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1. Coniochaeta elegans sp. nov., Coniochaeta montana sp. nov. and Coniochaeta nivea sp. nov., three new species of endophytes with distinctive morphology and functional traits

   https://doi.org/10.1099/ijsem.0.005003  

   Arnold, A. Elizabeth ; Harrington, Alison H. ; Huang, Yu-Ling ; U'Ren, Jana M. ; Massimo, Nicholas C. ; Knight-Connoni, Victoria ; Inderbitzin, Patrik ( November 2021 , International Journal of Systematic and Evolutionary Microbiology)

   A growing interest in fungi that occur within symptom-less plants and lichens (endophytes) has uncovered previously uncharacterized species in diverse biomes worldwide. In many temperate and boreal forests, endophytic Coniochaeta (Sacc.) Cooke ( Coniochaetaceae , Coniochaetales, Sordariomycetes , Ascomycota ) are commonly isolated on standard media, but rarely are characterized. We examined 26 isolates of Coniochaeta housed at the Gilbertson Mycological Herbarium. The isolates were collected from healthy photosynthetic tissues of conifers, angiosperms, mosses and lichens in Canada, Sweden and the United States. Their barcode sequences (nuclear ribosomal internal transcribed spacer and 5.8S; ITS rDNA) were ≤97% similar to any documented species available through GenBank. Phylogenetic analyses based on two loci (ITS rDNA and translation elongation factor 1-alpha) indicated that two isolates represented Coniochaeta cymbiformispora , broadening the ecological niche and geographic range of a species known previously from burned soil in Japan. The remaining 24 endophytes represented three previously undescribed species that we characterize here: Coniochaeta elegans sp. nov., Coniochaeta montana sp. nov. and Coniochaeta nivea sp. nov. Each has a wide host range, including lichens, bryophytes and vascular plants. C. elegans sp. nov. and C. nivea sp. nov. have wide geographic ranges. C. montana sp. nov. occurs inmore »the Madrean biome of Arizona (USA), where it is sympatric with the other species described here. All three species display protease, chitinase and cellulase activity in vitro . Overall, this study provides insight into the ecological and evolutionary diversity of Coniochaeta and suggests that these strains may be amenable for studies of traits relevant to a horizontally transmitted, symbiotic lifestyle.« less
2. Haraldiophyllum hawaiiense sp. nov. (Delesseriaceae, Rhodophyta): a new mesophotic genus record for the Hawaiian Islands

   https://doi.org/https://doi.org/10.4490/algae.2020.35.11.5  

   Paiano, M.O. ; Huisman, J.M. ; Cabrera, F.P. ; Spalding, H.L. ; Kosaki, R.K. ; Sherwood, A.R. ( October 2020 , Algae)

   Haraldiophyllum hawaiiense sp. nov. is described as a new mesophotic alga and a new genus record for the Hawaiian Islands. Six specimens were collected at a depth range of 81-93 m from Papahānaumokuākea Marine National Monument, and their morphology investigated, as well as molecular phylogenetic analyses of the plastidial ribulose-1,5- bisphosphate carboxylase–oxygenase large-subunit (rbcL) gene and a concatenated alignment of rbcL and nuclear large-subunit rRNA gene (LSU) sequences. Phylogenetic analyses supported H. hawaiiense sp. nov. as a distinct lineage within the genus Haraldiophyllum, and sister to a large clade containing the type species, H. bonnemaisonii, as well as H. crispatum and an undescribed European specimen. The six Hawaiian specimens were shown to be identical, but unique among other species of the genus as well as the recently segregated genus Neoharaldiophyllum, which comprises half of the species previously included in Haraldiophyllum. The vegetative morphology of H. hawaiiense sp. nov. resembles Neoharaldiophyllum udoense (formerly H. udoensis); however, no female or post-fertilization structures were found in the Hawaiian specimens to allow a more comprehensive comparison. The molecular phylogenies demonstrate that Haraldiophyllum is paraphyletic, suggesting either that the Myriogrammeae tribe includes undescribed genera, including Haraldiophyllum sensu stricto, or that Neoharaldiophyllum species should be transferredmore »into the genus Haraldiophyllum. However, based on vegetative morphology and molecular analyses, and pending resolution of this taxonomic issue, the Hawaiian specimens are placed within the genus Haraldiophyllum. This new record for the Hawaiian Islands highlights the novel biodiversity from mesophotic depths, reaffirming the need for further investigation into the biodiversity of Mesophotic Coral Ecosystems.« less
3. Endosymbiotic adaptations in three new bacterial species associated with Dictyostelium discoideum : Paraburkholderia agricolaris sp. nov., Paraburkholderia hayleyella sp. nov., and Paraburkholderia bonniea sp. nov

   https://doi.org/10.7717/peerj.9151  

   Brock, Debra A. ; Noh, Suegene ; Hubert, Alicia N.M. ; Haselkorn, Tamara S. ; DiSalvo, Susanne ; Suess, Melanie K. ; Bradley, Alexander S. ; Tavakoli-Nezhad, Mahboubeh ; Geist, Katherine S. ; Queller, David C. ; et al ( January 2020 , PeerJ)

   Here we give names to three new species of Paraburkholderia that can remain in symbiosis indefinitely in the spores of a soil dwelling eukaryote, Dictyostelium discoideum . The new species P. agricolaris sp. nov. , P. hayleyella sp. nov. , and P. bonniea sp. nov . are widespread across the eastern USA and were isolated as internal symbionts of wild-collected D. discoideum . We describe these sp. nov. using several approaches. Evidence that they are each a distinct new species comes from their phylogenetic position, average nucleotide identity, genome-genome distance, carbon usage, reduced length, cooler optimal growth temperature, metabolic tests, and their previously described ability to invade D. discoideum amoebae and form a symbiotic relationship . All three of these new species facilitate the prolonged carriage of food bacteria by D. discoideum, though they themselves are not food. Further studies of the interactions of these three new species with D. discoideum should be fruitful for understanding the ecology and evolution of symbioses.
4. Combining ultraconserved elements and mtDNA data to uncover lineage diversity in a Mexican highland frog ( Sarcohyla ; Hylidae)

   https://doi.org/10.7717/peerj.6045  

   Zarza, Eugenia ; Connors, Elizabeth M. ; Maley, James M. ; Tsai, Whitney L. E. ; Heimes, Peter ; Kaplan, Moises ; McCormack, John E. ( December 2018 , PeerJ)

   Molecular studies have uncovered significant diversity in the Mexican Highlands, leading to the description of many new endemic species. DNA approaches to this kind of species discovery have included both mitochondrial DNA (mtDNA) sequencing and multilocus genomic methods. While these marker types have often been pitted against one another, there are benefits to deploying them together, as linked mtDNA data can provide the bridge between uncovering lineages through rigorous multilocus genomic analysis and identifying lineages through comparison to existing mtDNA databases. Here, we apply one class of multilocus genomic marker, ultraconserved elements (UCEs), and linked mtDNA data to a species complex of frogs (Sarcohyla bistincta, Hylidae) found in the Mexican Highlands. We generated data from 1,891 UCEs, which contained 1,742 informative SNPs forS. bistinctaand closely related species and captured mitochondrial genomes for most samples. Genetic analyses based on both whole loci and SNPs agree there are six to seven distinct lineages within what is currently described asS. bistincta. Phylogenies from UCEs and mtDNA mostly agreed in their topologies, and the few differences suggested a more complex evolutionary history of the mtDNA marker. Our study demonstrates that the Mexican Highlands still hold substantial undescribed diversity, making their conservation a particularly urgentmore »goal. The Trans-Mexican Volcanic Range stands out as a significant geographic feature inSarcohylaand may have acted as a dispersal corridor forS. bistinctato spread to the north. Combining multilocus genomic data with linked mtDNA data is a useful approach for identifying potential new species and associating them with already described taxa, which will be especially important in groups with undescribed subadult phenotypes and cryptic species.

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5. Diversity, taxonomic composition, and functional aspects of fungal communities in living, senesced, and fallen leaves at five sites across North America

   https://doi.org/10.7717/peerj.2768  

   U’Ren, Jana M. ; Arnold, A. Elizabeth ( December 2016 , PeerJ)

   Fungal endophytes inhabit symptomless, living tissues of all major plant lineages to form one of earth’s most prevalent groups of symbionts. Many reproduce from senesced and/or decomposing leaves and can produce extracellular leaf-degrading enzymes, blurring the line between symbiotrophy and saprotrophy. To better understand the endophyte–saprotroph continuum we compared fungal communities and functional traits of focal strains isolated from living leaves to those isolated from leaves after senescence and decomposition, with a focus on foliage of woody plants in five biogeographic provinces ranging from tundra to subtropical scrub forest.

   We cultured fungi from the interior of surface-sterilized leaves that were living at the time of sampling (i.e., endophytes), leaves that were dead and were retained in plant canopies (dead leaf fungi, DLF), and fallen leaves (leaf litter fungi, LLF) from 3–4 species of woody plants in each of five sites in North America. Our sampling encompassed 18 plant species representing two families of Pinophyta and five families of Angiospermae. Diversity and composition of fungal communities within and among leaf life stages, hosts, and sites were compared using ITS-partial LSU rDNA data. We evaluated substrate use and enzyme activity by a subset of fungi isolated only from living tissues vs. fungi isolatedmore »only from non-living leaves.

   Across the diverse biomes and plant taxa surveyed here, culturable fungi from living leaves were isolated less frequently and were less diverse than those isolated from non-living leaves. Fungal communities in living leaves also differed detectably in composition from communities in dead leaves and leaf litter within focal sites and host taxa, regardless of differential weighting of rare and abundant fungi. All focal isolates grew on cellulose, lignin, and pectin as sole carbon sources, but none displayed ligninolytic or pectinolytic activityin vitro. Cellulolytic activity differed among fungal classes. Within Dothideomycetes, activity differed significantly between fungi from living vs. non-living leaves, but such differences were not observed in Sordariomycetes.

   Although some fungi with endophytic life stages clearly persist for periods of time in leaves after senescence and incorporation into leaf litter, our sampling across diverse biomes and host lineages detected consistent differences between fungal assemblages in living vs. non-living leaves, reflecting incursion by fungi from the leaf exterior after leaf death and as leaves begin to decompose. However, fungi found only in living leaves do not differ consistently in cellulolytic activity from those fungi detected thus far only in dead leaves. Future analyses should consider Basidiomycota in addition to the Ascomycota fungi evaluated here, and should explore more dimensions of functional traits and persistence to further define the endophytism-to-saprotrophy continuum.

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