Knock-Out of IKKepsilon Ameliorates Atherosclerosis and Fatty Liver Disease by Alterations of Lipid Metabolism in the PCSK9 Model in Mice.

The inhibitor-kappaB kinase epsilon (IKKε) represents a non-canonical IκB kinase that modulates NF-κB activity and interferon I responses. Inhibition of this pathway has been linked with atherosclerosis and metabolic dysfunction-associated steatotic liver disease (MASLD), yet the results are contradictory. In this study, we employed a combined model of hepatic PCSK9D377Y overexpression and a high-fat diet for 16 weeks to induce atherosclerosis and liver steatosis. The development of atherosclerotic plaques, serum lipid concentrations, and lipid metabolism in the liver and adipose tissue were compared between wild-type and IKKε knock-out mice. The formation and progression of plaques were markedly reduced in IKKε knockout mice, accompanied by reduced serum cholesterol levels, fat deposition, and macrophage infiltration within the plaque. Additionally, the development of a fatty liver was diminished in these mice, which may be attributed to decreased levels of multiple lipid species, particularly monounsaturated fatty acids, triglycerides, and ceramides in the serum. The modulation of several proteins within the liver and adipose tissue suggests that de novo lipogenesis and the inflammatory response are suppressed as a consequence of IKKε inhibition. In conclusion, our data suggest that the knockout of IKKε is involved in mechanisms of both atherosclerosis and MASLD. Inhibition of this pathway may therefore represent a novel approach to the treatment of cardiovascular and metabolic diseases.

Photon-counting computed tomography for paediatric congenital heart defects yields images of high diagnostic quality with low radiation doses at both 70 kV and 90 kV.

BACKGROUND: Photon-counting computed tomography (PCCT) is a new clinical method that may show better diagnostic quality at lower radiation doses than conventional CT. OBJECTIVE: To investigate the diagnostic quality and radiation dose of paediatric cardiovascular PCCT for diagnosis of congenital heart defects at 70 kV and 90 kV. MATERIALS AND METHODS: This retrospective assessment included clinical non-gated paediatric PCCT examinations for assessment of congenital heart defects. Radiation doses were recorded, and overall and specific diagnostic quality (1-4) were scored by four paediatric radiologists. Agreement, differences, and trends were assessed by percent rater agreement, intraclass correlation, Mann-Whitney tests, and Jonckheere-Terpstra tests. RESULTS: Seventy children with congenital heart defects were examined at 70 kV (n = 35; age 2 days-16 years; 63% boys) or 90 kV (n = 35; age 2 days-17 years; 51% boys). All observers gave a median score of 4 (high diagnostic quality) for both 70 kV and 90 kV, with no difference in median values between tube voltages (all P > 0.06). Agreement for overall scores was 66-94% for 70 kV and 60-77% for 90 kV. Agreement for specific scores was 80-97% for 70 kV and 83-89% for 90 kV. Size-dependent dose estimate was 0.68 mGy (0.25-2.02 mGy) for 70 kV and 1.10 mGy (0.58-2.71 mGy; P < 0.001) for 90 kV. Effective dose was 0.30 mSv (0.15-0.82 mSv) for 70 kV and 0.39 mSv (0.22-1.51 mSv; P = 0.01) for 90 kV. CONCLUSION: Paediatric cardiovascular PCCT yields images for congenital heart defects of high diagnostic quality with low radiation dose at both 70 kV and 90 kV.

Mmp12 Is Translationally Regulated in Macrophages during the Course of Inflammation.

Despite the importance of rapid adaptive responses in the course of inflammation and the notion that post-transcriptional regulation plays an important role herein, relevant translational alterations, especially during the resolution phase, remain largely elusive. In the present study, we analyzed translational changes in inflammatory bone marrow-derived macrophages upon resolution-promoting efferocytosis. Total RNA-sequencing confirmed that apoptotic cell phagocytosis induced a pro-resolution signature in LPS/IFNγ-stimulated macrophages (Mϕ). While inflammation-dependent transcriptional changes were relatively small between efferocytic and non-efferocytic Mϕ; considerable differences were observed at the level of de novo synthesized proteins. Interestingly, translationally regulated targets in response to inflammatory stimuli were mostly downregulated, with only minimal impact of efferocytosis. Amongst these targets, pro-resolving matrix metallopeptidase 12 (Mmp12) was identified as a translationally repressed candidate during early inflammation that recovered during the resolution phase. Functionally, reduced MMP12 production enhanced matrix-dependent migration of Mϕ. Conclusively, translational control of MMP12 emerged as an efficient strategy to alter the migratory properties of Mϕ throughout the inflammatory response, enabling Mϕ migration within the early inflammatory phase while restricting migration during the resolution phase.

Hypoxia-altered cholesterol homeostasis enhances the expression of interferon-stimulated genes upon SARS-CoV-2 infections in monocytes.

Hypoxia contributes to numerous pathophysiological conditions including inflammation-associated diseases. We characterized the impact of hypoxia on the immunometabolic cross-talk between cholesterol and interferon (IFN) responses. Specifically, hypoxia reduced cholesterol biosynthesis flux and provoked a compensatory activation of sterol regulatory element-binding protein 2 (SREBP2) in monocytes. Concomitantly, a broad range of interferon-stimulated genes (ISGs) increased under hypoxia in the absence of an inflammatory stimulus. While changes in cholesterol biosynthesis intermediates and SREBP2 activity did not contribute to hypoxic ISG induction, intracellular cholesterol distribution appeared critical to enhance hypoxic expression of chemokine ISGs. Importantly, hypoxia further boosted chemokine ISG expression in monocytes upon infection with severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2). Mechanistically, hypoxia sensitized toll-like receptor 4 (TLR4) signaling to activation by SARS-CoV-2 spike protein, which emerged as a major signaling hub to enhance chemokine ISG induction following SARS-CoV-2 infection of hypoxic monocytes. These data depict a hypoxia-regulated immunometabolic mechanism with implications for the development of systemic inflammatory responses in severe cases of coronavirus disease-2019 (COVID-19).

Functional RNA Dynamics Are Progressively Governed by RNA Destabilization during the Adaptation to Chronic Hypoxia.

Previous studies towards reduced oxygen availability have mostly focused on changes in total mRNA expression, neglecting underlying transcriptional and post-transcriptional events. Therefore, we generated a comprehensive overview of hypoxia-induced changes in total mRNA expression, global de novo transcription, and mRNA stability in monocytic THP-1 cells. Since hypoxic episodes often persist for prolonged periods, we further compared the adaptation to acute and chronic hypoxia. While total mRNA changes correlated well with enhanced transcription during short-term hypoxia, mRNA destabilization gained importance under chronic conditions. Reduced mRNA stability not only added to a compensatory attenuation of immune responses, but also, most notably, to the reduction in nuclear-encoded mRNAs associated with various mitochondrial functions. These changes may prevent the futile production of new mitochondria under conditions where mitochondria cannot exert their full metabolic function and are indeed actively removed by mitophagy. The post-transcriptional mode of regulation might further allow for the rapid recovery of mitochondrial capacities upon reoxygenation. Our results provide a comprehensive resource of functional mRNA expression dynamics and underlying transcriptional and post-transcriptional regulatory principles during the adaptation to hypoxia. Furthermore, we uncover that RNA stability regulation controls mitochondrial functions in the context of hypoxia.

Delineation of Paraburkholderia tuberum sensu stricto and description of Paraburkholderia podalyriae sp. nov. nodulating the South African legume Podalyria calyptrata.

Since the discovery of Paraburkholderia tuberum, an indigenous South African species and one of the first beta-rhizobia described, several other South African rhizobial Paraburkholderia species have been recognized. Here, we investigate the taxonomic status of 31 rhizobial isolates from the root nodules of diverse South African legume hosts in the Core Cape Subregion, which were initially identified as P. tuberum. These isolates originate from the root nodules of genera in the Papilionoideae as well as Vachellia karroo, from the subfamily Caesalpinioideae. Genealogical concordance analysis of five loci allowed delineation of the isolates into two putative species clusters (A and B). Cluster A included P. tuberum STM678T, suggesting that this monophyletic group represents P. tuberum sensu stricto. Cluster B grouped sister to P. tuberum and included isolates from the Paarl Rock Nature Reserve in the Western Cape Province. Average Nucleotide Identity (ANI) analysis further confirmed that isolates of Cluster A shared high genome similarity with P. tuberum STM678T compared to Cluster B and other Paraburkholderia species. The members of Cluster B associated with a single species of Podalyria, P. calyptrata. For this new taxon we accordingly propose the name Paraburkholderia podalyriae sp. nov., with the type strain WC7.3bT (= LMG 31413T; SARCC 750T). Based on our nodA and nifH phylogenies, P. podalyriae sp. nov. and strains of P. tuberum sensu stricto (including one from V. karroo) belong to symbiovar africana, the symbiotic loci of which have a separate evolutionary origin to those of Central and South American Paraburkholderia strains.

Mouth magnetoencephalography: A unique perspective on the human hippocampus.

Traditional magnetoencephalographic (MEG) brain imaging scanners consist of a rigid sensor array surrounding the head; this means that they are maximally sensitive to superficial brain structures. New technology based on optical pumping means that we can now consider more flexible and creative sensor placement. Here we explored the magnetic fields generated by a model of the human hippocampus not only across scalp but also at the roof of the mouth. We found that simulated hippocampal sources gave rise to dipolar field patterns with one scalp surface field extremum at the temporal lobe and a corresponding maximum or minimum at the roof of the mouth. We then constructed a fitted dental mould to accommodate an Optically Pumped Magnetometer (OPM). We collected data using a previously validated hippocampal-dependant task to test the empirical utility of a mouth-based sensor, with an accompanying array of left and right temporal lobe OPMs. We found that the mouth sensor showed the greatest task-related theta power change. We found that this sensor had a mild effect on the reconstructed power in the hippocampus (~10% change) but that coherence images between the mouth sensor and reconstructed source images showed a global maximum in the right hippocampus. We conclude that augmenting a scalp-based MEG array with sensors in the mouth shows unique promise for both basic scientists and clinicians interested in interrogating the hippocampus.

Paraburkholderia youngii sp. nov. and 'Paraburkholderia atlantica' - Brazilian and Mexican Mimosa-associated rhizobia that were previously known as Paraburkholderia tuberum sv. mimosae.

Previous studies have recognized South and Central/Latin American mimosoid legumes in the genera Mimosa, Piptadenia and Calliandra as hosts for various nodulating Paraburkholderia species. Several of these species have been validly named in the last two decades, e.g., P. nodosa, P. phymatum, P. diazotrophica, P. piptadeniae, P. ribeironis, P. sabiae and P. mimosarum. There are still, however, a number of diverse Paraburkholderia strains associated with these legumes that have an unclear taxonomic status. In this study, we focus on 30 of these strains which originate from the root nodules of Brazilian and Mexican Mimosa species. They were initially identified as P. tuberum and subsequently placed into a symbiovar (sv. mimosae) based on their host preferences. A polyphasic approach for the delineation of these strains was used, consisting of genealogical concordance analysis (using atpD, gyrB, acnA, pab and 16S rRNA gene sequences), together with comparisons of Average Nucleotide Identity (ANI), DNA G+C content ratios and phenotypic characteristics with those of the type strains of validly named Paraburkholderia species. Accordingly, these 30 strains were delineated into two distinct groups, of which one is conspecific with 'P. atlantica' CNPSo 3155T and the other new to Science. We propose the name Paraburkholderia youngii sp. nov. with type strain JPY169T (= LMG 31411T; SARCC751T) for this novel species.

Impaired theta phase coupling underlies frontotemporal dysconnectivity in schizophrenia.

Frontotemporal dysconnectivity is a key pathology in schizophrenia. The specific nature of this dysconnectivity is unknown, but animal models imply dysfunctional theta phase coupling between hippocampus and medial prefrontal cortex (mPFC). We tested this hypothesis by examining neural dynamics in 18 participants with a schizophrenia diagnosis, both medicated and unmedicated; and 26 age, sex and IQ matched control subjects. All participants completed two tasks known to elicit hippocampal-prefrontal theta coupling: a spatial memory task (during magnetoencephalography) and a memory integration task. In addition, an overlapping group of 33 schizophrenia and 29 control subjects underwent PET to measure the availability of GABAARs expressing the α5 subunit (concentrated on hippocampal somatostatin interneurons). We demonstrate-in the spatial memory task, during memory recall-that theta power increases in left medial temporal lobe (mTL) are impaired in schizophrenia, as is theta phase coupling between mPFC and mTL. Importantly, the latter cannot be explained by theta power changes, head movement, antipsychotics, cannabis use, or IQ, and is not found in other frequency bands. Moreover, mPFC-mTL theta coupling correlated strongly with performance in controls, but not in subjects with schizophrenia, who were mildly impaired at the spatial memory task and no better than chance on the memory integration task. Finally, mTL regions showing reduced phase coupling in schizophrenia magnetoencephalography participants overlapped substantially with areas of diminished α5-GABAAR availability in the wider schizophrenia PET sample. These results indicate that mPFC-mTL dysconnectivity in schizophrenia is due to a loss of theta phase coupling, and imply α5-GABAARs (and the cells that express them) have a role in this process.

Data-driven model optimization for optically pumped magnetometer sensor arrays.

Optically pumped magnetometers (OPMs) have reached sensitivity levels that make them viable portable alternatives to traditional superconducting technology for magnetoencephalography (MEG). OPMs do not require cryogenic cooling and can therefore be placed directly on the scalp surface. Unlike cryogenic systems, based on a well-characterised fixed arrays essentially linear in applied flux, OPM devices, based on different physical principles, present new modelling challenges. Here, we outline an empirical Bayesian framework that can be used to compare between and optimise sensor arrays. We perturb the sensor geometry (via simulation) and with analytic model comparison methods estimate the true sensor geometry. The width of these perturbation curves allows us to compare different MEG systems. We test this technique using simulated and real data from SQUID and OPM recordings using head-casts and scanner-casts. Finally, we show that given knowledge of underlying brain anatomy, it is possible to estimate the true sensor geometry from the OPM data themselves using a model comparison framework. This implies that the requirement for accurate knowledge of the sensor positions and orientations a priori may be relaxed. As this procedure uses the cortical manifold as spatial support there is no co-registration procedure or reliance on scalp landmarks.

High-precision magnetoencephalography for reconstructing amygdalar and hippocampal oscillations during prediction of safety and threat.

Learning to associate neutral with aversive events in rodents is thought to depend on hippocampal and amygdala oscillations. In humans, oscillations underlying aversive learning are not well characterised, largely due to the technical difficulty of recording from these two structures. Here, we used high-precision magnetoencephalography (MEG) during human discriminant delay threat conditioning. We constructed generative anatomical models relating neural activity with recorded magnetic fields at the single-participant level, including the neocortex with or without the possibility of sources originating in the hippocampal and amygdalar structures. Models including neural activity in amygdala and hippocampus explained MEG data during threat conditioning better than exclusively neocortical models. We found that in both amygdala and hippocampus, theta oscillations during anticipation of an aversive event had lower power compared to safety, both during retrieval and extinction of aversive memories. At the same time, theta synchronisation between hippocampus and amygdala increased over repeated retrieval of aversive predictions, but not during safety. Our results suggest that high-precision MEG is sensitive to neural activity of the human amygdala and hippocampus during threat conditioning and shed light on the oscillation-mediated mechanisms underpinning retrieval and extinction of fear memories in humans.

Neural Competitive Queuing of Ordinal Structure Underlies Skilled Sequential Action.

Fluent retrieval and execution of movement sequences is essential for daily activities, but the neural mechanisms underlying sequence planning remain elusive. Here participants learned finger press sequences with different orders and timings and reproduced them in a magneto-encephalography (MEG) scanner. We classified the MEG patterns for each press in the sequence and examined pattern dynamics during preparation and production. Our results demonstrate the "competitive queuing" (CQ) of upcoming action representations, extending previous computational and non-human primate recording studies to non-invasive measures in humans. In addition, we show that CQ reflects an ordinal template that generalizes across specific motor actions at each position. Finally, we demonstrate that CQ predicts participants' production accuracy and originates from parahippocampal and cerebellar sources. These results suggest that the brain learns and controls multiple sequences by flexibly combining representations of specific actions and interval timing with high-level, parallel representations of sequence position.

Mesorhizobium carmichaelinearum sp. nov., isolated from Carmichaelineae spp. root nodules.

Five strains of Gram-stain-negative, rod-shaped bacteria were isolated from Carmichaelia and Montigena root nodules. Based on 16S rRNA gene phylogeny, they were shown to belong to the genus Mesorhizobium, and to be most closely related to Mesorhizobium jarvisii ATCC 33669T (100-99.6 % sequence similarity), Mesorhizobium huakuii IAM 14158T (99.9-99.6 %), Mesorhizobium japonicum MAFF303099T (99.8-99.6 %) and Mesorhizobium erdmanii USDA 3471T (99.8-99.5 %). Additionally, the strains formed distinct groups based on housekeeping gene analysis and were most closely related to M. jarvisii ATCC 33669T (89.6-89.5 and 97.6-97.3 % sequence similarity for glnII and recA, respectively), M. erdmanii USDA 3471T (94.3-94.0 and 94.9-94.1 %), M. japonicum MAFF303099T (90.0-89.9 and 96.7-96.2 %) and M. huakuii IAM 14158T (89.9-90.0 and 95.4-94.9 %). Chemotaxonomic data supported the assignment of the strains to the genus Mesorhizobium and DNA-DNA hybridizations, average nucleotide identity analysis, matrix-assisted laser desorption ionization time-of-flight MS analysis, physiological and biochemical tests differentiated them genotypically and phenotypically from their nearest neighbouring species. Therefore, these strains are considered to represent a novel species, for which the name Mesorhizobium carmichaelinearum sp. nov. is proposed. The type strain is ICMP 18942T (=MonP1N1T=LMG 28414T).

Lamina-specific cortical dynamics in human visual and sensorimotor cortices.

Distinct anatomical and spectral channels are thought to play specialized roles in the communication within cortical networks. While activity in the alpha and beta frequency range (7 - 40 Hz) is thought to predominantly originate from infragranular cortical layers conveying feedback-related information, activity in the gamma range (>40 Hz) dominates in supragranular layers communicating feedforward signals. We leveraged high precision MEG to test this proposal, directly and non-invasively, in human participants performing visually cued actions. We found that visual alpha mapped onto deep cortical laminae, whereas visual gamma predominantly occurred more superficially. This lamina-specificity was echoed in movement-related sensorimotor beta and gamma activity. These lamina-specific pre- and post- movement changes in sensorimotor beta and gamma activity suggest a more complex functional role than the proposed feedback and feedforward communication in sensory cortex. Distinct frequency channels thus operate in a lamina-specific manner across cortex, but may fulfill distinct functional roles in sensory and motor processes.

Diversity of endemic rhizobia on Christmas Island: Implications for agriculture following phosphate mining.

Given that phosphate supplies may diminish and become uneconomic to mine after 2020, there is a compelling need to develop alternative industries to support the population on Christmas Island. Former mine sites could be turned into productive agricultural land, however, large-scale commercial agriculture has never been attempted, and, given the uniqueness of the island, the diversity of rhizobia prior to introducing legumes needed evaluation. Therefore, 84 rhizobia isolates were obtained from nine different hosts, both crop and introduced legumes, located at seven sites across the island. Based on 16S rRNA and recA gene sequence analysis, the isolates grouped into 13 clades clustering within the genus Bradyrhizobium, Ensifer, Cupriavidus and Rhizobium. According to the sequences of their symbiosis genes nodC and nifH, the isolates were classified into 12 and 11 clades, respectively, and clustered closest to tropical or crop legume isolates. Moreover, the symbiosis gene phylogeny and Multi Locus Sequence Analysis gene phylogeny suggested vertical transmission in the Alpha-rhizobia but horizontal transmission within the Beta-rhizobia. Furthermore, this study provides evidence of a large diversity of endemic rhizobia associated with both crop and introduced legumes, and highlights the necessity of inoculation for common bean, chickpea and soybean on the Island.

Quantifying the performance of MEG source reconstruction using resting state data.

In magnetoencephalography (MEG) research there are a variety of inversion methods to transform sensor data into estimates of brain activity. Each new inversion scheme is generally justified against a specific simulated or task scenario. The choice of this scenario will however have a large impact on how well the scheme performs. We describe a method with minimal selection bias to quantify algorithm performance using human resting state data. These recordings provide a generic, heterogeneous, and plentiful functional substrate against which to test different MEG recording and reconstruction approaches. We used a Hidden Markov model to spatio-temporally partition data into self-similar dynamic states. To test the anatomical precision that could be achieved, we then inverted these data onto libraries of systematically distorted subject-specific cortical meshes and compared the quality of the fit using cross validation and a Free energy metric. This revealed which inversion scheme was able to identify the least distorted (most accurate) anatomical models, and allowed us to quantify an upper bound on the mean anatomical distortion accordingly. We used two resting state datasets, one recorded with head-casts and one without. In the head-cast data, the Empirical Bayesian Beamformer (EBB) algorithm showed the best mean anatomical discrimination (3.7 mm) compared with Minimum Norm/LORETA (6.0 mm) and Multiple Sparse Priors (9.4 mm). This pattern was replicated in the second (conventional dataset) although with a marginally poorer (non-significant) prediction of the missing (cross-validated) data. Our findings suggest that the abundant resting state data now commonly available could be used to refine and validate MEG source reconstruction methods and/or recording paradigms.

Cognitive neuroscience using wearable magnetometer arrays: Non-invasive assessment of language function.

Recent work has demonstrated that Optically Pumped Magnetometers (OPMs) can be utilised to create a wearable Magnetoencephalography (MEG) system that is motion robust. In this study, we use this system to map eloquent cortex using a clinically validated language lateralisation paradigm (covert verb generation: 120 trials, ∼10 min total duration) in healthy adults (n = 3). We show that it is possible to lateralise and localise language function on a case by case basis using this system. Specifically, we show that at a sensor and source level we can reliably detect a lateralising beta band (15-30 Hz) desynchronization in all subjects. This is the first study of human cognition using OPMs and not only highlights this technology's utility as tool for (developmental) cognitive neuroscience but also its potential to contribute to surgical planning via mapping of eloquent cortex, especially in young children.

Horizontal Transfer of Symbiosis Genes within and Between Rhizobial Genera: Occurrence and Importance.

Rhizobial symbiosis genes are often carried on symbiotic islands or plasmids that can be transferred (horizontal transfer) between different bacterial species. Symbiosis genes involved in horizontal transfer have different phylogenies with respect to the core genome of their ‘host’. Here, the literature on legume⁻rhizobium symbioses in field soils was reviewed, and cases of phylogenetic incongruence between rhizobium core and symbiosis genes were collated. The occurrence and importance of horizontal transfer of rhizobial symbiosis genes within and between bacterial genera were assessed. Horizontal transfer of symbiosis genes between rhizobial strains is of common occurrence, is widespread geographically, is not restricted to specific rhizobial genera, and occurs within and between rhizobial genera. The transfer of symbiosis genes to bacteria adapted to local soil conditions can allow these bacteria to become rhizobial symbionts of previously incompatible legumes growing in these soils. This, in turn, will have consequences for the growth, life history, and biogeography of the legume species involved, which provides a critical ecological link connecting the horizontal transfer of symbiosis genes between rhizobial bacteria in the soil to the above-ground floral biodiversity and vegetation community structure.

Symbiotic and non-symbiotic Paraburkholderia isolated from South African Lebeckia ambigua root nodules and the description of Paraburkholderia fynbosensis sp. nov.

Nine Gram-negative, rod-shaped bacteria were isolated from Lebeckia ambigua root nodules. All strains were able to nodulate and fix nitrogen with Lebeckia ambigua apart from WSM4178T, WSM4181 and WSM4182. Based on the 16S rRNA gene phylogeny, all strains were closely related to Paraburkholderia species (98.4-99.9 %), belonging to the Betaproteobacteria class and Burkholderiaceae family. According to 16S rRNA gene phylogeny the closest relative for WSM4174-WSM4177 and WSM4179-WSM4180 was Paraburkholderia tuberum(99.80-99.86 %), for WSM4178T was Paraburkholderia caledonica (98.42 %) and for WSM4181-WSM4182 was Paraburkholderia graminis (99.79 %). Analysis of the gyrB and recA housekeeping genes supported the assignment of WSM4181-WSM4182 to P. graminis and the other investigated strains could be assigned to the genus Paraburkholderia. The results of DNA-DNA hybridization, physiological and biochemical tests allowed genotypic and phenotypic differentiation of WSM4178T from the closest validly published Paraburkholderia species. However, WSM4174-WSM4177 and WSM4179-WSM4180 could not reliably be distinguished from its closest neighbour and therefore complete genome comparison was performed between WSM4176 and P. tuberum STM678T which gave ANI values of 96-97 %. Chemotaxonomic data, including fatty acid profiles and quinone data supported the assignment of the strains to the genus Paraburkholderia. On the basis of genotypic and phenotypic data one novel species, Paraburkholderiafynbosensis sp. nov. (WSM4178T=LMG 27177T=HAMBI 3356T), is proposed and the isolation of P. tuberum and P. graminis from root nodules of Lebeckia ambigua is reported.

Genetic diversity and symbiotic effectiveness of Phaseolus vulgaris-nodulating rhizobia in Kenya.

Phaseolus vulgaris (common bean) was introduced to Kenya several centuries ago but the rhizobia that nodulate it in the country remain poorly characterised. To address this gap in knowledge, 178 isolates recovered from the root nodules of P. vulgaris cultivated in Kenya were genotyped stepwise by the analysis of genomic DNA fingerprints, PCR-RFLP and 16S rRNA, atpD, recA and nodC gene sequences. Results indicated that P. vulgaris in Kenya is nodulated by at least six Rhizobium genospecies, with most of the isolates belonging to Rhizobium phaseoli and a possibly novel Rhizobium species. Infrequently, isolates belonged to Rhizobium paranaense, Rhizobium leucaenae, Rhizobium sophoriradicis and Rhizobium aegyptiacum. Despite considerable core-gene heterogeneity among the isolates, only four nodC gene alleles were observed indicating conservation within this gene. Testing of the capacity of the isolates to fix nitrogen (N2) in symbiosis with P. vulgaris revealed wide variations in effectiveness, with ten isolates comparable to Rhizobium tropici CIAT 899, a commercial inoculant strain for P. vulgaris. In addition to unveiling effective native rhizobial strains with potential as inoculants in Kenya, this study demonstrated that Kenyan soils harbour diverse P. vulgaris-nodulating rhizobia, some of which formed phylogenetic clusters distinct from known lineages. The native rhizobia differed by site, suggesting that field inoculation of P. vulgaris may need to be locally optimised.