Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome is thought to play an important role in promoting citrus growth and health. Here, we report a comprehensive analysis of the structural and functional composition of the citrus rhizosphere microbiome. We use both amplicon and deep shotgun metagenomic sequencing of bulk soil and rhizosphere samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes. The core citrus rhizosphere microbiome comprises Pseudomonas, Agrobacterium, Cupriavidus, Bradyrhizobium, Rhizobium, Mesorhizobium, Burkholderia, Cellvibrio, Sphingomonas, Variovorax and Paraburkholderia, some of which are potential plant beneficial microbes. We also identify over-represented microbial functional traits mediating plant-microbe and microbe-microbe interactions, nutrition acquisition and plant growth promotion in citrus rhizosphere. The results provide valuable information to guide microbial isolation and culturing and, potentially, to harness the power of the microbiome to improve plant production and health.

Sordariomycetes is one of the largest classes of Ascomycota that comprises a highly diverse range of fungi characterized mainly by perithecial ascomata and inoperculate unitunicate asci. The class includes many important plant pathogens, as well as endophytes, saprobes, epiphytes, coprophilous and fungicolous, lichenized or lichenicolous taxa. They occur in terrestrial, freshwater and marine habitats worldwide. This paper reviews the 107 families of the class Sordariomycetes and provides a modified backbone tree based on phylogenetic analysis of four combined loci, with a maximum five representative taxa from each family, where available. This paper brings together for the first time, since Barrs’ 1990 Prodromus, descriptions, notes on the history, and plates or illustrations of type or representative taxa of each family, a list of accepted genera, including asexual genera and a key to these taxa of Sordariomycetes. Delineation of taxa is supported where possible by molecular data. The outline is based on literature to the end of 2015 and the Sordariomycetes now comprises six subclasses, 32 orders, 105 families and 1331 genera. The family Obryzaceae and Pleurotremataceae are excluded from the class.

The recent realistic estimate of fungal numbers which used various algorithms was between 2.2 and 3.8 million. There are nearly 100,000 accepted species of Fungi and fungus-like taxa, which is between 2.6 and 4.5% of the estimated species. Several forums such as Botanica Marina series, Fungal Diversity notes, Fungal Biodiversity Profiles, Fungal Systematics and Evolution—New and Interesting Fungi, Mycosphere notes and Fungal Planet have enhanced the introduction of new taxa and nearly 2000 species have been introduced in these publications in the last decade. The need to define a fungal species more accurately has been recognized, but there is much research needed before this can be better clarified. We address the evidence that is needed to estimate the numbers of fungi and address the various advances that have been made towards its understanding. Some genera are barely known, whereas some plant pathogens comprise numerous species complexes and numbers are steadily increasing. In this paper, we examine ten genera as case studies to establish trends in fungal description and introduce new species in each genus. The genera are the ascomycetes Colletotrichum and Pestalotiopsis (with many species or complexes), Atrocalyx, Dothiora, Lignosphaeria, Okeanomyces, Rhamphoriopsis, Thozetella, Thyrostroma (relatively poorly studied genera) and the basidiomycete genus Lepiota. We provide examples where knowledge is incomplete or lacking and suggest areas needing further research. These include (1) the need to establish what is a species, (2) the need to establish how host-specific fungi are, not in highly disturbed urban areas, but in pristine or relatively undisturbed forests, and (3) the need to establish if species in different continents, islands, countries or regions are different, or if the same fungi occur worldwide? Finally, we conclude whether we are anywhere near to flattening the curve in new species description.

Diaporthalesis an important ascomycetous order comprising phytopathogenic, saprobic, and endophytic fungi, but interfamilial taxonomic relationships are still ambiguous. Despite its cosmopolitan distribution and high diversity with distinctive morphologies, this order has received relativelyiaceae,Macrohilaceae,Melanconidaceae,Pseudoplagiostomaceae,Schizoparmaceae,StilbosporaceaeandSydowiellaceae. Taxonomic uncertainties among genera are also clarified and recurrent discrepancies in the taxonomic position of families within theDiaporthalesare discussed. An updated outline and key to families and genera of the order is presented.

The previous phylogenies of Sordariomycetes by M.E. Barr, O.E. Eriksson and D.L. Hawksworth, and T. Lumbsch and S. Huhndorf, were mainly based on morphology and thus were somewhat subjective. Later outlines by T. Lumbsch and S. Huhndorf, and Maharachchikumbura and co-authors, took into account phylogenetic evidence. However, even these phylogenetic driven arrangements for Sordariomycetes, were somewhat subjective, as the arrangements in trees depended on many variables, such as number of taxa, different gene regions and methods used in the analyses. What is needed is extra evidence to help standardize ranking in the fungi. Estimation of divergence times using molecular clock methods has been proposed for providing additional rational for higher ranking of taxa. Thus, in Sordariomycetes, a divergence period (i.e. 200–300 MYA) can be used as criteria to judge when a group of related taxa evolved and what rank they should be given. In this paper, we provide an updated classification of accepted subclasses, orders of Sordariomycetes and use divergence times to provide additional evidence to stabilize ranking of taxa in the class. We point out and discuss discrepancies where the phylogenetic tree conflicts with the molecular clock.