Polyphasic taxonomic characterization of lactic acid bacteria isolated from spontaneous sorghum fermentations used to produce ting, a traditional South African food

Ting, an indigenous cooked fermented food made from sorghum flour, is consumed extensively in South Africa. Due to the spontaneous nature of the sorghum fermentation considerable variations in the sensory and microbial quality of the end-product may occur, thus hampering large-scale production of this food. The use of starter cultures purified from the fermented sorghum may be an alternative approach to obtain ting of consistent quality. The aim of this study was therefore to identify the lactic acid bacteria (LAB) associated with ting fermentation using a polyphasic approach. Phenotypic characterization and sequence analysis of the genes encoding the 16S subunit of the ribosomal RNA (rrs) and phenylalanyl tRNA synthase (pheS) were used. The results of these analyses showed that ting fermentation involved at least three different species of LAB, i.e. Lactobacillus fermentum, L. plantarum and L. rhamnosus. To our knowledge, this is the first report of polyphasic taxonomic characterization of LAB from this food. This research forms an essential first step towards the development of relevant starter cultures to produce ting of consistent quality

Phylogenomic analyses predict sistergroup relationship of nucleariids and Fungi and paraphyly of zygomycetes with significant support

Abstract Background Resolving the evolutionary relationships among Fungi remains challenging because of their highly variable evolutionary rates, and lack of a close phylogenetic outgroup. Nucleariida, an enigmatic group of amoeboids, have been proposed to emerge close to the fungal-metazoan divergence and might fulfill this role. Yet, published phylogenies with up to five genes are without compelling statistical support, and genome-level data should be used to resolve this question with confidence. Results Our analyses with nuclear (118 proteins) and mitochondrial (13 proteins) data now robustly associate Nucleariida and Fungi as neighbors, an assemblage that we term 'Holomycota'. With Nucleariida as an outgroup, we revisit unresolved deep fungal relationships. Conclusion Our phylogenomic analysis provides significant support for the paraphyly of the traditional taxon Zygomycota, and contradicts a recent proposal to include Mortierella in a phylum Mucoromycotina. We further question the introduction of separate phyla for Glomeromycota and Blastocladiomycota, whose phylogenetic positions relative to other phyla remain unresolved even with genome-level datasets. Our results motivate broad sampling of additional genome sequences from these phyla

Draft genome sequences of <i>Pantoea agglomerans</i> and <i>Pantoea vagans</i> isolates associated with termites

The genus Pantoea incorporates many economically and clinically important species. The plant-associated species, Pantoea agglomerans and Pantoea vagans, are closely related and are often isolated from similar environments. Plasmids conferring certain metabolic capabilities are also shared amongst these two species. The genomes of two isolates obtained from fungus-growing termites in South Africa were sequenced, assembled and annotated. A high number of orthologous genes are conserved within and between these species. The difference in genome size between P. agglomerans MP2 (4,733,829 bp) and P. vagans MP7 (4,598,703 bp) can largely be attributed to the differences in plasmid content. The genome sequences of these isolates may shed light on the common traits that enable P. agglomerans and P. vagans to co-occur in plant- and insect-associated niches.The Danish Council for Independent Research, Natural Sciences (STENO grant: Michael Poulsen), the National Research Foundation (NRF) (RCA Fellowship: Pieter De Maayer) and the NRF/Dept. of Science and Technology Centre of Excellence in Tree Health Biotechnology (CTHB), South Africa.http://www.standardsingenomics.org/index.php/sigenam2016Forestry and Agricultural Biotechnology Institute (FABI)Microbiology and Plant Patholog

Symbiotic performance and characterization of Pigeonpea (Cajanus cajan L. Millsp.) Rhizobia occurring in South African soils

Pigeonpea (Cajanus cajan (L.) Millsp.) is an important grain legume, which, like several other legumes, depends on the process of biological nitrogen fixation for its nitrogen (N2 ) requirement by forming a symbiotic association with rhizobia. Compared to other tropical legumes, however, the productivity of pigeonpea in South Africa is low, despite the extensive interests in developing it for wider markets. To assist this process, the objectives of the current study were to (i) characterize putative indigenous rhizobial strains that were previously derived from local soils with no previous history of legume cultivation and (ii) confirm their nodulation abilities on a local landrace and a genetically improved (exotic) genotype of pigeonpea. DNA-based analyses using the 16S rRNA and recA genes showed that the strains predominantly represented Rhizobium and Bradyrhizobium, although we also recovered Phyllobacterium and Paraburkholderia. These rhizobia nodulated both the local landrace and the improved pigeonpea genotype that were included for comparative purposes. In many cases, rhizobia performed similarly on the two genotypes, although the locally sourced landrace mostly performed better in terms of nodulation and plant biomass. While the current study generated vital information regarding the diversity of indigenous rhizobia associating with pigeonpea, further screening (including field inoculation trials) would be necessary to identify possible elite nitrogen-fixing rhizobial strains for development as inoculants to enhance South African pigeonpea production.The University of Venda Research and Publications Committee.The University of Venda Research and Publications CommitteeBiochemistryGenetic

Roots and Nodules Response Differently to P Starvation in the Mediterranean-Type Legume Virgilia divaricata

Virgilia divaricata is a tree legume that grows in the Cape Floristic Region (CFA) in poor nutrient soils. A comparison between high and low phosphate growth conditions between roots and nodules was conducted and evaluated for the plants ability to cope under low phosphate stress conditions in V. divaricata. We proved that the plant copes with low phosphate stress through an increased allocation of resources, reliance on BNF and enhanced enzyme activity, especially PEPC. Nodules had a lower percentage decline in P compared to roots to uphold its metabolic functions. These strategies partly explain how V. divaricata can sustain growth despite LP conditions. Although the number of nodules declined with LP, their biomass remained unchanged in spite of a plant decline in dry weight. This is achieved via the high efficiency of BNF under P stress. During LP, nodules had a lower % decline at 34% compared to the roots at 88%. We attribute this behavior to P conservation strategies in LP nodules that imply an increase in a metabolic bypass that operates at the PEP branch point in glycolysis. The enhanced activities of nodule PEPC, MDH, and ME, whilst PK declines, suggests that under LP conditions an adenylate bypass was in operation either to synthesize more organic acids or to mediate pyruvate via a non-adenylate requiring metabolic route. Both possibilities represent a P-stress adaptation route and this is the first report of its kind for legume trees that are indigenous to low P, acid soils. Although BNF declined by a small percentage during LP, this P conservation was evident in the unchanged BNF efficiency per weight, and the increase in BNF efficiency per mol of P. It appears that legumes that are indigenous to acid soils, may be able to continue their reliance on BNF via increased allocation to nodules and also due to increase their efficiency for BNF on a P basis, owing to P-saving mechanisms such as the organic acid routes

Phylogenomic resolution of the bacterial genus Pantoea and its relationship with Erwinia and Tatumella

Erworben im Rahmen der Schweizer Nationallizenzen (http://www.nationallizenzen.ch

Burkholderia kirstenboschensis sp. nov. nodulates papilionoid legumes indigenous to South Africa

Despite the diversity of Burkholderia species known to nodulate legumes in introduced and native regions, relatively few taxa have been formally described. For example, the Cape Floristic Region of South Africa is thought to represent one of the major centres of diversity for the rhizobial members of Burkholderia, yet only five species have been described from legumes occurring in this region and numerous are still awaiting taxonomic treatment. Here, we investigated the taxonomic status of 12 South African root-nodulating Burkholderia isolates from native papilionoid legumes (Hypocalyptus coluteoides, H. oxalidifolius, H. sophoroides and Virgilia oroboides). Analysis of four gene regions (16S rRNA, recA, atpD and rpoB) revealed that the isolates represent a genealogically unique and exclusive assemblage within the genus. Its distinctness was supported by all other aspects of the polyphasic approach utilized, including the genome-based criteria DNA−DNA hybridization (≥70.9%) and average nucleotide identities (≥96%). We accordingly propose the name B. kirstenboschensis sp. nov. for this taxon with isolate Kb15T (=LMG 28727T; =SARC 695T) as its type strain. Our data showed that intraspecific genome size differences (≥0.81 Mb) and the occurrence of large DNA regions that are apparently unique to single individuals (16−23% of an isolate's genome) can significantly limit the value of data obtained from DNA−DNA hybridization experiments. Substitution of DNA−DNA hybridization with whole genome sequencing as a prerequisite for the description of Burkholderia species will undoubtedly speed up the pace at which their diversity are documented, especially in hyperdiverse regions such as the Cape Floristic Region.South African National Research Foundation (NRF) and the Department of Science and Technology.http://www.elsevier.de/syapm2016-12-31hb201

IMA Genome - F16 – Draft genome assemblies of Fusarium marasasianum, Huntiella abstrusa, two Immersiporthe knoxdaviesiana isolates, Macrophomina pseudophaseolina, Macrophomina phaseolina, Naganishia randhawae, and Pseudocercospora cruenta

Draft genome assembly of Fusarium marasasianum Introduction Many plants are thought to have at least one Fusarium-associated disease with more than 80% of economically important plants affected by at least one Fusarium disease (Leslie and Summerell 2006). The socioeconomic importance of Fusarium is particularly evident when considering the Fusarium fujikuroi species complex (FFSC, sensu Geiser et al. 2021). This monophyletic group contains 65 species and numerous cryptic species (Yilmaz et al. 2021). More than 50 species in the FFSC have publicly available genomes (www.ncbi.nlm.nih.gov), indicative of their economic importance. A number of recent studies showed that the FFSC complex contains four large clades (Herron et al. 2015; Sandoval-Denis et al. 2018; Yilmaz et al. 2021). One of these corresponds to the so-called “American” clade that was initially proposed to reflect the biogeography of the species it contains (O’Donnell et al. 1998). For example, Fusarium circinatum, the pine pitch canker pathogen, is thought to be native to Mexico and Central America (Drenkhan et al. 2020), where it likely co-evolved with its Pinus hosts (Herron et al. 2015; O’Donnell et al. 1998; Wikler and Gordon 2000). The American clade also includes five additional species associated with Pinus species in Colombia. These species are F. fracticaudum, F. pininemorale, F. parvisorum, F. marasasianum, and F. sororula, of which F. parvisorum, F. marasasianum, and F. sororula displayed levels of pathogenicity that were comparable to those of F. circinatum on susceptible Pinus species (Herron et al. 2015). The risk that the various American clade species pose to forestry in Colombia and globally has provided the impetus for projects aiming to sequence their genomes. To complement the genomic resources available for F. circinatum (Fulton et al. 2020; van der Nest et al. 2014a; Van Wyk et al. 2018; Wingfield et al. 2012, 2018a), the genomes of F. pininemorale (Wingfield et al. 2017), F. fracticaudum (Wingfield et al. 2018b) and F. sororula (van der Nest et al. 2021) have been published. Here we present the whole genome sequence for the pine pathogen F. marasasianum, named after the late South African professor Walter “Wally” F.O. Marasas (Wingfield and Crous 2012) who specialised in the taxonomy of Fusarium species and their associated mycotoxins