Bacterial community changes in response to oil contamination and perennial crop cultivation

We investigated bacterial community dynamics in response to used motor oil contamination and perennial crop cultivation by 16S rRNA gene amplicon sequencing in a 4-year field study. Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes were the major bacterial phyla, and Rhodococcus was the most abundant genus. Initially, oil contamination decreased the overall bacterial diversity. Actinobacteria, Betaproteobacteria, and Gammaproteobacteria were sensitive to oil contamination, exhibiting clear succession with time. However, bacterial communities changed over time, regardless of oil contamination and crop cultivation. The abundance difference of most OTUs between oil-contaminated and non-contaminated plots remained the same in later sampling years after the initial abundance difference induced by oil spike. The abundances of three oil-favored actinobacteria (Lysinimonas, Microbacteriaceae, and Marmoricola) and one betaproteobacterium (Aquabacterium) changed in different manner over time in oil-contaminated and non-contaminated soil. We propose that these taxa are potential bio-indicators for monitoring recovery from motor oil contamination in boreal soil. The effect of crop cultivation on bacterial communities became significant only after the crops achieved stable growth, likely associated with plant material decomposition by Bacteroidetes, Armatimonadetes and Fibrobacteres.Peer reviewe

Response of Soil Bacterial Community Diversity and Composition to Time, Fertilization, and Plant Species in a Sub-Boreal Climate

Pastures are an important part of crop and food systems in cold climates. Understanding how fertilization and plant species affect soil bacterial community diversity and composition is the key for understanding the role of soil bacteria in sustainable agriculture. To study the response of soil bacteria to different fertilization and cropping managements, a 3-year (2013-2015) field study was established. In the split-plot design, fertilizer treatment (unfertilized control, organic fertilizer, and synthetic fertilizer) was the main plot factor, and plant treatment [clear fallow, red clover (Trifolium pratense), timothy (Phleum pratense), and a mixture of red clover and timothy] was the sub-plot factor. Soil bacterial community diversity and composition, soil properties, and crop growth were investigated through two growing seasons in 2014 and 2015, with different nitrogen input levels. The community diversity measures (richness, Shannon diversity, and Shannon evenness) and composition changed over time (P<0.05) and at different time scales. The community diversity was lower in 2014 than in 2015. The temporal differences were greater than the differences between treatments. The overall correlations of Shannon diversity to soil pH, NO3-, NH4+, and surplus nitrogen were positive and that of bacterial richness to crop dry matter yield was negative (P<0.05). The major differences in diversity and community composition were found between fallow and planted treatments and between organic and synthetic fertilizer treatments. The differences between the planted plots were restricted to individual operational taxonomic units (OTUs). Soil moisture, total carbon content, and total nitrogen content correlated consistently with the community composition (P<0.05). Compared to the unfertilized control, the nitrogen fertilizer loading enhanced the temporal change of community composition in pure timothy and in the mixture more than that in red clover, which further emphasizes the complexity of interactions between fertilization and cropping treatments on soil bacteria.Peer reviewe

Draft genome sequences of Bradyrhizobium shewense sp nov ERR11(T) and Bradyrhizobium yuanmingense CCBAU 10071(T)

The type strain of the prospective Bradyrhizobium shewense sp. nov. ERR11(T), was isolated from a nodule of the leguminous tree Erythrina brucei native to Ethiopia. The type strain Bradyrhizobium yuanmingense CCBAU 10071(T), was isolated from the nodules of Lespedeza cuneata in Beijing, China. The genomes of ERR11(T) and CCBAU 10071(T) were sequenced by DOE-JGI and deposited at the DOE-JGI genome portal as well as at the European Nucleotide Archive. The genome of ERR11(T) is 9,163,226 bp in length and has 102 scaffolds, containing 8548 protein-coding and 86 RNA genes. The CCBAU 10071(T) genome is arranged in 108 scaffolds and consists of 8,201,522 bp long and 7776 protein-coding and 85 RNA genes. Both genomes contain symbiotic genes, which are homologous to the genes found in the complete genome sequence of Bradyrhizobium diazoefficiens USDA110(T). The genes encoding for nodulation and nitrogen fixation in ERR11(T) showed high sequence similarity with homologous genes found in the draft genome of peanut-nodulating Bradyrhizobium arachidis LMG 26795(T). The nodulation genes nolYAnodD2D1YABCSUIJ-nolO-nodZ of ERR11(T) and CCBAU 10071(T) are organized in a similar way to the homologous genes identified in the genomes of USDA110(T), Bradyrhizobium ottawaense USDA 4 and Bradyrhizobium liaoningense CCBAU 05525. The genomes harbor hupSLCFHK and hypBFDE genes that code the expression of hydrogenase, an enzyme that helps rhizobia to uptake hydrogen released by the N2-fixation process and genes encoding denitrification functions napEDABC and norCBQD for nitrate and nitric oxide reduction, respectively. The genome of ERR11(T) also contains nosRZDFYLX genes encoding nitrous oxide reductase. Based on multilocus sequence analysis of housekeeping genes, the novel species, which contains eight strains formed a unique group close to the B. ottawaense branch. Genome Average Nucleotide Identity (ANI) calculated between the genome sequences of ERR11(T) and closely related sequences revealed that strains belonging to B. ottawaense branch (USDA4 and CCBAU15615), were the closest strains to the strain ERR11(T) with 95.2% ANI. Type strain ERR11(T) showed the highest DDH predicted value with CCBAU15615 (58.5%), followed by USDA 4 (53.1%). Nevertheless, the ANI and DDH values obtained between ERR11(T) and CCBAU 15615 or USDA 4 were below the cutoff values (ANI = 96.5%; DDH = 70%) for strains belonging to the same species, suggesting that ERR11(T) is a new species. Therefore, based on the phylogenetic analysis, ANI and DDH values, we formally propose the creation of B. shewense sp. nov. with strain ERR11(T) (HAMBI 3532(T)= LMG 30162(T)) as the type strain.Peer reviewe

Genetically diverse lentil- and faba bean-nodulating rhizobia are present in soils across Central and Southern Ethiopia

In total 196 bacterial isolates were obtained from root nodules of lentil (Lens culinaris) and faba bean (Vicia faba) grown on soil samples collected from 10 different sites in central and southern parts of Ethiopia. All isolates were identified as members of the genus Rhizobium by using recA gene sequence analysis. In the recA phylogenetic tree 195 rhizobial strains were classified into nine genospecies. The phylogeny of symbiotic genes nodC and nifH revealed five and six distinct groups respectively, largely dominated by symbiovar viciae. A multivariate analysis showed that environmental variables of the sampling sites considered in this study had more effect on the distribution and composition of the genospecies than the host legumes of the strains. Twenty representative strains, selected based on their isolation site, host plant and nodC group, were able to nodulate all lentil, faba bean, field pea (Pisum abyssinicum) and grass pea (Lathyrus sativus) plants in a greenhouse test in axenic conditions. The majority of the rhizobial strains were effective nitrogen-fixing symbionts for all tested legumes, indicating their potential to serve as broad host-range inoculants in agriculture. The present work suggests the presence of taxonomically and symbiotically diverse rhizobial species for legumes in the Viciae tribe in Ethiopia.Peer reviewe

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

Implications of wetland degradation for the potential denitrifying activity and bacterial populations with nirS genes as found in a succession in Qinghai Tibet plateau, China

Alpine wetland in the Zoige Plateau has suffered from serious degradation during"the last 30 years due to global climate change and anthropogenic impact. Denitrification is a key nitrogen removal process which can be performed by different microorganisms, including bacteria harboring ttirS-genes. In this study, a degradation succession was used to study the effect on potential denitrification activity (PDA) and on bacterial communities harboring nirS genes. Based on the determination of the PDA, the abundance, structural diversity, and phylogenetic identity of the soil bacteria with nirS genes were further assessed by qPCR, terminal restriction fragment length polymorphism (T-RFLP), and DNA-sequencing, respectively. The results showed that soil PDA ranged from 8.78 to 52.77 ng N20-N g(-1) dry soil h(-1), being lowest in sandy soil and highest in swamp soil. The abundance of nirS genes (copies g(-1) soil) were also the lowest in the sandy soil while highest in the swamp soil. The average Shannon-Wiener diversity index of the nirS denitrifying bacterial structural ranged from 2.20 in the meadow soil to 3.07 in the swamp soil. Redundancy analysis (RDA) showed that the nirS denitrifying bacterial community correlated with soil water content and available phosphorus, with water content as the major factor in shaping the nirS denitrifying bacterial community. The results of this study suggest that the wetland degradation would decrease soil PDA, and abundance and structural diversity of the denitrifying bacteria with nirS genes. These findings can contribute to support a theoretical foundation for predicting the potential influences of wetland degradation on soil denitrifying bacteria in alpine wetlands. (C) 2017 Elsevier Masson SAS. All rights reserved.Peer reviewe

Low adherence with antihypertensives in actual practice: the association with social participation – a multilevel analysis

BACKGROUND: Low adherence is a key factor in explaining impaired effectiveness and efficiency in the pharmacological treatment of hypertension. However, little is known about which factors determine low adherence in actual practice. The purpose of this study is to examine whether low social participation is associated with low adherence with antihypertensive medication, and if this association is modified by the municipality of residence. METHODS: 1288 users of antihypertensive medication were identified from The Health Survey in Scania 2000, Sweden. The outcome was low adherence with antihypertensives during the last two weeks. Multilevel logistic regression with participants at the first level and municipalities at the second level was used for analyses of the data. RESULTS: Low social participation was associated with low adherence with antihypertensives during the last two weeks (OR = 2.05, 95% CI: 1.05–3.99), independently of low educational level. However, after additional adjustment for poor self-rated health and poor psychological health, the association between low social participation and low adherence with antihypertensives during the last two weeks remained but was not conclusive (OR = 1.80, 95% CI: 0.90–3.61). Furthermore, the association between low social participation and low adherence with antihypertensives during the last two weeks varied among municipalities in Scania (i.e., cross-level interaction). CONCLUSION: Low social participation seems to be associated with low adherence with antihypertensives during the last two weeks, and this association may be modified by the municipality of residence. Future studies aimed at investigating health-related behaviours in general and low adherence with medication in particular might benefit if they consider area of residence

Physical activity, exercise and self-rated health: a population-based study from Sweden

<p>Abstract</p> <p>Background</p> <p>In order to screen for the most inactive individuals in the population and target health-related interventions where they are most needed it is important to assess different forms of physical activity in population-based studies. The aims were (1) to identify the most inactive individuals in the population by assessing two dimensions of physical activity, (2) to investigate the correlation between exercise and total physical activity and (3) to investigate the association between exercise, total physical activity and good self-rated health.</p> <p>Methods</p> <p>A simple random sample of the Swedish population aged 25–64 years were interviewed about their living conditions, health and lifestyle in a survey performed by Statitics Sweden. In total 1876 women and 1880 men completed the survey during 1999 (response rate 76.6%) when two different questions about physical activity assessed exercise and total physical activity in all domains (e.g. transportation, exercise, and at work). Logistic regression models were used to estimate odds ratios.</p> <p>Results</p> <p>The most inactive individuals (no exercise and total physical activity ≤ 2 hours per week) constituted 4.3% of the sample. The correlation between exercise and total physical activity was low (gamma = 0.4, <it>p = </it>0.02). There were significant associations between higher levels of exercise, total physical activity and good self-rated health after adjustment for age, gender, country of birth, education, employment, marital status, housing tenure, smoking and BMI.</p> <p>Conclusion</p> <p>Both exercise and total physical activity were independently associated with good self-rated health. It seems to be advantageous to use more than one question in population based surveys in order to evaluate several dimensions of physical activity and identify the most inactive individuals.</p

Effect of a primary health-care-based controlled trial for cardiorespiratory fitness in refugee women

BACKGROUND: Refugee women have a high risk of coronary heart disease with low physical activity as one possible mediator. Furthermore, cultural and environmental barriers to increasing physical activity have been demonstrated. The aim of the study was to evaluate the combined effect of an approximate 6-month primary health care- and community-based exercise intervention versus an individual written prescription for exercise on objectively assessed cardiorespiratory fitness in low-active refugee women. METHODS: A controlled clinical trial, named "Support for Increased Physical Activity", was executed among 243 refugee women recruited between November 2006 and April 2008 from two deprived geographic areas in southern Stockholm, Sweden. One geographic area provided the intervention group and the other area the control group. The control group was on a higher activity level at both baseline and follow-up, which was taken into consideration in the analysis by applying statistical models that accounted for this. Relative aerobic capacity and fitness level were assessed as the two main outcome measures. RESULTS: The intervention group increased their relative aerobic capacity and the percentage with an acceptable fitness level (relative aerobic capacity > 23 O2 mlxkgxmin-1) to a greater extent than the control group between baseline and the 6-month follow-up, after adjusting for possible confounders (P = 0.020). CONCLUSIONS: A combined primary health-care and community-based exercise programme (involving non-profit organizations) can be an effective strategy to increase cardiorespiratory fitness among low-active refugee women. TRIAL REGISTRATION: ClinicalTrials.gov ID: NCT00747942