The history and distribution of nodulating Paraburkholderia, a potential inoculum for Fynbos forage species

Legumes in the Fynbos vegetation of the Western Cape of South Africa have emerged as candidates for domestication, particularly for their adaptation to acidic and infertile soils. However, South African rhizobia have been shown to be very diverse and unique, and a detailed understanding of them is essential to success in forage breeding programs that seek to exploit these “new” legumes. Symbionts of legumes in South Africa that belong to traditional rhizobial genera have been shown to have a unique origin for their symbiotic loci in comparison to members sampled from other regions of the world. Some of the legume tribes in the Fynbos have also been shown to associate predominantly with unique species in the Betaproteobacterial genus Paraburkholderia. The rhizobial members of this genus have two main centres of diversity, of which South Africa is one. In this centre, the legume hosts are principally from the Papilionoideae subfamily while hosts from the mimosoid clade (now in the Caesalpinioideae) are abundant in the South American centre. Not only do these rhizobia differ in terms of host, but their symbiotic loci also show separate origins. The dominance and uniqueness of the Paraburkholderia symbionts, in the context of indigenous South African legumes, makes understanding the history and factors that affect the distribution of this genus essential if successful adaptation and effective nodulation of these legumes in Agriculture are to be achieved globally.http://wileyonlinelibrary.com/journal/gfsam2022BiochemistryGeneticsMicrobiology and Plant Patholog

Rhizosphere diazotrophs and other bacteria associated with native and encroaching legumes in the succulent Karoo biome in South Africa

SUPPLEMENTARY MATERIAL : TABLE S1: Statistical analysis of soil chemical properties of the study sites showing main effects of different legume species and sites, TABLE S2: Diverse bacterial phyla in the Succulent Karoo biome in South Africa, their inherent properties and possible impacts on plant communities, TABLE S3: Families containing diazotrophic bacteria (nifH gene) in the rhizosphere soils examined and their possible roles in plant growth promotion of legume species in the Succulent Karoo biome in South Africa, TABLE S4: Analysis of variance (ANOVA) and Permutations analysis of variance (PERMANOVA) to test the effects of factors ‘legume species’, ‘sites’ and their interactions on the respective alpha and beta diversity matrices, using the 16S rRNA and nifH gene barcodes.Total and diazotrophic bacteria were assessed in the rhizosphere soils of native and encroaching legumes growing in the Succulent Karoo Biome (SKB), South Africa. These were Calobota sericea, Lessertia diffusa, Vachellia karroo, and Wiborgia monoptera, of Fabaceae family near Springbok (Northern Cape Province) and neighboring refugia of the Fynbos biome for C. sericea for comparison purposes. Metabarcoding approach using 16S rRNA gene revealed Actinobacteria (26.7%), Proteobacteria (23.6%), Planctomycetes, and Acidobacteria (10%), while the nifH gene revealed Proteobacteria (70.3%) and Cyanobacteria (29.5%) of the total sequences recovered as the dominant phyla. Some of the diazotrophs measured were assigned to families; Phyllobacteriaceae (39%) and Nostocaceae (24.4%) (all legumes), Rhodospirillaceae (7.9%), Bradyrhizobiaceae (4.6%) and Methylobacteriaceae (3%) (C. sericea, V. karroo, W. monoptera), Rhizobiaceae (4.2%; C. sericea, L. diffusa, V. Karroo), Microchaetaceae (4%; W. monoptera, V. karroo), Scytonemataceae (3.1%; L. diffusa, W. monoptera), and Pseudomonadaceae (2.7%; V. karroo) of the total sequences recovered. These families have the potential to fix the atmospheric nitrogen. While some diazotrophs were specific or shared across several legumes, a member of Mesorhizobium species was common in all rhizosphere soils considered. V. karroo had statistically significantly higher Alpha and distinct Beta-diversity values, than other legumes, supporting its influence on soil microbes. Overall, this work showed diverse bacteria that support plant life in harsh environments such as the SKB, and shows how they are influenced by legumes.DSI-NRF Centre of Excellence in Plant Health and Biotechnology (CPHB) through the Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa.https://www.mdpi.com/journal/microorganismsam2023BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Fate of Salmonella Typhimurium in laboratory-scale drinking water biofilms

Investigations were carried out to evaluate and quantify colonization of laboratory-scale drinking water biofilms by a chromosomally green fluorescent protein (gfp)-tagged strain of Salmonella Typhimurium. Gfp encodes the green fluorescent protein and thus allows in situ detection of undisturbed cells and is ideally suited for monitoring Salmonella in biofilms. The fate and persistence of non-typhoidal Salmonella in simulated drinking water biofilms was investigated. The ability of Salmonella to form biofilms in monoculture and the fate and persistence of Salmonella in a mixed aquatic biofilm was examined. In monoculture S. Typhimurium formed loosely structured biofilms. Salmonella colonized established multi-species drinking water biofilms within 24 hours, forming micro-colonies within the biofilm. S. Typhimurium was also released at high levels from the drinking water-associated biofilm into the water passing through the system. This indicated that Salmonella could enter into, survive and grow within, and be released from a drinking water biofilm. The ability of Salmonella to survive and persist in a drinking water biofilm, and be released at high levels into the flow for recolonization elsewhere, indicates the potential for a persistent health risk to consumers once a network becomes contaminated with this bacterium.This research was supported by a grant from the Water Research Commission of South Africa (WRC K5/1276) to VSB and SNV, and National Research Foundation (NRF) grant 2046811 to VSB. LMS was supported by a scholarship from the NRF of South Africa.http://www.iwaponline.com/jwh/default.htmhb201

An evaluation of the bacterial diversity at Tshipise, Mphephu and Sagole hot water springs, Limpopo Province, South Africa

Tshipise, Mphephu and Sagole are thermal hot water springs in the Limpopo Province of South Africa with temperatures of 58, 43 and 45°C; and pH of 8.85, 8.08 and 9.70, respectively. The bacterial diversity of the hot water springs was determined by pyrosequencing of the two 16S rRNA hypervariable regions V1-3 and V4-7. Analyses of the community DNA revealed that bacterial populations as detectable by the V1-3 or V4-7 region, respectively were dominated by the Bacteriodetes and Proteobacteria for Mphephu, and Proteobacteria and Cyanobacteria for both Tshipise and Sagole. The major differences in the bacterial diversity between the springs was that no Cyanobacteria were detected for Mphephu and the level of Bacteriodetes detected for both Tshipise and Sagole was much lower compared to the levels detected at Mphephu. The Firmicutes were detected at all the springs but at a much lower abundance compared to the other main phyla detected. Various other phyla were detected at the hot springs at levels below 0.20% of the total sequences obtained. It is interesting that very diverse bacterial genera exist in the three hot water springs studied.This research was supported through a grant from Water Research Commission (WRC, SA, Project K5/1959/1).http://www.academicjournals.org/AJM

All ANIs are not created equal : implications for prokaryotic species boundaries and integration of ANIs into polyphasic taxonomy

In prokaryotic taxonomy, a set of criteria is commonly used to delineate species. These criteria are generally based on cohesion at the phylogenetic, phenotypic and genomic levels. One such criterion shown to have promise in the genomic era is average nucleotide identity (ANI), which provides an average measure of similarity across homologous regions shared by a pair of genomes. However, despite the popularity and relative ease of using this metric, ANI has undergone numerous refinements, with variations in genome fragmentation, homologue detection parameters and search algorithms. To test the robustness of a 95–96 % species cut-off range across all the commonly used ANI approaches, seven different methods were used to calculate ANI values for intra- and interspecies datasets representing three classes in the Proteobacteria . As a reference point, these methods were all compared to the widely used blast-based ANI (i.e. ANIb as implemented in JSpecies), and regression analyses were performed to investigate the correlation of these methods to ANIb with more than 130000 individual data points. From these analyses, it was clear that ANI methods did not provide consistent results regarding the conspecificity of isolates. Most of the methods investigated did not correlate perfectly with ANIb, particularly between 90 and 100% identity, which includes the proposed species boundary. There was also a difference in the correlation of methods for the different taxon sets. Our study thus suggests that the specific approach employed needs to be considered when ANI is used to delineate prokaryotic species. We furthermore suggest that one would first need to determine an appropriate cut-off value for a specific taxon set, based on the intraspecific diversity of that group, before conclusions on conspecificity of isolates can be made, and that the resulting species hypotheses be confirmed with analyses based on evolutionary history as part of the polyphasic approach to taxonomy.The National Research Foundation (ZA), the US National Science Foundation, Environmental Biology and the DST-NRF Centre Of Excellence In Tree Health Biotechnology.https://www.microbiologyresearch.org/content/journal/ijsemhj2021BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Solar salterns as model systems to study the units of bacterial diversity that matter for ecosystem functioning

Microbial communities often harbor overwhelming species and gene diversity, making it challenging to determine the important units to study this diversity. We argue that the reduced, and thus tractable, microbial diversity of manmade salterns provides an ideal system to advance this cornerstone issue. We review recent time-series genomic and metagenomic studies of the saltern-dominating bacterial and archaeal taxa to show that these taxa form persistent, sequence-discrete, species-like populations. While these populations harbor extensive intra-population gene diversity, even within a single saltern site, only a small minority of these genes appear to be functionally important during environmental perturbations. We outline an approach to detect and track such populations and their ecologically important genes that should be broadly applicable.The US National Science Foundation, the Spanish Ministry of Science, Innovation and Universities which were supported with European Regional Development Fund (FEDER) funds.http://www.journals.elsevier.com/current-opinion-in-biotechnologyhj2021BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Niche preference of Escherichia coli in a peri-urban pond ecosystem

Escherichia coli comprises diverse strains with a large accessory genome, indicating functional diversity and the ability to adapt to a range of niches. Specific strains would display greatest fitness in niches matching their combination of phenotypic traits. Given this hypothesis, we sought to determine whether E. coli in a peri-urban pond and associated cattle pasture display niche preference. Samples were collected from water, sediment, aquatic plants, water snails associated with the pond, as well as bovine feces from cattle in an adjacent pasture. Isolates (120) were obtained after plating on Membrane Lactose Glucuronide Agar (MLGA). We used the uidA and mutS sequences for all isolates to determine phylogeny by maximum likelihood, and population structure through gene flow analysis. PCR was used to allocate isolates to phylogroups and to determine the presence of pathogenicity/virulence genes (stxI, stxII, eaeA, hlyA, ST, and LT). Antimicrobial resistance was determined using a disk diffusion assay for Tetracycline, Gentamicin, Ciprofloxacin, Meropenem, Ceftriaxone, and Azithromycin. Our results showed that isolates from water, sediment, and water plants were similar by phylogroup distribution, virulence gene distribution, and antibiotic resistance while both snail and feces populations were significantly different. Few of the feces isolates were significantly similar to aquatic ones, and most of the snail isolates were also different. Population structure analysis indicated three genetic backgrounds associated with bovine, snail, and aquatic environments. Collectively these data support niche preference of E. coli isolates occurring in this ecosystem.SUPPLEMENTARY MATERIAL : Figure S1: Multinomial log-linear regression analysis of phylogroup distribution of isolates across sample types. Phylogrouping was performed according to the scheme of Clermont et al., 2013. The X axis denotes phylogroups and the Y-axis represents proportion of isolates. Sed–sediment, W–water, WP–water plant, SN–snail, Figure S2: Virulence gene distribution across isolates allocate to phylogroups based on the scheme of Clermont et al., 2013. The number of isolates for each phylogroup is given in parentheses on the x axis, Figure S3: Distribution of sensitive (0) and isolates displaying Intermediate resistance to 1, 2, 3, 4 or 5 antibiotics from the five sampling sites, Table S1: Primers used for determining the uidA and mutS genes, and for phylogrouping, Table S2: Primers used for amplification of virulence genes.The South Dakota Agricultural Experiment Stationhttps://www.mdpi.com/journal/lifeam2022BiochemistryGeneticsMicrobiology and Plant Patholog

Bradyrhizobium xenonodulans sp. nov. isolated from nodules of Australian Acacia species invasive to South Africa

DATA AVAILABILITY : Data will be made available on request.Please read abstract in the article.https://www.elsevier.com/locate/syapmhj2023BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Antifungal actinomycetes associated with the pine bark beetle, Orthotomicus erosus, in South Africa

Actinomycete bacteria are often associated with insects that have a mutualistic association with fungi. These bacteria are believed to be important to this insect–fungus association as they produce antibiotics that exclude other saprophytic fungi from the immediate environment. The aim of this study was to investigate the presence of potentially protective actinomycetes associated with Orthotomicus erosus, an alien invasive pine bark beetle, in South Africa. This bark beetle and its relatives have an association with Ophiostomatales species which are often the only fungi found in the bark beetle galleries. We hypothesised that antibiotic-producing actinomycetes could be responsible for the paucity of other fungi in the galleries by producing compounds to which the Ophiostoma spp. are tolerant. Several actinomycetes in the genus Streptomyces and one Gordonia sp. were isolated from the beetle. Interestingly, most isolates were from the same species as actinomycetes associated with other pine-infesting insects from other parts of the world, including bark beetles and the woodwasp Sirex noctilio. Most actinomycetes isolated had strong antifungal properties against the selected test fungi, including Ophiostoma ips, which is the most common fungal symbiont of Orthotomicus erosus. Although the actinomycetes did not benefit Ophiostoma ips and the hypothesis was not supported, their sporadic association with Orthotomicus erosus suggests that they could have some impact on the composition of the fungal communities present in the bark beetle galleries, which is at present poorly understood. SIGNIFICANCE : • Discovery of four putative undescribed Streptomyces spp. with antibiotic potential • First record of the introduction of actinomycete bacteria with pine-infesting insects into South Africa • Actinomycetes from South Africa group with undescribed Streptomyces spp. from pine-infesting insects of North AmericaDST-NRF Centre of Excellence in Tree Health Biotechnology, the National Research Foundation (South Africa) and the University of Pretoria.http://www.sajs.co.zaam2017Forestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Fire impacts bacterial composition in Protea repens (Proteaceae) infructescences

The diverse bacterial communities in and around plants provide important benefits, such as protection against pathogens and cycling of essential minerals through decomposition of moribund plant biomass. Biodiverse fynbos landscapes generally have limited deadwood habitats due to the absence of large trees and frequent fire. In this study, we determined the effect of a fire disturbance on the bacterial communities in a fynbos landscape dominated by the shrub Protea repens using 16S ribosomal RNA amplicon sequencing. The bacterial community composition in newly formed fruiting structures (infructescences) and soil at a recently burnt site was different from that in an unburnt site. Bacteria inhabiting P. repens infructescences were similar to well-known taxa from decomposing wood and litter. This suggests a putative role for these aboveground plant structures as reservoirs for postfire decomposer bacteria. The results imply that inordinately frequent fires, which are commonplace in the Anthropocene, are a significant disturbance to bacterial communities and could affect the diversity of potentially important microbes from these landscapes.The National Research Foundation (NRF) and the Department of Science and Innovation (DSI)/NRF Centre of Excellence in Tree Health Biotechnology (CTHB).https://academic.oup.com/femsle2022-10-09hj2022BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog