant interactions: parasitic with Orobanche, and symbiosis with arbuscular mycorrhiza fungi (AMF), and the involvement of a newly define plant hormones, strigolactones (SLs), in these plant interactions. In addition to strigolactones role in regulation of above-ground plant architecture, they are also known to be secreted from roots, and to be a signal for seed germination of the parasitic plants Orobanche. Moreover, secreted strigolactones were recognized as inducers of AMFhyphae branching. The present work was aimed at Generation of RNAi mutants of both tomato and Medicago, targeting multiple genes that may be involved in strigolactone production, carotenoid biosynthesis pathway, Pi signaling or other metabolic pathways, and hence affect AMF colonization and/or Orobanche resistance. Following the newly formed and existing RNAi mutants were examined for AMF colonization and Orobanche resistance. At the first phase of this project Orobanche seed germination assays and AMF colonization were examined in intact plants. These assays were shown to be effective and resulted with enhancement of Orobanche seed germination and AMF colonization in WT tomato plants, whereas roots of strigolactones impaired lines did not result with Orobanche seed germination and mycorrhiza colonization. Unexpectedly, root organ cultures (ROC) that were produced from the same wild type (WT) and mutant lines did not induce the Orobanche seed germination and AMFhyphal branching. This implies that under in vitro conditions ROC cultures are missing an important component for induction of Orobanche seed germination and AMFhyphal branching. In another line of experiments we have tested transgenic lines of Medicagotruncatula for AMFhuyphal branching and Orobanche seed germination assays. These lines included lines silenced for a GRAS transcription factor (RNAi 1845), an NBS-LRR type resistance gene (RNAi 1847), a kinase (RNAi 2403) and a protein of unknown function (RNAi 2417). In all cases, five independent transgenic root lines showed altered AMFphenotypes with reduced or aberrant colonization patterns. Following, we transformed tomato plants with the M. truncatulaTC 127050 PhosphoinositidekinaseRNAi construct. Transgenic lines that contained GUS constructs were used as control. All transgenic lines showed reduced level of Orobanche seed germination, masking any strigoalctones-specific effect. The research demonstrated that SLs production may not be examined in ROC –based bioassays. It was shown by the 3 independent assays employed in this project that none of the recognized characters of SLs may be reflected in these bioassays. However, when the whole plant root exudates were examined, SLs activity in root exudates was demonstrated. Hence, it can be concluded that the presence of an intact shoot, and possibly, shoot factors, may be necessary for production of SLs in roots. Another point of interest that rises from these results is that the presence of SLs is not necessary for AMF completion of life cycle. Hence, it may be concluded that SLs are important for AMFhyphal branching, before symbiosis, but not essential for AMF colonization and life cycle completion under ROC system conditions.