Author: Bernard Goffinet

New publication on HGT from fungi to mosses

Sun G., S. Bai, Y. Guan, Q. Wang, S. Wang, Y. Liu, H. Liu, B. Goffinet, Y. Zhou, M. Paoletti, X. Hu, F. Haas, N. Fernendez-Pozo, A. Czyrt, H. Sun, S. Rensing & J. Huang. 2020. Are fungi-derived genomic regions related to antagonism toward fungi in mosses? New Phytologist 228: 1169–1175. pdf

In this article the authors “report two genomic regions in the nuclear genome of the moss Physcomitrium patens, previously Physcomitrella patens (Medina et al., 2019; Rensing et al., 2020), that contain mostly fungi-specific genes and mobile genetic elements. These two regions were identified in our genome screening for horizontally acquired genes in P. patens. Available evidence indicates that these fungi-specific genes are likely involved in the interaction between mosses and fungi. We discuss how these fungi-specific genes might have contributed to the defense against fungal and other microbial pathogens, as well as the loss of MFAs in mosses.”

On-line article on Sub-Antarctic bryophytes and lichens

View of region of Aysen, Sub-Antarctic ChileIntroduction to article “Los pioneros vegetales del Estrecho de Magallanes” published on-line by the NGO Laderasur reads (google translation): Thousands of years ago, the Strait of Magellan was not what we know now, but rather an ice field. Thanks to the deglaciation, large lakes originated and the soils were covered with the pioneering organisms of the place: liquids, bryophytes and fungi. In this article, the scientists Laura Sánchez-Jardón, Bernard Goffinet, Ricardo Rozzi and the photographer Felipe Soza describe some representatives of these pioneers from the subantarctic region of Chile, relating them to the process of human colonization, recounting three successive discoveries that were made in the Strait of Magellan.

 

Visit article for nice pictures! Below is an English translation:

Thousands of years ago, the Strait of Magellan was not what we know now, but rather an ice field. Thanks to the deglaciation, large lakes originated and the soils were covered with the pioneering organisms of the place: liquids, bryophytes and fungi. In this article, scientists Laura Sánchez-Jardón, Bernard Goffinet, Ricardo Rozzi and photographer Felipe Soza describe some of the representatives of these pioneers from the region where they were made in the Strait of Magellan.

 

Twenty thousand years ago the Strait of Magellan was not such, but a vast field of ice. During the deglaciation started some sixteen thousand years ago, the retreat of the ice in its central part and surrounding areas gave rise to large lakes and terrestrial ecosystems whose rocks and soils were progressively covered by pioneering organisms: lichens, bryophytes and fungi.

 

This first discovery of the Strait of Magellan, associated with the melting of the ice cover, was producing unique processes of ecological succession led by small colonizing organisms, plant pioneers that generated the first ecosystems with a unique biota whose exuberance at the “end of the world” it is greater than in any other region of the planet.

 

When Hernando de Magallanes arrived at the southern tip of America five hundred years ago, there was a second discovery of the biota of the strait that today bears his name. The promise of riches offered by the New World, Terra Incognita, motivated scientists to explore the region, who were surprised by the abundance and diversity of lichens, mosses and fungi that grew on the ground and the trunks of subantarctic forests.

 

Some of these unique species are Ganoderma australe, which grows on coigües, lengas and ñires and is striking for its tongue or ear shape; in fact, they are known as “stick ears”; Cortinarius magellanicus, whose surprising color (bright purple) awakens the imaginations of scientists, tourists, and various Magellan co-inhabitants; some are even associated with algae and form lichens: Peltigera patagonica, one of the few species that appears on the tree line in the upper part of the mountain range and whose endemic distribution in the subantarctic region makes this species characteristic of it; Protousnea magellanica or “old man’s beard”, as this lichen is commonly called, abundant and widely distributed in subantarctic forests; along with Pseudocyphellaria berberina, they are endemic to the Southern Cone of South America.

 

In February 1834, Charles Darwin continued his navigation through the strait towards Puerto del Hambre aboard the Beagle, exploring the Shoal cove sector along the way. The British noted that this landscape represents a transition zone between aridity and humidity, between «Patagonia and Tierra del Fuego; many plants from these regions grow here ». The next day they arrived in Puerto del Hambre and on February 6 of that year, the young naturalist made his memorable ascent to Mount Tarn, recording in his Diary: I found a second species in other beech species in Chile; and Dr. Hooker informs me that a third species has recently been discovered in Van Diemen’s Land [Tasmania]. How unique is this relationship between parasitic fungi and the trees on which they grow, in the farthest parts of the world! In Tierra del Fuego, the fungus in its smooth and mature state is collected in large quantities by women and children, and is eaten without cooking.

 

The young naturalist was referring here to the digueñes or dihueñes (Cyttaria spp.), Also recognized in other scientific expeditions by the southern hemisphere during the 19th century. These endemic fungi, metaphorically called “Indian bread”, that grew on the trunks and branches of the coigüe and lenga, both trees of the dominant Nothofagus genus in the region, were already discovered by the first human populations that reached the strait and other areas from the Magellan subantarctic ecoregion, who found in them a unique food source.

 

Indeed, little by little, the extreme richness of fungi was revealed, as well as the exceptional diversity of small plants in the sub-Antarctic region of the Strait of Magellan: mosses, liverworts and hornworts, which together are called bryophytes. These small organisms facilitated the recolonization of life once the ice was removed in the Strait of Magellan, sheltering in the neighboring territories the original peoples that arrived more than ten thousand years ago.

 

Just twenty years ago, a third discovery of the Magallanes region south of the strait, in the Cape Horn archipelagos, happened fortuitously, leading to the identification of this sub-Antarctic region as a world center of diversity of bryophytes and lichens. The unique biodiversity that inhabits these archipelagos is of great value for life on the planet and we must jointly take care of this biota and ecosystems that contribute to planetary health.

 

Among these species are the Dendroligotrichum dendroides or “pinito moss”, with the appearance of a miniature tree – up to 20 centimeters the largest -; Bartramia mossmaniana; Sphagnum magellanicum, an endemic species of the southern hemisphere that proliferates locally on accumulations of dead organic matter, forming a particular type of ecosystem called «peatland», extraordinarily important in carbon fixation and in the retention of water and nutrients; in especially humid and shady places are also found hornwort like Phaeomegaceros chiloensis.

 

These miniature forests of fungi, lichens and bryophytes, in addition to all the associated fauna of invertebrates, have accompanied the three discoveries of the Strait of Magellan. From an ethical point of view, they can be considered as Magellanic co-inhabitants: literally, they have shared the habitats of the strait with humans since the first settlement and have had a leading role in their food, health, fire source, water, culture and , lately, in the scientific vanguard. From the south of the world, the knowledge of the great Magellanic flora will contribute to its conservation and the sustainability of the planet in the scenario of global socio-environmental change. About the authors: Laura Sanchez-Jardón, is a Doctor in ecology and environment at the Complutense University of Madrid; Ricardo Rozzi is a Doctor in Ecology and a Master in Philosophy from the University of Connecticut; Bernard Goffinet is a Doctor in Botany University of Connecticut and Jorge Felipe Soza Soza (Instagram: @felipesozaphotography)

 

New publication on comparative transcriptomics

Potential reductions series in sporophyte size in Funariaceae: A. Funaria, B. Physcomitrium pyriforme. C: P. serratum (capsule hidden among leaves).
Potential reductions series in sporophyte size in Funariaceae: A. Funaria, B. Physcomitrium pyriforme. C: P. serratum (capsule hidden among leaves). From Vanderpoorten & Goffinet 2009.

Kirbis A., M. Waller, M. Ricca, Z. Bont, A. Neubauer, B. Goffinet & P. Szövényi. 2020. The transcriptomic landscape of differential sporophyte development in two mosses, Physcomitrium (Physcomitrellapatens and Funaria hygrometrica. Frontiers in Plant Sciences11: 747. pdf

Abstract readsUnderstanding the molecular basis of morphological shifts is a fundamental question of evolutionary biology. New morphologies may arise through the birth/death of genes (gene gain/loss) or by reutilizing existing gene sets. Yet, the relative contribution of these two processes to radical morphological shifts is still poorly understood. Here, we use the model system of two mosses, Funaria hygrometrica and Physcomitrium (Physcomitrella) patens, to investigate the molecular mechanisms underlying contrasting sporophyte architectures. We used comparative analysis of time-series expression data for four stages of sporophyte development in both species to address this question in detail. We found that large-scale differences in sporophytic architecture are mainly governed by orthologous (i.e., shared) genes frequently experiencing temporal gene expression shifts between the two species. While the absolute number of species-specific genes expressed during sporophyte development is somewhat smaller, we observed a significant increase of their proportion in preferentially sporophyte expressed genes, suggesting a fundamental role in the sporophyte phase. However, further functional studies are necessary to determine their contribution to diverging sporophyte morphologies. Our results add to the growing set of studies suggesting that radical changes in morphology may rely on the heterochronic expression of conserved regulators. 

Two new publications on lichens

Emmanuelia patinifera (photo Lücking)
Emmanuelia patinifera (photo Lücking)

We propose a new genus to accommodate some species of lichenized fungi from the New World, including the Southeastern United States, in a new genus, as part of the ongoing studies of the evolution of the Lobariaceae.

Simon A., R. Lücking, B. Moncada, J.A. Mercado-Díaz, F. Bungartz, M. Cáceres, E. Gumboski, S. Maria de Azevedo Martinsi, D. Parker & B. Goffinet. 2020. Emmanuelia, a new genus of lobarioid lichen-forming fungi (lichenized Ascomycota: Peltigerales). Plant and Fungal Systematics 65: 76–94. pdf

Abstract reads: The former family Lobariaceae, now included in Peltigeraceae as subfamily Lobarioideae, has undergone substantial changes in its generic classification in recent years, based on phylogenetic inferences highlighting the polyphyly of the speciose genera Lobaria, Pseudocyphellaria and Sticta. Here we introduce the new genus Emmanuelia, named in honor of Prof. Emmanuël Sérusiaux for his extensive work on the Peltigerales. Emmanuelia currently comprises twelve species. It is superficially similar to the lobarioid genus Ricasolia, but differs by its apothecia, rimmed by overarching and often crenulate to lobulate margins, with the parathecium (proper excipulum) and the amphithecium (thalline excipulum formed by the thallus cortex) apically separated and of a different structure. Also, ascospore dimensions and shape differ between the two genera, with the ascospores of Emmanuelia being longer and narrower. Molecular phylogenetic analyses using DNA nucleotide sequences of the internal transcribed spacer region (ITS) and the small subunit of mitochondrial ribosomal DNA (mtSSU) confirm that Emmanuelia belongs to the Lobaria s.lat. clade and forms a monophyletic group sister to the lineage consisting of Dendriscosticta, Lobariella and Yoshimuriella. None of the available generic names of lobarioid lichens can be applied to this group, and consequently a new name is proposed for this new genus, which is typified with E. ravenelii comb. nov. Eleven other species are transferred to Emmanuelia: E. americana comb. nov., E. conformis comb. nov., E. cuprea comb. nov., E. elaeodes comb. nov., E. erosa comb. nov., E. excisa comb. nov., E. lobulifera comb. nov., E. ornata comb. nov., E. patinifera comb. nov., E. pseudolivacea comb. nov. and E. tenuis comb. nov. The genus is represented in North America by three species, including E. lobulifera, which is resurrected from synonymy with E. (Lobaria) tenuis, a South American species, and E. ornata, whose populations were previously treated under E. (Lobaria) ravenelii.

 

Suspected to represent a new species, populations of Peltigera from Papua New Guinea are now recognized as P. serusiauxii: Magain N., B. Goffinet, A. Simon, J. Seelan Sathiya, I. Medeiros, F. Lutzoni & J. Miadlikowska. 2020. Peltigera serusiauxii, a new species in section Polydactylon from Papua New Guinea and Malaysia (Lecanoromycetes, Ascomycota). Plant and Fungal Systematics 65: 139–146. pdf

Abstract reads: Peltigera serusiauxii is proposed here as a new species from Papua New Guinea and Sabah, northern Borneo (Malaysia). The species belongs to the polydactyloid clade of section Polydactylon. Because of its large thalli with a glabrous upper surface, this species was previously identified as P. dolichorhiza, but it differs by its polydactylon-type lower surface and the high amount of dolichorrhizin. It appears to be a strict specialist in its association with Nostoc phylogroup IX throughout its known distribution. This is one of many undescribed species remaining to be formally described within the genus Peltigera,especially in Asia and Australasia.

 

New publication on tardigrades!

mple of the possible mechanism of endozoochorous dispersal of tardigrades by White-bellied Seedsnipe (Attagis malouinus).

It started with a search for bryophyte fragments in the feces of high Andean birds on Navarino island (see post) when Michael Robertson and Nicholas Russo (former EEB student now at UCLA) discovered tardigrades in the samples. Their observation are now published in Polar Biology.

Robertson M.W., N.J. Russo, S.J. McInnes, B. Goffinet & J.E. Jiménez. 2020. Potential dispersal of tardigrades by birds through endozoochory: evidence from sub-Antarctic White-bellied Seedsnipe (Attagis malouinus). Polar Biology in press.

Abstract reads: Tardigrades are potentially dispersed by birds, but the extent of the interactions between birds and tardigrades is virtually unknown. We discovered nine tardigrades within feces of White-bellied Seedsnipe (Attagis malouinus) collected from high Andean tundra on Navarino Island, Chile. Eight of the tardigrade specimens began moving once rehydrated. Two specimens belonged to the genus Adropion (Hypsibiidae), one to the Macrobiotus (Macrobiotidae), and five could not be identified. A ninth specimen was a species of Isohypsibius in an embryonic egg state. These tardigrades could have passed through the avian digestive tract after incidental ingestion or burrowed into the feces post-defecation to feed on microorganisms and undigested plant matter present in the feces. To our knowledge, this is the first discovery of tardigrades in bird feces and may have implications for tardigrade distributions if birds transport tardigrades endogenously.

New publication on bryophytes

Juan Carlos Villarreal published the last chapter of his dissertation, focused on the population genetic study of Nothoceros aenigmaticus, a clonal hornwort with allopatric sexual populations. The study was picked up and completed by Juan Carlos’ postdoc, Marta Alonso Garcia, who had visited our lab when she was finishing her Ph.D. in Murcia, Spain. Alonso Garcia M., Villarreal J.C., K. McFarland & B. Goffinet. 2020. Population genomics confirms extreme sex ratio of a clonal bryophyte. Frontiers in Plant Science 11: 495. pdf

 

Abstract reads: The southern Appalachian (SA) is one of the most biodiversity−rich areas in North America and has been considered a refugium for many disjunct plant species, from the last glacial period to the present. Our study focuses on the SA clonal hornwort, Nothoceros aenigmaticus J.C. Villarreal & K.D. McFarland. This hornwort was described from North Carolina and is widespread in the SA, growing on rocks near or submerged in streams in six and one watersheds of the Tennessee (TR) and Alabama (AR) Rivers, respectively. Males and female populations occur in different watersheds, except in the Little Tennessee (TN) River where an isolated male population exists ca. 48 km upstream from the female populations. The sex ratio of 1:0 seems extreme in each population. In this study, we use nuclear and organellar microsatellites from 250 individuals from six watersheds (seven populations) in the SA region and two populations from Mexico (23 individuals). We, then, selected 86 individuals from seven populations and used genotyping by sequencing to sample over 600 bi-allelic markers. Our results suggest that the SA N. aenigmaticus and Mexican plants are a nested within a clade of sexual tropical populations. In the US populations, we confirm an extreme sex ratio and only contiguous US watersheds share genotypes. The phylogenetic analysis of SNP data resolves four clusters: Mexican populations, male plants (Little Pigeon and Pigeon river watersheds) and two clusters of female plants; one from the Little Tennessee and Hiwassee Rivers (TR) and the other from the Ocoee (TR) and Coosa (AR) Rivers. All clusters are highly differentiated (Fst values over 0.9). In addition, our individual assignment analyses and PCAs reflect the phylogenetic results grouping the SA samples in three clades and recovering males and female plants with high genetic differentiation (Fst values between 0.5 and 0.9 using microsatellites and bi-allelic markers). Our results point to Pleistocene events shaping the biogeographical pattern seen in US populations. The extreme sex ratio reflects isolation and highlights the high vulnerability of the populations in the SA.

Zach’s fieldwork funded by ABLS!

Niebla sp. from California

Zachary Muscavitch joined the Lewis and Goffinet lab to pursue his interests in the lichen symbiosis, with a focus on both symbionts, the green alga and the fungus. By December he designed a project focused on Niebla and Vermilacinia, endemic to Western North America, conducted preliminary fieldwork in California and generated encouraging data to further develop his project. He is planning on sampling populations in Baja California, Mexico. His project is now supported by the American Bryological and Lichenological Society. Congratulations Zach, and let’s hope you can travel to this Niebla and Vermilacinia hotspot.

Summer Fellowships to Olivia

Olivia LemieuxOlivia Lemieux, who joined the lab last fall to conduct an independent study was awarded a Summer Undergraduate Research Fellowship from UCONN for her project entitled “Hybridization in the Physcomitrium pyriforme complex: Identifying maternal and paternal progenitors of hybrid species” Congratulations and let’s hope you can pursue this project this summer!

New publication

Rensing S.A., B. Goffinet, R. Meyberg, S.-Z. Wu & M. Bezanilla. 2020. The moss Physcomitrium(Physcomitrella) patens: a model organism for non-seed plants. The Plant Cell 32: 1361–1376. pdf

Abstract reads: Since the discovery two decades ago that transgenes are efficiently integrated into the genome of Physcomitrella patens by homologous recombination, this moss has been a premier model system to study evolutionary developmental biology (evo-devo) questions, stem cell reprogramming, and the biology of non-vascular plants. P. patens was the first non-seed plant to have its genome sequenced. With this level of genomic information together with increasing molecular genetic tools, a large number of reverse genetic studies have propelled the use of this model system. A number of technological advances have recently opened the door to forward genetics as well as extremely efficient and precise genome editing in P. patens. Additionally, careful phylogenetic studies with increased resolution have suggested that P. patens emerged from within Physcomitrium. Thus, rather than Physcomitrella patens, the species should be named Physcomitrium patens. Here we review these advances and describe the areas where P. patens has had the most impact on plant biology.

Chapter on Ecotourism with a hand-lens is out!

Cover of book Rozzi R., M.T. La Valle, S. Russell, B. Goffinet & F. Massardo. 2020. Ecotourism with a hand-lens: a field environmental philosophy experience from the South of the world. Pages: 222–239. In R. Frodeman & E. Brister (eds.), A Guide to Field Philosophy. Case Studies and Practical Strategies (1st edition). Routledge, a Taylor and Francis Group. Link to book

 

The chapters starts with: Earth is not only a biophysical entity; it is also a word that influences the way we understand and relate to the biophysical reality of the planet. Scientists often forget the gravity of words and focus on the biophysical reality. Conversely, philosophers often focus on examining the language of cultural reality, ignoring the biophysical realm. Biocultural ethics unites biological and cultural realities in one conceptual framework (Rozzi, 2001). In addition, it promotes a contextual and systemic approach that shows consideration for the vast biophysical and cultural diversity found in different regions of the world.

In this chapter, we focus on a transdisciplinary endeavor launched in 1999. This long-term project advocates for a biocultural perspective at the southern end of the American continent, in the Cape Horn County of Chile. A team of philosophers, scientists, artists, members of the Yahgan indigenous community, government authorities, Navy officers, schoolteachers, and members of the local community in the world’s southernmost city, Puerto Williams, created the Omora Ethnobotanical Park.1 This endeavor has resulted in changes in the local sciences, arts, and humanities curricula and educational activities at all levels of formal education, as well as with tourists, members of the public, and policymakers from inside and outside Chile.