Early efforts to classify Mortierellaceae were based on macro-and micromorphology, but sequencing and phylogenetic studies with ribosomal DNA (rDNA) markers have demonstrated conflicting taxonomic groupings and polyphyletic genera. Although some taxonomic confusion in the family has been clarified, rDNA data alone is unable to resolve higher level phylogenetic relationships within Mortierellaceae. In this study, we applied two parallel approaches to resolve the Mortierellaceae phylogeny: low coverage genome (LCG) sequencing and high-throughput, multiplexed targeted amplicon sequencing to generate sequence data for multi-gene phylogenetics. We then combined our datasets to provide a well-supported genome-based phylogeny having broad sampling depth from the amplicon dataset. Resolving the Mortierellaceae phylogeny into monophyletic genera resulted in 13 genera, 7 of which are newly proposed. Low-coverage genome sequencing proved to be a relatively cost-effective means of generating a high-confidence phylogeny. The multi-gene phylogenetics approach enabled much greater sampling depth and breadth than the LCG approach, but has limitations too. We present this work to resolve some of the taxonomic confusion and provide a genus-level framework to empower future studies on Mortierellaceae diversity and evolution.

Bacterial interactions with animals and plants have been examined for over a century; by contrast, the study of bacterial-fungal interactions has received less attention. Bacteria interact with fungi in diverse ways, and endobacteria that reside inside fungal cells represent the most intimate interaction. The most significant bacterial endosymbionts that have been studied are associated with Mucoromycota and include two main groups: Burkholderia-related and Mycoplasma-related endobacteria (MRE). Examples of Burkholderia-related endobacteria have been reported in the three Mucoromycota subphyla. By contrast, MRE have only been identified in Glomeromycotina and Mucoromycotina. This study aims to understand whether MRE dwell in Mortierellomycotina and, if so, to determine their impact on the fungal host. We carried out a large-scale screening of 394 Mortierellomycotina strains and employed a combination of microscopy, molecular phylogeny, next-generation sequencing and qPCR. We detected MRE in 12 strains. These endosymbionts represent novel bacterial phylotypes and show evidence of recombination. Their presence in Mortierellomycotina demonstrates that MRE occur within fungi across Mucoromycota and they may have lived in their common ancestor. We cured the fungus of its endosymbionts with antibiotics and observed improved biomass production in isogenic lines lacking MRE, demonstrating that these endobacteria impose some fitness costs to their fungal host. Here we provided the first functional insights into the lifestyle of MRE. Our findings indicate that MRE may be antagonistic to their fungal hosts, and adapted to a non-lethal parasitic lifestyle in the mycelium of Mucoromycota. However, context-dependent adaptive benefits to their host at minimal cost cannot not be excluded. Finally, we conclude that Mortierellomycotina represent attractive model organisms for exploring interactions between MRE and fungi.

The aboveground parts of terrestrial plants are colonized by a variety of microbes that collectively constitute the phyllosphere microbiota. Decades of pioneering work using individual phyllosphere microbes, including commensals and pathogens, have provided foundational knowledge about how individual microbes adapt to the phyllosphere environment and their role in providing biological control against pathogens. Recent studies have revealed a more complete repertoire of phyllosphere microbiota across plant taxa and how plants respond to and regulate the level and composition of phyllosphere microbiota. Importantly, the development of several gnotobiotic systems is allowing causative and mechanistic studies to determine the contributions of microbiota to phyllosphere health and productivity. New insights into how the phyllosphere carries out key biological processes, including photosynthesis, biomass accumulation, reproduction, and defense against biotic and abiotic insults, in either the presence or absence of a normal microbiota could unleash novel plant- and microbiota-based technologies to improve agriculturally relevant traits of crop plants. Expected final online publication date for the Annual Review of Plant Biology, Volume 74 is May 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

their size and physiology, and they belong to many different phylogenetic groups that are distinct from plants. [1] Microalgae are the subset of algae that are unicellular and range in size from several to a few hundred micrometers. Most microalgae diversity resides in freshwater or marine systems. Microalgae can grow in extreme environments such as deserts and polar regions, [2] and often show greater efficiency in synthesizing bioproducts compared to land plants. [3] Moreover, algae produce oxygen and sequester the greenhouse gas carbon dioxide at globally relevant scales, [4] and account for half of the oceans' net primary production. [5] They grow fast and can produce high-value biomass. [6] While microalgae are phylogenetically diverse, most biotechnology interest applies to the green algae (Chlorophyceae), diatoms (Bacillariophyceae), blue-green algae (Cyanobacteria), and Eustigmatophyceae (including Nannochloropsis), which are well-characterized species for valuable bioproducts. 1.2. Microalgae as Sustainable Biofactories Microalgae have the potential to produce large amounts of valuable products sustainably, since they do not require arable land and can be produced using seawater, wastewater, or brackish water. Reduction in environmental impacts of fuels and food products will be important for the mitigation of climate change. [7] Microalgae are also being used in powerplants as a means to capture carbon dioxide and sequester it into biomass, which may provide opportunities for large-scale production of carbon-neutral energy and products. [8] Vaccines and other pharmaceutical proteins are among the most high-value products that microalgae are used to produce, as well as effectively store and orally administer those products. [9] Other high-value products derived from microalgae include cosmetics, [10] food supplements and additives, [11] cooking oils, [12] and animal feed. [13,14] These have been developed as potentially more sustainable alternatives to synthetic or animal-derived products. Microalgae also provide feedstocks for biodiesel [15] and ethanol, [16] contributing to renewable and sustainable energy resource developments that may displace fossil fuels and food-derived fuels. Genetic and synthetic biology approaches can accelerate the development of microalgae strains capable of producing novel specialty products [17-19] or producing conventional products with improved lipid content, [20] growth rate, and production efficiency. [21,22] Unlike field-grown transgenic crops, multi ple Microalgae are promising biological factories for diverse natural products. Microalgae tout high productivity, and their biomass has value in industrial products ranging from biofuels, feedstocks, food additives, cosmetics, pharmaceuticals, and as alternatives to synthetic or animal-derived products. However, harvesting microalgae to extract bioproducts is challenging given their small size and suspension in liquid growth media. In response, technologic developments have relied upon mechanical, chemical, thermal, and b...

Summary CONSTAX - the CONSensus TAXonomy classifier - was developed for accurate and reproducible taxonomic annotation of fungal rDNA amplicon sequences and is based upon a consensus approach of RDP, SINTAX, and UTAX algorithms. CONSTAX2 extends these features to classify prokaryotes as well as eukaryotes and incorporates BLAST-based classifiers to reduce classification errors. Additionally, CONSTAX2 implements a conda-installable command line tool with improved classification metrics, faster training, multithreading support, capacity to incorporate external taxonomic databases, and new isolate matching and high-level taxonomy tools, replete with documentation and example tutorials. Availability CONSTAX2 is available at https://github.com/liberjul/CONSTAXv2, and is packaged for Linux and MacOS from Bioconda with use under the MIT License. A tutorial and documentation are available at https://constax.readthedocs.io/en/latest/. Supplementary information Supplementary data are available at Bioinformatics online.