The ecology of lichenicolous lichens: a case-study in Italy.

This paper, with Italy as a case-study, provides a general overview on the ecology of lichenicolous lichens, i.e. those which start their life-cycle on the thallus of other lichens. It aims at testing whether some ecological factors do exert a positive selective pressure on the lichenicolous lifestyle. The incidence of some biological traits (photobionts, growth-forms and reproductive strategies) in lichenicolous and non-lichenicolous lichens was compared, on a set of 3005 infrageneric taxa potentially occurring in Italy, 189 of which are lichenicolous. Lichenicolous lichens have a much higher incidence of coccoid (non-trentepohlioid) green algae, crustose growth-forms and sexual reproduction. A matrix of the 2762 species with phycobionts and some main ecological descriptors was subjected to ordination. Lichenicolous lichens occupy a well-defined portion of the ecological space, tending to grow on rocks in dry, well-lit habitats where a germinating spore is likely to have a short life-span, at all altitudes. This corroborates the hypothesis that at least some of them are not true "parasites", as they are often called, but gather the photobionts - which have already adapted to local ecological conditions - from their hosts, eventually developing an independent thallus.

The Dolichens database: the lichen biota of the Dolomites.

The Dolichens project provides the first dynamic inventory of the lichens of the Dolomites (Eastern Alps, Italy). Occurrence records were retrieved from published and grey literature, reviewed herbaria, unpublished records collected by the authors, and new sampling campaigns, covering a period from 1820 to 2022. Currently, the dataset contains 56,251 records, referring to 1,719 infrageneric taxa, reported from 1820 to 2022, from hilly to nival belts, and corresponding to about half of the species known for the whole Alpine chain. Amongst them, 98% are georeferenced, although most of them were georeferenced a posteriori. The dataset is available through the Global Biodiversity Information Facility (GBIF; https://www.gbif.org/es/dataset/cea3ee2c-1ff1-4f8e-bb37-a99600cb4134) and through the Dolichens website (https://italic.units.it/dolichens/). We expect that this open floristic inventory will contribute to tracking the lichen diversity of the Dolomites over the past 200 years, and providing the basis for future taxonomic, biogeographical, and ecological studies.

The dataset of the CLU lichen herbarium (Calabria, Italy).

Background: Calabria, the southernmost tip of the Italian Peninsula, is a biogeographically very interesting region for lichenologists, characterised by the abundance of oceanic and suboceanic species with subtropical affinities, but also by the presence of the southernmost outposts of several boreal species on the highest peaks. The lichen biota of Calabria, which began to be intensively studied only from the 1980s, hosts more than 1000 infrageneric taxa. The lichen herbarium of the Botanical Garden of the University of Calabria (CLU) is the most relevant lichen collection from this region. It was established in 1985 and it presently includes 16926 specimens, most of which were collected in Calabria, although there are also several specimens from other parts of Italy and from abroad. New information: This dataset contains 16926 records of lichens for a total of 1316 species. Of the 15219 georeferenced specimens, 10254 were collected in Calabria, while 4965 in other administrative regions of Italy. The dataset is available through GBIF, as well as in ITALIC, the Information System of Italian Lichens.

Aggregation of Italian Lichen Data in ITALIC 7.0.

The creation of a coordinated publishing and aggregation system of biodiversity data is a challenging task, which calls for the adoption of open data standards. ITALIC, the information system on Italian lichens, originated from the conversion of the first Italian checklist into a database. While the first version was "frozen", the present version is continuously updated and provides access to several other data sources and services, such as ecological indicator values, ecological notes and information, traits, images, digital identification keys, etc. The identification keys especially are an ongoing work that will lead to a complete national flora by 2026. Last year, new services were added, one for aligning lists of names with the national checklist, the other for aggregating occurrence data deriving from the digitization of 13 Italian herbaria, forming a total of ca. 88,000 records, which are distributed under a CC BY license and can be exported as CSV files in the Darwin Core format. An aggregator for lichen data will encourage the national community of lichenologists to produce and aggregate further data sets, and it will stimulate data reuse according to the paradigms of open science.

Freshwater Lichens, Including New Species in the Genera Verrucaria, Placopyrenium and Circinaria, Associated with Lobothallia hydrocharis (Poelt & Nimis) Sohrabi & Nimis from Watercourses of Sardinia.

This work summarizes the results of the exploration of freshwater lichen biota on the island of Sardinia associated with the regional flagship species Lobothallia hydrocharis, a large-sized crustose lichen from the splash zone along mountain streams, so far known from Sardinia only. Molecular data were used to confirm its distinctiveness from other taxa and its systematic placement and to identify critical taxa among its associated lichen biota. We found 25 species of lichenized fungi, including three species new to science in the genera Verrucaria, Placopyrenium, and Circinaria, and seven species new to Sardinia (Hydropunctaria rheithrophila, Ionaspis chrysophana, I. odora, Verrucaria aquatilis, V. collematodes, V. pseudovirescens), or new to Southern Europe (V. devensis). Specific traits for the freshwater lichen biota of Sardinia were identified and compared to those reported from freshwater sites in the Alps and Carpathian mountains, e.g., a relative scarcity of subgelatinous lichens. Parasitic or epilichenic interactions were found frequently but only in the splash zone and not in the permanently submerged zone, i.e., two parasitic Placopyrenium species, and clearly lichenicolous thalli of Kuettlingeria atroflava and Lobothallia hydrocharis. Due to its specific trait profile and the great potential for the discovery of new species, we recommend the inclusion of Sardinian and further Mediterranean sites in continental-scale monitoring programs for freshwater lichens.

The Italian lichens dataset from the TSB herbarium (University of Trieste).

Background: The "Herbarium Universitatis Tergestinae" (TSB), with a total of ca. 50,000 specimens, includes the largest modern collection of lichens in Italy, with 25,796 samples collected from all over the country since 1984, representing 74% of all taxa known to occur in Italy. Almost all specimens have been georeferenced "a posteriori". The dataset is available through GBIF, as well as in ITALIC, the Information System of Italian Lichens. New information: The TSB Herbarium hosts the largest modern lichen collection in Italy, with a total of ca. 50,000 specimens. This dataset contains all of the 25,796 specimens collected within the administrative borders of Italy. Amongst them, 98% are georeferenced and 87% have the date of collection. The dataset includes several type specimens (isotypes and holotypes) and exsiccata.

Antibiotic and Nematocidal Metabolites from Two Lichen Species Collected on the Island of Lampedusa (Sicily).

The antibiotic and nematocidal activities of extracts from two coastal lichen species collected on Lampedusa Island (Sicily), Ramalina implexa Nyl. and Roccella phycopsis Ach., were tested. Methyl orsellinate, orcinol, (+)-montagnetol, and for the first time 4-chlororcinol were isolated from Roccella phycopsis. (+)-Usnic acid was obtained from Ramalina implexa. The crude organic extract of both lichen species showed strong antibiotic activity against some bacterial species and nematocidal activity. Among all the pure metabolites tested against the infective juveniles (J2) of the root-knot nematode (RKN) Meloydogine incognita, (+)-usnic acid, orcinol, and (+)-montagnetol had significant nematocidal activity, comparable with that of the commercial nematocide Velum® Prime, and thus they showed potential application in agriculture as a biopesticide. On the contrary, methyl orsellinate and 4-chlororcinol had no nematocidal effect. These results suggest that the substituent pattern at ortho-para-position in respect to both hydroxyl groups of resorcine moiety, which is present in all metabolites, seems very important for nematocidal activity. The organic extracts of both lichens were also tested against some Gram-positive and Gram-negative bacteria. Both extracts were active against Gram-positive species. The extract of Ramalina implexa showed, among Gram-negative species, activity against Escherichia coli and Acinetobacter baumannii, while that from Roccella phycopsis was effective towards all test strains, with the exception of Pseudomonas aeruginosa. The antimicrobial activity of (+)-usnic acid, methyl orsellinate, and (+)-montagnetol is already known, so tests were focused on orcinol and 4-chlororcinol. The former showed antibacterial activity against all Gram positive and Gram-negative test strains, with the exception of A. baumannii and K. pneumoniae, while the latter exhibited a potent antibacterial activity against Gram-positive test strains and among Gram-negative strains, was effective against A. baumannii and K. pneumonia. These results suggest, for orcinol and 4-chlororcinol, an interesting antibiotic potential against both Gram-positive and Gram-negative bacterial strains.

A hotspot of lichen diversity and lichenological research in the Alps: the Paneveggio-Pale di San Martino Natural Park (Italy).

A checklist of 916 lichenised taxa is reported from the Paneveggio-Pale di San Martino Natural Park and its surroundings (Trentino-Alto Adige, N Italy), based on 7351 records from: (a) 72 literature sources, (b) eight public and private herbaria and (c) field observations by some of the authors. The study area appears as a hotspot of lichen diversity, hosting 30.1% of the lichen biota of the Alps in a territory that has 0.064% of their total surface area. This is mainly due to its high climatical, geological and orographic heterogeneity, but also to the long history of lichenological exploration, that started in the 19th century with Ferdinand Arnold and is still ongoing. The present work highlights the importance of detailed species inventories to support knowledge of biodiversity patterns, taxonomy and ecology and to properly address conservation issues. Fuscideamollisvar.caesioalbescens, Hydropunctariascabra, Protoparmeliabadiavar.cinereobadia and Variosporapaulii are new to Italy, 18 other taxa are new to Trentino-Alto Adige.

Refining the picture: new records to the lichen biota of Italy.

Based on the analysis of both historical and recent collections, this paper reports an annotated list of taxa which are new to the lichen biota of Italy or of its administrative regions. Specimens were identified using a dissecting and a compound microscope; routine chemical spot tests and standardized thin-layer chromatography (TLC or HPTLC). The list includes 225 records of 153 taxa. Twenty taxa are new to Italy, the others are new to one or more administrative regions, with 15 second records and 5 third records for Italy. Some of the species belong to recently-described taxa, others are poorly known, sterile or ephemeral lichens which were largely overlooked in Italy. Several species are actually rare, either because of the rarity of their habitats (e.g. old-growth forests), or because in Italy they are at the margins of their bioclimatic distribution. The picture of the lichen biota of Italy has now new pixels, but its grain is still coarse. Further analysis of historical collections, increased efforts in the exploration of some areas, and the taxonomic revision of critical groups are still necessary to provide more complete distributional data for new biogeographic hypotheses, taxonomic and ecological research, and biodiversity conservation.

Match Algorithms for Scientific Names in FlorItaly, the Portal to the Flora of Italy.

Scientific names are not part of everyday language in any modern country, and their input as strings in a query system can be easily associated with typographical errors. While globally unique identifiers univocally address a taxon name, they can hardly be used for querying a database manually. Thus, matching algorithms are often used to overcome misspelled names in query systems in several data repositories worldwide. In order to improve users' experience in the use of FlorItaly, the Portal to the Flora of Italy, a near match algorithm to resolve misspelled scientific names has been integrated in the query systems. In addition, a novel tool in FlorItaly, capable of rapidly aligning any list of names to the nomenclatural backbone provided by the national checklists, has been developed. This manuscript aims at describing the potential of these new tools.

The lichens of the Majella National Park (Central Italy): an annotated checklist.

The botanical exploration of the Majella National Park has a long tradition dating back to the eighteenth century. However, the lichen biota of this area is still poorly investigated. To provide a baseline for future investigations, in this annotated checklist, we summarised all available information on the occurrence of lichens in the Majella National Park, retrieved from previous literature, herbarium material and original data produced by recent research. The checklist includes 342 infrageneric taxa. However, seven taxa are considered as dubious, thus setting the number of accepted taxa at 335, i.e. 45.8% of those currently known to occur in the Abruzzo Region. This checklist provides a baseline of the lichens known to occur in the Majella National Park, highlighting the potential of this area as a hotspot of lichen biodiversity, especially from a biogeographical point of view as indicated by the occurrence of several arctic-alpine species that form disjunct populations in the summit area of the massif.

FlorItaly - the portal to the Flora of Italy.

Digital data concerning the flora of Italy are largely fragmented among different resources hosted on different platforms, and often with different data standards, which are neither connected by a common access point, nor by web services, thus constituting a relevant obstacle to data access and usage. Taxonomic incongruences add a further complication. This paper describes "FlorItaly", an online information system which allows to access and query updated information on the checklist of the flora of Italy, aiming at becoming an aggregator for Italian botanical resources. "FlorItaly" was developed in a collaborative effort by more than 50 taxonomists, with the support of the Italian Botanical Society, and of Project "Dryades" (University of Trieste), to provide a better and reliable organization of botanical knowledge in Italy, as well as a relevant simplification for data retrieval, and a further stimulus towards a more collaborative approach in botanical research.

The lichens of the Alps - an annotated checklist.

This is the first attempt to provide an overview of the lichen diversity of the Alps, one of the biogegraphically most important and emblematic mountain systems worldwide. The checklist includes all lichenised species, plus a set of non- or doubtfully lichenised taxa frequently treated by lichenologists, excluding non-lichenised lichenicolous fungi. Largely based on recent national or regional checklists, it provides a list of all infrageneric taxa (with synonyms) hitherto reported from the Alps, with data on their distribution in eight countries (Austria, France, Germany, Liechtenstein, Monaco, Italy, Slovenia, Switzerland) and in 42 Operational Geographic Units, mostly corresponding to administrative subdivisions within the countries. Data on the main substrates and on the altitudinal distribution are also provided. A short note points to the main ecological requirements of each taxon and/or to open taxonomic problems. Particularly poorly known taxa are flagged and often provided with a short description, to attract the attention of specialists. The total number of infrageneric taxa is 3,163, including 117 non- or doubtfully lichenised taxa. The richness of the lichen biota fairly well corresponds with the percent of the Alpine area occupied by each country: Austria (2,337 taxa), Italy (2,169), France (2,028), Switzerland (1,835), Germany (1,168), Slovenia (890) and Lichtenstein (152), no lichen having ever been reported from Monaco. The number of poorly known taxa is quite high (604, 19.1% of the total), which indicates that, in spite of the Alps being one of the lichenologically most studied mountain systems worldwide, much work is still needed to reach a satisfactory picture of their real lichen diversity. Thirteen new combinations are proposed in the genera Agonimia, Aspicilia, Bagliettoa, Bellemerea, Carbonea, Lepra, Miriquidica, Polysporina, Protothelenella, Pseudosagedia and Thelidium.

Airborne trace elements near a petrochemical industrial complex in Thailand assessed by the lichen Parmotrema tinctorum (Despr. ex Nyl.) Hale.

Several trace elements discharged by the petrochemical industry are toxic to humans and the ecosystem. In this study, we assessed airborne trace elements in the vicinity of the Map Ta Phut petrochemical industrial complex in Thailand by transplanting the lichen Parmotrema tinctorum to eight industrial, two rural, and one clean air sites between October 2013 and June 2014. After 242 days, the concentrations of As, Cd, Co, Cr, Cu, Hg, Mo, Ni, Pb, Sb, Ti, V, and Zn in lichens at most industrial sites were higher than those at the rural and the control sites; in particular, As, Cu, Mo, Sb, V, and Zn were significantly higher than at the control site (p < 0.05). Contamination factors (CFs) indicated that Cd, Cu, Mo, and Sb, which have severe health impacts, heavily contaminated at most industrial sites. Principal component analysis (PCA) showed that most elements were associated with industry, with lesser contributions from traffic and agriculture. Based on the pollution load indexes (PLIs), two industrial sites were highly polluted, five were moderately polluted, and one had a low pollution level, whereas the pollution load at the rural sites was comparable to background levels. This study reinforces the utility of lichens as cost-effective biomonitors of airborne elements, suitable for use in developing countries, where adequate numbers of air monitoring instruments are unavailable due to financial, technical, and policy constraints.

From local checklists to online identification portals: a case study on vascular plants.

Checklists, the result of time-consuming exploration and painstaking bibliographic research, can be easily converted into online databases, which have the advantage of being updatable online in real time, and of reaching a much wider audience. However, thousands of local checklists (Natural Parks, protected areas, etc.) are still available on paper only, and most of those published online appear as dry lists of latin names, which strongly reduces their outreach for a wider audience. The University of Trieste has recently started the publication of several local checklists in a way that may be more appealing for the general public, by linking species' names to archives of digital resources, and especially to digital identification tools produced by software FRIDA (FRiendly IDentificAtion). The query interfaces were developed on the basis of feedback from a wide range of users. The result is no longer a simple list of names accessible on the Web, but a veritable multimedial, interactive portal to the biodiversity of a given area. This paper provides an example of how relevant added value can be given to local lists of taxa by embedding them in a complex system of biodiversity-related resources, making them usable for a much wider audience than a restricted circle of specialists, as testified by the almost 1.000.000 unique visitors reached in 2014. A critical mass of digital resources is also put at disposal of the scientific community by releasing them under a Creative Commons license.

Development of a standard protocol for monitoring trace elements in continental waters with moss bags: inter- and intraspecific differences.

This paper is a contribution for validating a standard method for trace element monitoring based on transplants and analysis of aquatic bryophytes, in the framework of the EC Directive 2000/60. It presents the results of an experiment carried out to assess significant differences in the amount and variability of As, Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb and Zn in three moss species (Cinclidotus aquaticus, Fontinalis antipyretica, Platyhypnidium riparioides) and two different parts of the moss (whole plant vs apical tips). Mosses were caged in bags made of a plastic net and transplanted for 2 weeks to an irrigation canal impacted by a waste water treatment plant. Trace element concentrations were measured by inductively coupled plasma optical emission spectrometry (ICP-OES) and inductively coupled plasma mass spectrometry (ICP-MS) before and after exposure to the experimental and control sites in five samples. Enrichment factors >>2 were found for Cu, Ni, Mn, Pb and Zn in all moss species, lower in C. aquaticus, intermediate in F. antipyretica and higher in P. riparioides (the species we recommend to use). The analysis of apical tips after exposure instead of the whole plant led to (I) lower concentrations of As, Co, Cr, Fe and Zn in C. aquaticus (-7 to -30%) and of Fe and Pb (-13, -18%) in P. riparioides, (II) higher concentrations of Cu, Ni and Zn (+14 to +18%) in P. riparioides, while (III) no significant difference (p > 0.05) in F. antipyretica. Data variability after exposure was generally lower in apical tips, especially in C. aquaticus and in F. antipyretica, less in P. riparioides. In the aim of standardizing the moss-bag technique, the analysis of apical tips is recommended.

Moss bags as sentinels for human safety in mercury-polluted groundwaters.

An equation to estimate Hg concentrations of <4 µg/L in groundwaters of a polluted area in NE Italy was set out by using transplants of the aquatic moss Rhynchostegium riparioides as trace element bioaccumulators. The equation is derived from a previous mathematical model which was implemented under laboratory conditions. The work aimed at (1) checking the compliance of the uptake kinetics with the model, (2) improving/adapting the model for groundwater monitoring, (3) comparing the performances of two populations of moss collected from different sites, and (4) assessing the environmental impact of Hg contamination on a small river. The main factors affecting Hg uptake in the field were-as expected-water concentration and time of exposure, even though the uptake kinetics in the field were slightly different from those which were previously observed in the lab, since the redox environmental conditions influence the solubility of cationic Fe, which is a negative competitor of Hg(2+). The equation was improved by including the variable 'dissolved oxygen concentration'. A numerical parameter depending on the moss collection site was also provided, since the differences in uptake efficiency were observed between the two populations tested. Predicted Hg concentrations well fitted the values measured in situ (approximately ±50%), while a notable underestimation was observed when the equation was used to predict Hg concentration in a neighbouring river (-96%), probably due to the organic pollution which hampers metal uptake by mosses.

Implementation of an active 'bryomonitoring' network for chemical status and temporal trend assessment under the Water Framework Directive in the Chiampo Valley's tannery district (NE Italy).

An innovative network based on transplanted bryophytes providing a continuous monitoring of the priority substances Cd, Hg, Ni, and Pb and other trace elements (Co, Cr, Cu, Fe, Mn, Zn) was designed for the watercourses flowing across an industrial district of NE Italy where both permitted and illegal wastes cause sporadic, intermittent or chronic events of environmental alteration. During a two-year preliminary survey, over 300 biomonitoring actions ('moss bag' transplantation and recovery) were successfully carried out at 25 stations: 190 of them occurred under acceptable conditions and provided results suitable for comparisons. Five environmental priorities were assessed and characterized in space and time. For these situations local authorities drafted a protocol for data management, to plan official controls and dissuasive actions. The 'moss bag' technique allows a flexible approach for both surveillance monitoring (trend assessment) and investigations (point source detection) in compliance with the Water Framework Directive 2000/60/EC as suggested by the recent Guidance Document on chemical monitoring of sediment and biota.

DNA barcoding as an effective tool in improving a digital plant identification system: a case study for the area of Mt. Valerio, Trieste (NE Italy).

BACKGROUND: Identification keys are decision trees which require the observation of one or more morphological characters of an organism at each step of the process. While modern digital keys can overcome several constraints of classical paper-printed keys, their performance is not error-free. Moreover, identification cannot be always achieved when a specimen lacks some morphological features (i.e. because of season, incomplete development or miss-collecting). DNA barcoding was proven to have great potential in plant identification, while it can be ineffective with some closely related taxa, in which the relatively brief evolutionary distance did not produce differences in the core-barcode sequences. METHODOLOGY/PRINCIPAL FINDINGS: In this paper, we investigated how the DNA barcoding can support the modern digital approaches to the identification of organisms, using as a case study a local flora, that of Mt. Valerio, a small hill near the centre of Trieste (NE Italy). The core barcode markers (plastidial rbcL and matK), plus the additional trnH-psbA region, were used to identify vascular plants specimens. The usefulness of DNA barcoding data in enhancing the performance of a digital identification key was tested on three independent simulated scenarios. CONCLUSIONS/SIGNIFICANCE: Our results show that the core barcode markers univocally identify most species of our local flora (96%). The trnH-psbA data improve the discriminating power of DNA barcoding among closely related plant taxa. In the multiparametric digital key, DNA barcoding data improves the identification success rate; in our simulation, DNA data overcame the absence of some morphological features, reaching a correct identification for 100% of the species. FRIDA, the software used to generate the digital key, has the potential to combine different data sources: we propose to use this feature to include molecular data as well, creating an integrated identification system for plant biodiversity surveys.