Terrestrial fungi play critical roles in nutrient cycling and food webs and can shape macroorganism communities as parasites and mutualists. Although estimates for the number of fungal species on the planet range from 1.5 to over 5 million, likely fewer than 10% of fungi have been identified so far. To date, a relatively small percentage of described species are associated with marine environments, with ∼1,100 species retrieved exclusively from the marine environment. Nevertheless, fungi have been found in nearly every marine habitat explored, from the surface of the ocean to kilometers below ocean sediments. Fungi are hypothesized to contribute to phytoplankton population cycles and the biological carbon pump and are active in the chemistry of marine sediments. Many fungi have been identified as commensals or pathogens of marine animals (e.g., corals and sponges), plants, and algae. Despite their varied roles, remarkably little is known about the diversity of this major branch of eukaryotic life in marine ecosystems or their ecological functions. This perspective emerges from a Marine Fungi Workshop held in May 2018 at the Marine Biological Laboratory in Woods Hole, MA. We present the state of knowledge as well as the multitude of open questions regarding the diversity and function of fungi in the marine biosphere and geochemical cycles.

BackgroundZostera marina (also known as eelgrass) is a foundation species in coastal and marine ecosystems worldwide and is a model for studies of seagrasses (a paraphyletic group in the order Alismatales) that include all the known fully submerged marine angiosperms. In recent years, there has been a growing appreciation of the potential importance of the microbial communities (i.e., microbiomes) associated with various plant species. Here we report a study of variation in Z. marina microbiomes from a field site in Bodega Bay, CA.MethodsWe characterized and then compared the microbial communities of root, leaf and sediment samples (using 16S ribosomal RNA gene PCR and sequencing) and associated environmental parameters from the inside, edge and outside of a single subtidal Z. marina patch. Multiple comparative approaches were used to examine associations between microbiome features (e.g., diversity, taxonomic composition) and environmental parameters and to compare sample types and sites.ResultsMicrobial communities differed significantly between sample types (root, leaf and sediment) and in sediments from different sites (inside, edge, outside). Carbon:Nitrogen ratio and eelgrass density were both significantly correlated to sediment community composition. Enrichment of certain taxonomic groups in each sample type was detected and analyzed in regard to possible functional implications (especially regarding sulfur metabolism).DiscussionOur results are mostly consistent with prior work on seagrass associated microbiomes with a few differences and additional findings. From a functional point of view, the most significant finding is that many of the taxa that differ significantly between sample types and sites are closely related to ones commonly associated with various aspects of sulfur and nitrogen metabolism. Though not a traditional model organism, we believe that Z. marina can become a model for studies of marine plant-microbiome interactions.

SignificanceChondrodystrophy, characterized by short limbs and intervertebral disc disease (IVDD), is a common phenotype in many of the most popular dog breeds, including the dachshund, beagle, and French bulldog. Here, we report the identification of a FGF4 retrogene insertion on chromosome 12, the second FGF4 retrogene reported in the dog, as responsible for chondrodystrophy and IVDD. Identification of the causative mutation for IVDD will impact an incredibly large proportion of the dog population and provides a model for IVDD in humans, as FGF-associated mutations are responsible for IVDD and short stature in human achondroplasia. This is a report of a second retrogene copy of the same parental gene, each causing complementary disease phenotypes in a mammalian species.

Seed treatment. Seeds of spring wheat were surface -sterilized as follows: seeds were washed in 0.1% Triton X-100 detergent with shaking for 10 min; the detergent was NATURE MICROBIOLOGY

42Seagrasses are globally distributed marine flowering plants that are foundation species in coastal 43 ecosystems. Seagrass beds play essential roles as habitats and hatcheries, in nutrient cycling and 44 in protecting the coastline from erosion. Although many studies have focused on seagrass 45 ecology, only a limited number have investigated their associated fungi. In terrestrial systems, 46 fungi can have beneficial and detrimental effects on plant fitness. However, not much is known 47 about marine fungi and even less is known about seagrass associated fungi. Here we used 48 culture-independent sequencing of the ribosomal internal transcribed spacer (ITS) region to 49 characterize the taxonomic diversity of fungi associated with the seagrass, Zostera marina. We 50 sampled from two Z. marina beds in Bodega Bay over three time points to investigate fungal 51 diversity within and between plants. Our results indicate that there are many fungal taxa for 52 which a taxonomic assignment cannot be made living on and inside Z. marina leaves, roots and 53 rhizomes and that these plant tissues harbor distinct fungal communities. The most prevalent ITS 54 amplicon sequence variant (ASV) associated with Z. marina leaves was classified as fungal, but 55 could not initially be assigned to a fungal phylum. We then used PCR with a primer targeting 56 unique regions of the ITS2 region of this ASV and an existing primer for the fungal 28S rRNA 57 gene to amplify part of the 28S rRNA gene region and link it to this ASV. Sequencing and 58 phylogenetic analysis of the resulting partial 28S rRNA gene revealed that the organism that this 59 ASV comes from is a member of Novel Clade SW-I in the order Lobulomycetales in the phylum 60 Chytridiomycota. This clade includes known parasites of freshwater diatoms and algae and it is 61 possible this chytrid is directly infecting Z. marina leaf tissues. This work highlights a need for 62 further studies focusing on marine fungi and the potential importance of these understudied 63 communities to the larger seagrass ecosystem.64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 109 110In contrast to their apparent lack of mycorrhizal associations, some studies of seagrasses have 111 observed associations with novel fungal endophytes similar to dark septate endophytes (DSE) 112 common in land plants (Borovec and Vohník, 2018; Torta et al., 2015; Vohník et al., 2015 Vohník et al., , 2016 Vohník et al., , 113 2017 Vohník et al., , 2019). DSE are a morphology based type and not a phylogenetic group, and are largely 114 uncharacterized. In some cases, DSEs have been shown to transfer nitrogen and receive carbon 115 from plants as well as increase overall plant nutrient content and growth (Porras-Alfaro and 116 Bayman, 2011; Usuki and Narisawa, 2007). DSEs are not the only fungi that have been observed 117to form associations with seagrasses. Additional culture based studies have found fungi 118 associated with the leaves, roots and rhizomes of different seagrasses; however, many of these 119...

Culture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refined, corrected and revolutionized understanding of the tree of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and microbial diversity. We assembled genomes of bacteria and archaea using DNA that had previously been characterized via 16S rRNA gene clone libraries. We recovered 36 MAGs, 29 of medium to high quality, and inferred their placement in a phylogenetic tree consisting of 3,240 publicly available microbial genomes. We highlight MAGs that were taxonomically assigned to groups previously underrepresented in available genome data. This includes several archaea ( Korarchaeota, Bathyarchaeota and Aciduliprofundum ) and one potentially new species within the bacterial genus Sulfurihydrogenibium . Putative functions in both pools were compared and are discussed in the context of their diverging geochemistry. This study adds comprehensive information about phylogenetic diversity and functional potential within two hot springs in the caldera of Kamchatka.

Snake fungal disease (SFD; ophidiomycosis), caused by the pathogen Ophidiomyces ophiodiicola (Oo), has been documented in wild snakes in North America and Eurasia, and is considered an emerging disease in the eastern United States of America. However, a lack of historical disease data has made it challenging to determine whether Oo is a recent arrival to the USA or whether SFD emergence is due to other factors. Here, we examined the genomes of 82 Oo strains to determine the pathogen’s history in the eastern USA. Oo strains from the USA formed a clade (Clade II) distinct from European strains (Clade I), and molecular dating indicated that these clades diverged too recently (approximately 2,000 years ago) for transcontinental dispersal of Oo to have occurred via natural snake movements across Beringia. A lack of nonrecombinant intermediates between clonal lineages in Clade II indicates that Oo has actually been introduced multiple times to North America from an unsampled source population, and molecular dating indicates that several of these introductions occurred within the last few hundred years. Molecular dating also indicated that the most common Clade II clonal lineages have expanded recently in the USA, with time of most recent common ancestor mean estimates ranging from 1985 to 2007 CE. The presence of Clade II in captive snakes worldwide demonstrates a potential mechanism of introduction and highlights that additional incursions are likely unless action is taken to reduce the risk of pathogen translocation and spillover into wild snake populations.

The “gamification” of science has gained a lot of traction in recent years, and games that convey scientific concepts or themes are increasingly popular. While a number of existing games touch on microbiology, very few consider the beneficial (as opposed to the detrimental) aspects of microbes. We designed a board game called “Gut Check: The Microbiome Game” to fill this gap. The game is meant to be both educational as well as challenging and fun. Here we discuss the development of the game, some of the logistics of game development in this context, and offer suggestions for others thinking of similar projects.