Revised taxonomy of the family Rhizobiaceae, and phylogeny of mesorhizobia nodulating Glycyrrhiza spp.

ABSTRACT Studies of the taxonomy of bacteria were initiated in the last quarter of the 19th century when bacteria were classified in six genera placed in four tribes based on their morphological appearance. Since then the taxonomy of bacteria has been revolutionized several times. At present, 30 phyla belong to the domain Bacteria , which includes over 9600 species. Unlike many eukaryotes, bacteria lack complex morphological characters and practically phylogenetically informative fossils. It is partly due to these reasons that bacterial taxonomy is complicated. Due to the improvement of methods to obtain sequence level characters plus new methods for their analyses, the taxonomy of bacteria has also been improved. However, there is still no official classification of prokaryotes. Biological nitrogen fixation (BNF) is a process in which bacteria reduce inert nitrogen gas to biologically useful ammonia. The symbiotic interaction between rhizobia and legumes (Fabaceae or Leguminosae) is important both in natural systems and in agriculture. Rhizobia is a general name for a group of bacteria that can enter symbiosis with legumes. Until 1982, all these were classified into one single bacterial genus, Rhizobium. The number of rhizobial genera increased to 17 by the year 2011, from which five genera, Rhizobium, Allorhizobium, Agrobacterium, Ensifer (syn. Sinorhizobium), and Shinella were accommodated in the family Rhizobiaceae. The genus Agrobacterium, a group of mostly pathogenic bacteria, was placed among the beneficial nitrogen-fixing bacteria (rhizobia) in the family Rhizobiaceae. That resulted in several taxonomic issues regarding the family Rhizobiaceae. The main nomenclatural issue regarding the genus Agrobacterium resulted from transferring this genus to the genus Rhizobium. Moreover, the phylogenetic position of the former nitrogen-fixing Rhizobium galegae complex was not clear. This group of bacteria was in previous studies clustered with either Agrobacterium or Rhizobium or placed in a lineage separately from other genera of the family Rhizobiaceae. During the last decade, the number of the rhizobial species increased dramatically, especially in the genus Rhizobium. However, Rhizobium is an inappropriate genus name for some of the species assigned to the genus. To resolve some of the major taxonomic uncertainties of the family Rhizobiaceae, two separate multilocus sequencing analyses (MLSA) were performed. In the first study, an MLSA of 114 rhizobial strains was performed by using six housekeeping genes (atpD, glnA, glnII, recA, rpoB, and thrC). The first MLSA study was focusing on the phylogeny of the taxa belonging to the former Rhizobium galegae complex and the genus Agrobacterium. In the second MLSA, a total of 100 strains representing 81 species of the family Rhizobiaceae were studied using four housekeeping genes namely 16S rRNA, atpD, recA, and rpoB. Based on these results, we proposed delineation of two new genera, Neorhizobium gen. nov. and Pararhizobium gen. nov., and 16 new species combinations, Neorhizobium galegae comb. nov., Neorhizobium huautlense comb. nov., Neorhizobium alkalisoli comb. nov., Agrobacterium nepotum comb. nov., Agrobacterium pusense comb. nov., Agrobacterium skierniewicense comb. nov., Allorhizobium vitis comb. nov., Allorhizobium taibaishanense comb. nov., Allorhizobium paknamense comb. nov., Allorhizobium oryzae comb. nov., Allorhizobium pseudoryzae comb. nov., Allorhizobium borbori comb. nov., Pararhizobium giardinii comb. nov., Pararhizobium capsulatum comb. nov., Pararhizobium herbae comb. nov., and Pararhizobium sphaerophysae comb. nov. (Paper I and II). A total of 159 bacterial strains were isolated from the nodules of the Chinese specimens of the plant genus Glycyrrhiza L. The results of the study showed that 29 true symbiotic strains belong to the genus Mesorhizobium. To estimate the phylogenetic position of the 29 isolates an MLSA was performed for 59 mesorhizobial strains by using three housekeeping genes 16S rRNA, recA, and rpoB. Moreover, the phylogeny of three symbiotic genes (nodA, nodC, and nifH) of these 59 mesorhizobial strains was investigated. The results of MLSA showed that 21 test strains belong to the species M. tianshanense, M. gobiense, M. temperatum, M. muleiense, M. amorphae, M. alhagi, and M. camelthorni, whereas eight test strains might belong to a novel species of Mesorhizobium. The results of the analyses of accessory genes in this study showed that the mesorhizobial strains isolated from the plant genus Glycyrrhiza have probably acquired some genetic material from other rhizobia co-evolving with Glycyrrhiza and other legumes (Paper III).

The Comparative Analysis of the Effect of Magic Spell on Prophet Muhammad (PBUH) in Sahih Bukhari and Sahih Muslim with Regard to the Circumstance of Revelation for Surah an-Nas and Surah al-Falaq

Some of the Ahadith in Sahih al-Bukhari and Sahih al-Muslim about casting a magic spell on Prophet Muhammad have made Sunni commentators and Muhaddithin relate the circumstance of revelation for Surah al-Falaq and Surah an-Nas to casting a magic spell on Prophet Muhammad by someone called Labid bin A’sam Yahudi. Sunni commentators thus recognize that this event is not against the infallibility of the Holy Prophet and his dignity of Nabuwwat. This article aims to answer this research question: Can the event of casting a magic spell on the Holy Prophet by Labid bin A’sam in Medina, as it is mentioned in some of the Ahadith, be the circumstance of revelation for Surah an-Nas and Surah al-Falaq? The results of the study show that due to some discrepancies between commentators on whether these chapters are Makki or Madani, some contradictory traditions on their circumstance of revelation, the referential and conceptual weakness of  the traditions about the magic spell on the Prophet, and stylistics of the above chapters having a Makki context, it is concluded that the circumstance of revelation for the above chapters cannot be attributed to the event of casting a magic spell on the Holy Prophet. © Seyed Mousavi, S.H; Mortazawi, S.M; Abdollah Zadeh, S.H. (2020) The Comparative Analysis of the Effect of Magic Spell on Prophet Muhammad (PBUH) in Sahih Bukhari and Sahih Muslim with Regard to the Circumstance of Revelation for Surah an-Nas and Surah al-Falaq. Biannual Journal of Comparative Exegetical Researches, 6 (11) 253-276.  Doi: 10.22091/ptt.2020.3366.138

International Committee on Systematics of Prokaryotes, Subcommittee on the taxonomy of Rhizobia and Agrobacteria, minutes of the annual meeting by videoconference, 5 July 2021, followed by online discussion until 31 December 2021.

Minutes of the closed meeting of the International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria held by videoconference, 5 July 2021, followed by online discussion until 31 December 2021, and list of recent species

Characterization of Agrobacterium radiobacter, a new pathogen of pistachio

Crown and stem gall caused by agrobacterial species is one of the most devastating diseases on different crops worldwide. In spring 2018, an alert concerning a disease forming galls on seedlings of pistachio in nurseries was received from Rafsanjan county, Kerman province, Iran. After isolation of bacteria from the galls by using conventional bacteriological methods, bacterial colonies were purified and selected for further analyses including biochemical, pathogenicity and molecular tests. Pathogenicity tests of all isolates on test plants and carrot discs were evaluated positive. Based on the results of biochemical and pathogenicity tests, supported by molecular phylogenies of housekeeping and pathogenicity genes, the isolates were identified as Agrobacterium radiobacter. Since agrobacteria could be easily spread through seedlings and agricultural materials between different areas, the identified Agrobacterium strains could be considered as a latent threat to the pistachio nurseries of Iran. The present study is the first report on the occurrence of crown and stem gall on pistachio caused by A. radiobacter worldwide.Peer reviewe

Genomic features separating ten strains of Neorhizobium galegae with different symbiotic phenotypes

Background The symbiotic phenotype of Neorhizobium galegae, with strains specifically fixing nitrogen with either Galega orientalis or G. officinalis, has made it a target in research on determinants of host specificity in nitrogen fixation. The genomic differences between representative strains of the two symbiovars are, however, relatively small. This introduced a need for a dataset representing a larger bacterial population in order to make better conclusions on characteristics typical for a subset of the species. In this study, we produced draft genomes of eight strains of N. galegae having different symbiotic phenotypes, both with regard to host specificity and nitrogen fixation efficiency. These genomes were analysed together with the previously published complete genomes of N. galegae strains HAMBI 540T and HAMBI 1141. Results The results showed that the presence of an additional rpoN sigma factor gene in the symbiosis gene region is a characteristic specific to symbiovar orientalis, required for nitrogen fixation. Also the nifQ gene was shown to be crucial for functional symbiosis in both symbiovars. Genome-wide analyses identified additional genes characteristic of strains of the same symbiovar and of strains having similar plant growth promoting properties on Galega orientalis. Many of these genes are involved in transcriptional regulation or in metabolic functions. Conclusions The results of this study confirm that the only symbiosis-related gene that is present in one symbiovar of N. galegae but not in the other is an rpoN gene. The specific function of this gene remains to be determined, however. New genes that were identified as specific for strains of one symbiovar may be involved in determining host specificity, while others are defined as potential determinant genes for differences in efficiency of nitrogen fixation.Peer reviewe

Non-communicable diseases in the southwest of Iran: profile and baseline data from the Shahrekord PERSIAN Cohort Study

Background Critical inter-provincial differences within Iran in the pattern of non-communicable diseases (NCDs) and difficulties inherent to identifying prevention methods to reduce mortality from NCDs have challenged the implementation of the provincial health system plan. The Shahrekord Cohort Study (SCS) was designed to address these gaps in Chaharmahal and Bakhtiari, a province of high altitude in the southwest of Iran, characterized by its large Bakhtiari population, along with Fars and Turk ethnicity groups. Methods This ongoing cohort, a prospective, large-scale longitudinal study, includes a unique, rich biobank and was conducted for the first time in Chaharmahal and Bakhtiari Province in Iran. SCS is a part of the PERSIAN (Prospective Epidemiological Research Studies in IrAN) cohort. The study began in 2015, recruited 10075 participants (52.8% female, 47.2% male) from both urban (n=7034) and rural (n=3041) areas, and participants will be annually followed up for at least 15 years. A cross-sectional analysis was conducted using baseline data from the SCS, using descriptive statistics and logistic regression. Data analysis was performed using Stata software. Results The prevalence of NCDs was 9.8% for type 2 diabetes, 17.1% for hypertension, 11.6% for thyroid disease, 0.2% for multiple sclerosis and 5.7, 0.9 and 1.3% for ischemic heart disease, stroke and myocardial infarction, respectively. The prevalence of multimorbidity (>= 2 NCDs) was higher in women (39.1%) than men (24.9%). The means (standard deviations) of age, BMI, systolic blood pressure and fasting blood glucose were 49.5 (9) years, 27.6 (4.6) kg/m(2), 115.4 (17.3) mmHg and 96.7 (27.3) mg/dL, respectively. Logistic regression models showed that older age, female gender, living in an urban area, non-native ethnicity, high wealth index, unemployment, obesity, low physical activity, hypertriglyceridemia, high fasting blood sugar, alkaline urine pH and high systolic and diastolic blood pressure were associated with increased prevalence of NCDs. Conclusions The SCS provides a platform for epidemiological studies that will be useful to better control NCDs in the southwest of Iran and to foster research collaboration. The SCS will be an essential resource for identifying NCD risk factors in this region and designing relevant public health interventions

Mapping development and health effects of cooking with solid fuels in low-income and middle-income countries, 2000-18 : a geospatial modelling study

Background More than 3 billion people do not have access to clean energy and primarily use solid fuels to cook. Use of solid fuels generates household air pollution, which was associated with more than 2 million deaths in 2019. Although local patterns in cooking vary systematically, subnational trends in use of solid fuels have yet to be comprehensively analysed. We estimated the prevalence of solid-fuel use with high spatial resolution to explore subnational inequalities, assess local progress, and assess the effects on health in low-income and middle-income countries (LMICs) without universal access to clean fuels.Methods We did a geospatial modelling study to map the prevalence of solid-fuel use for cooking at a 5 km x 5 km resolution in 98 LMICs based on 2.1 million household observations of the primary cooking fuel used from 663 population-based household surveys over the years 2000 to 2018. We use observed temporal patterns to forecast household air pollution in 2030 and to assess the probability of attaining the Sustainable Development Goal (SDG) target indicator for clean cooking. We aligned our estimates of household air pollution to geospatial estimates of ambient air pollution to establish the risk transition occurring in LMICs. Finally, we quantified the effect of residual primary solid-fuel use for cooking on child health by doing a counterfactual risk assessment to estimate the proportion of deaths from lower respiratory tract infections in children younger than 5 years that could be associated with household air pollution.Findings Although primary reliance on solid-fuel use for cooking has declined globally, it remains widespread. 593 million people live in districts where the prevalence of solid-fuel use for cooking exceeds 95%. 66% of people in LMICs live in districts that are not on track to meet the SDG target for universal access to clean energy by 2030. Household air pollution continues to be a major contributor to particulate exposure in LMICs, and rising ambient air pollution is undermining potential gains from reductions in the prevalence of solid-fuel use for cooking in many countries. We estimated that, in 2018, 205000 (95% uncertainty interval 147000-257000) children younger than 5 years died from lower respiratory tract infections that could be attributed to household air pollution.Interpretation Efforts to accelerate the adoption of clean cooking fuels need to be substantially increased and recalibrated to account for subnational inequalities, because there are substantial opportunities to improve air quality and avert child mortality associated with household air pollution. Copyright (C) 2022 The Author(s). Published by Elsevier Ltd.Peer reviewe

Adolescent transport and unintentional injuries: a systematic analysis using the Global Burden of Disease Study 2019

Background: Globally, transport and unintentional injuries persist as leading preventable causes of mortality and morbidity for adolescents. We sought to report comprehensive trends in injury-related mortality and morbidity for adolescents aged 10–24 years during the past three decades. Methods: Using the Global Burden of Disease, Injuries, and Risk Factors 2019 Study, we analysed mortality and disability-adjusted life-years (DALYs) attributed to transport and unintentional injuries for adolescents in 204 countries. Burden is reported in absolute numbers and age-standardised rates per 100 000 population by sex, age group (10–14, 15–19, and 20–24 years), and sociodemographic index (SDI) with 95% uncertainty intervals (UIs). We report percentage changes in deaths and DALYs between 1990 and 2019. Findings: In 2019, 369 061 deaths (of which 214 337 [58%] were transport related) and 31·1 million DALYs (of which 16·2 million [52%] were transport related) among adolescents aged 10–24 years were caused by transport and unintentional injuries combined. If compared with other causes, transport and unintentional injuries combined accounted for 25% of deaths and 14% of DALYs in 2019, and showed little improvement from 1990 when such injuries accounted for 26% of adolescent deaths and 17% of adolescent DALYs. Throughout adolescence, transport and unintentional injury fatality rates increased by age group. The unintentional injury burden was higher among males than females for all injury types, except for injuries related to fire, heat, and hot substances, or to adverse effects of medical treatment. From 1990 to 2019, global mortality rates declined by 34·4% (from 17·5 to 11·5 per 100 000) for transport injuries, and by 47·7% (from 15·9 to 8·3 per 100 000) for unintentional injuries. However, in low-SDI nations the absolute number of deaths increased (by 80·5% to 42 774 for transport injuries and by 39·4% to 31 961 for unintentional injuries). In the high-SDI quintile in 2010–19, the rate per 100 000 of transport injury DALYs was reduced by 16·7%, from 838 in 2010 to 699 in 2019. This was a substantially slower pace of reduction compared with the 48·5% reduction between 1990 and 2010, from 1626 per 100 000 in 1990 to 838 per 100 000 in 2010. Between 2010 and 2019, the rate of unintentional injury DALYs per 100 000 also remained largely unchanged in high-SDI countries (555 in 2010 vs 554 in 2019; 0·2% reduction). The number and rate of adolescent deaths and DALYs owing to environmental heat and cold exposure increased for the high-SDI quintile during 2010–19. Interpretation: As other causes of mortality are addressed, inadequate progress in reducing transport and unintentional injury mortality as a proportion of adolescent deaths becomes apparent. The relative shift in the burden of injury from high-SDI countries to low and low–middle-SDI countries necessitates focused action, including global donor, government, and industry investment in injury prevention. The persisting burden of DALYs related to transport and unintentional injuries indicates a need to prioritise innovative measures for the primary prevention of adolescent injury. Funding: Bill & Melinda Gates Foundation

Measuring universal health coverage based on an index of effective coverage of health services in 204 countries and territories, 1990–2019 : A systematic analysis for the Global Burden of Disease Study 2019

Background Achieving universal health coverage (UHC) involves all people receiving the health services they need, of high quality, without experiencing financial hardship. Making progress towards UHC is a policy priority for both countries and global institutions, as highlighted by the agenda of the UN Sustainable Development Goals (SDGs) and WHO's Thirteenth General Programme of Work (GPW13). Measuring effective coverage at the health-system level is important for understanding whether health services are aligned with countries' health profiles and are of sufficient quality to produce health gains for populations of all ages. Methods Based on the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019, we assessed UHC effective coverage for 204 countries and territories from 1990 to 2019. Drawing from a measurement framework developed through WHO's GPW13 consultation, we mapped 23 effective coverage indicators to a matrix representing health service types (eg, promotion, prevention, and treatment) and five population-age groups spanning from reproductive and newborn to older adults (≥65 years). Effective coverage indicators were based on intervention coverage or outcome-based measures such as mortality-to-incidence ratios to approximate access to quality care; outcome-based measures were transformed to values on a scale of 0–100 based on the 2·5th and 97·5th percentile of location-year values. We constructed the UHC effective coverage index by weighting each effective coverage indicator relative to its associated potential health gains, as measured by disability-adjusted life-years for each location-year and population-age group. For three tests of validity (content, known-groups, and convergent), UHC effective coverage index performance was generally better than that of other UHC service coverage indices from WHO (ie, the current metric for SDG indicator 3.8.1 on UHC service coverage), the World Bank, and GBD 2017. We quantified frontiers of UHC effective coverage performance on the basis of pooled health spending per capita, representing UHC effective coverage index levels achieved in 2019 relative to country-level government health spending, prepaid private expenditures, and development assistance for health. To assess current trajectories towards the GPW13 UHC billion target—1 billion more people benefiting from UHC by 2023—we estimated additional population equivalents with UHC effective coverage from 2018 to 2023. Findings Globally, performance on the UHC effective coverage index improved from 45·8 (95% uncertainty interval 44·2–47·5) in 1990 to 60·3 (58·7–61·9) in 2019, yet country-level UHC effective coverage in 2019 still spanned from 95 or higher in Japan and Iceland to lower than 25 in Somalia and the Central African Republic. Since 2010, sub-Saharan Africa showed accelerated gains on the UHC effective coverage index (at an average increase of 2·6% [1·9–3·3] per year up to 2019); by contrast, most other GBD super-regions had slowed rates of progress in 2010–2019 relative to 1990–2010. Many countries showed lagging performance on effective coverage indicators for non-communicable diseases relative to those for communicable diseases and maternal and child health, despite non-communicable diseases accounting for a greater proportion of potential health gains in 2019, suggesting that many health systems are not keeping pace with the rising non-communicable disease burden and associated population health needs. In 2019, the UHC effective coverage index was associated with pooled health spending per capita (r=0·79), although countries across the development spectrum had much lower UHC effective coverage than is potentially achievable relative to their health spending. Under maximum efficiency of translating health spending into UHC effective coverage performance, countries would need to reach $1398 pooled health spending per capita (US$ adjusted for purchasing power parity) in order to achieve 80 on the UHC effective coverage index. From 2018 to 2023, an estimated 388·9 million (358·6–421·3) more population equivalents would have UHC effective coverage, falling well short of the GPW13 target of 1 billion more people benefiting from UHC during this time. Current projections point to an estimated 3·1 billion (3·0–3·2) population equivalents still lacking UHC effective coverage in 2023, with nearly a third (968·1 million [903·5–1040·3]) residing in south Asia. Interpretation The present study demonstrates the utility of measuring effective coverage and its role in supporting improved health outcomes for all people—the ultimate goal of UHC and its achievement. Global ambitions to accelerate progress on UHC service coverage are increasingly unlikely unless concerted action on non-communicable diseases occurs and countries can better translate health spending into improved performance. Focusing on effective coverage and accounting for the world's evolving health needs lays the groundwork for better understanding how close—or how far—all populations are in benefiting from UHC