Analyses of the Distribution Patterns of Burkholderia pseudomallei and Associated Phages in Soil Samples in Thailand Suggest That Phage Presence Reduces the Frequency of Bacterial Isolation

Melioidosis is a frequently fatal infectious disease caused by the Gram negative bacillus Burkholderia pseudomallei. Although it was originally discovered in Myanmar, the disease disappeared from sight for many decades. This study focuses on detection of B. pseudomallei in soil in selected sampling sites in an attempt to start to fill the gaps in the current status of our knowledge of the geographical distribution of B. pseudomallei in soil in Myanmar. This cross-sectional study consists of 400 soil samples from 10 selected study townships from two major paddy growing regions. Bacterial isolation was done using a simplified method for the isolation of Burkholderia pseudomallei from soil. In this study, only 1% (4/400) of soil samples were found to be positive; two of four were found at 90 cm depth and another two positive samples were found at 30 cm and 60 cm. This survey has confirmed the presence of environmental B. pseudomallei in Myanmar indicating that the conditions are in place for melioidosis acquisition.

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Evaluation of consensus method for the culture of Burkholderia pseudomallei in soil samples from Laos

Wellcome Open Research ◽

10.12688/wellcomeopenres.14851.2 ◽

2018 ◽

Vol 3 ◽

pp. 132 ◽

Cited By ~ 2

Author(s):

David A.B. Dance ◽

Michael Knappik ◽

Sabine Dittrich ◽

Viengmon Davong ◽

Joy Silisouk ◽

...

Keyword(s):

Environmental Samples ◽

Burkholderia Pseudomallei ◽

Enrichment Culture ◽

False Negative ◽

Culture Method ◽

Soil Samples ◽

Consensus Method ◽

Conventional Culture ◽

Two Samples ◽

Conventional Culture Method

Background: We have previously shown that PCR following enrichment culture is the most sensitive method to detect Burkholderia pseudomallei in environmental samples. Here we report an evaluation of the published consensus method for the culture of B. pseudomallei from Lao soil in comparison with our conventional culture method and with PCR with or without prior broth enrichment. Methods: One hundred soil samples were collected from a field known to contain B. pseudomallei and processed by: (i) the conventional method, (ii-iii) the consensus method using media prepared in either Laos or Thailand, and (iv) the consensus method performed in Thailand, as well as by (v) PCR following direct extraction of DNA from soil and (vi) PCR following broth pre-enrichment. Results: The numbers of samples in which B. pseudomallei was detected were 42, 10, 7, 6, 6 and 84, respectively. However, two samples were positive by the consensus method but negative by conventional culture, and one sample was negative by PCR following enrichment although B. pseudomallei was isolated by the conventional culture method. Conclusions/Discussion: The results show that no single method will detect all environmental samples that contain B. pseudomallei. People conducting environmental surveys for this organism should be aware of the possibility of false-negative results using the consensus culture method. An approach that entails screening using PCR after enrichment, followed by the evaluation of a range of different culture methods on PCR-positive samples to determine which works best in each setting, is recommended.

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No hints for abundance of Bacillus anthracis and Burkholderia pseudomallei in 100 environmental samples from Cameroon

European Journal of Microbiology and Immunology ◽

10.1556/1886.2021.00014 ◽

2021 ◽

Author(s):

Hagen Frickmann ◽

Sven Poppert

Keyword(s):

Nucleic Acid ◽

Bacillus Anthracis ◽

Real Time Pcr ◽

Environmental Samples ◽

Plant Material ◽

Burkholderia Pseudomallei ◽

Soil Samples ◽

Water Contact ◽

Dressing Room ◽

Proof Of Principle

Abstract Background Little is known on the abundance of the pathogens Bacillus anthracis and Burkholderia pseudomallei in environmental samples in Cameroon. Therefore, 100 respective samples were assessed in a proof-of-principle assessment. Methods DNA residuals from nucleic acid extractions of 100 environmental samples, which were collected between 2011 and 2013 in the Mapé Basin of Cameroon, were screened for B. anthracis and B. pseudomallei by real-time PCR. The samples comprised soil samples with water contact (n = 88), soil samples without water contact (n = 6), plant material with water contact (n = 3), water (n = 2), and soil from a hospital dressing room (n = 1). Results B. anthracis and B. pseudomallei were detected in none of the samples assessed. Conclusion The results indicate that at least a quantitatively overwhelming, ubiquitous occurrence of B. anthracis and B. pseudomallei in the environment in Cameroon is highly unlikely. However, the number and choice of the assessed samples limit the interpretability of the results.

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Comparison and interpretation of characteristics of Rhizosphere microbiomes of three blueberry varieties

BMC Microbiology ◽

10.1186/s12866-021-02092-7 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Yan Zhang ◽

Wei Wang ◽

Zhangjun Shen ◽

Jingjing Wang ◽

Yajun Chen ◽

...

Keyword(s):

Microbial Communities ◽

High Throughput Sequencing ◽

Rhizosphere Soil ◽

Alpha Diversity ◽

Distribution Patterns ◽

Soil Samples ◽

Bulk Soil ◽

Core Microbiome ◽

Rhizosphere Microbiome ◽

Vital Functions

Abstract Background Studies on the rhizosphere microbiome of various plants proved that rhizosphere microbiota carries out various vital functions and can regulate the growth and improve the yield of plants. However, the rhizosphere microbiome of commercial blueberry was only reported by a few studies and remains elusive. Comparison and interpretation of the characteristics of the rhizosphere microbiome of blueberry are critical important to maintain its health. Results In this study, a total of 20 rhizosphere soil samples, including 15 rhizosphere soil samples from three different blueberry varieties and five bulk soil samples, were sequenced with a high-throughput sequencing strategy. Based on these sequencing datasets, we profiled the taxonomical, functional, and phenotypic compositions of rhizosphere microbial communities for three different blueberry varieties and compared our results with a previous study focused on the rhizosphere microbiome of blueberry varieties. Our results demonstrated significant differences in alpha diversity and beta diversity of rhizosphere microbial communities of different blueberry varieties and bulk soil. The distribution patterns of taxonomical, functional, and phenotypic compositions of rhizosphere microbiome differ across the blueberry varieties. The rhizosphere microbial communities of three different blueberry varieties could be distinctly separated, and 28 discriminative biomarkers were selected to distinguish these three blueberry varieties. Core rhizosphere microbiota for blueberry was identified, and it contained 201 OTUs, which were mainly affiliated with Proteobacteria, Actinobacteria, and Acidobacteria. Moreover, the interactions between OTUs of blueberry rhizosphere microbial communities were explored by a co-occurrence network of OTUs from an ecological perspective. Conclusions This pilot study explored the characteristics of blueberry’s rhizosphere microbial community, such as the beneficial microorganisms and core microbiome, and provided an integrative perspective on blueberry’s rhizosphere microbiome, which beneficial to blueberry health and production.

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Sediment morphology and distribution in a restored riparian forest

Scientia Agricola ◽

10.1590/s0103-90162007000500006 ◽

2007 ◽

Vol 64 (5) ◽

pp. 486-494 ◽

Cited By ~ 3

Author(s):

Renata Santos Momoli ◽

Miguel Cooper ◽

Selene Cristina de Pierri Castilho

Keyword(s):

Particle Size ◽

Sugar Cane ◽

Riparian Forest ◽

Distribution Patterns ◽

Deposition Process ◽

Soil Samples ◽

Particle Size Distributions ◽

Statistical Parameters ◽

Sediment Distribution ◽

Deposition Processes

Sediment distribution patterns of riparian zones reflect the deposition dynamics and the type of deposition event. The purpose of this study is to characterize the morphology and distribution of sediments deposited in a restored riparian forest that were transported from adjacent areas cropped with sugar-cane. In order to study the deposition processes in a riparian forest located in the county of Iracemápolis state of São Paulo, Brazil, soil samples were collected on a transect for micromorphological as well as particle size distribution analyses, using Folk & Ward statistical parameters. Soil samples were dispersed with NaOH + sodium hexametaphosphate and water. The dispersion in water was made to simulate field transport conditions. Particle size distributions together with field and laboratory morphological analyses showed an irregular and non-uniform sediment deposition. This deposition process suggests the occurrence of high intensity erosive events that produce high amount of sediments and runoff characterized by a turbulent flow. The land use change in the riparian area marks the change in the preferential deposition location, which when sugar-cane dominated, corresponded to the alluvial plain and, after the restoration and development of the riparian forest, was dislocated 27 m upslope within the first few meters from the border of the forest.

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Distribution Characteristics of SOC, STN, and STP Contents Along a Slope Aspect Gradient of Loess Plateau in China

Frontiers in Soil Science ◽

10.3389/fsoil.2021.741000 ◽

2021 ◽

Vol 1 ◽

Author(s):

Minxia Liu ◽

Ruixin Yu ◽

Liang Li ◽

Lu Xu ◽

Ruolan Mu ◽

...

Keyword(s):

Loess Plateau ◽

Soil Nutrient ◽

Distribution Patterns ◽

Soil Samples ◽

Gansu Province ◽

Slope Aspect ◽

Northern Slope ◽

Southern Slope ◽

Soil Layers ◽

Correlation Degree

In this study, the effects of slope aspects and depths on soil organic carbon (SOC), soil total nitrogen (STN), and soil total phosphorus (STP) were quantified in disturbed restoration regions of Gaolan County, located in the Gansu Province of semi-arid loess Plateau of China. Soil samples were collected at 0–10, 10–20, 20–40, 40–60, 60–80, and 80–100 cm on southern, southwestern, western, northwestern, and northern slope aspects of three hills. A total of 75 soil profiles and 450 soil samples were analyzed. Results showed that the SOC, STN, and STP content varied from 1.65 to 12.87 g/kg, 0.45 to 1.53 g/kg, and 0.07 to 0.78 g/kg, and the SOCD, STND, and STPD at 0–100 cm varied from 3.9 to 9.5 kg/m2, 0.58 to 1.35 kg/m2, and 0.33 to 0.56 kg/m2, which increased from the southern to northern slope aspects. The SOC, STN, and STP contents and SOCD, STND, and STPD were mainly in the 0–60 and 60–100 cm soil layers. The vertical descent rate was γSOC > γSTN > γSTP for both content and density. For a single soil nutrient, the decline rate of its content and density on the northern slope aspect was greater than that on the southern slope aspect, that is γN > γ All > γS. The correlation degree between soil properties and SOC and STN content were above 0.6, the overall correlation with STP content was <0.6. These results confirmed that topography (slope aspects) was the most significant factor controlling the distribution patterns of SOC, STN, and STP in hill ecosystems. Overall, the northern slope aspect (vs. southern slope aspect) was more favorable to the preservation of SOC, STN, and STP. Accordingly, in the Loess Plateau and similar fragile environments, soil nutrient protection and vegetation restoration are selective to some extent.

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Evaluation of spatial spreading of phyto-available sulphur and micronutrients in cultivated coastal soils

PLoS ONE ◽

10.1371/journal.pone.0258166 ◽

2021 ◽

Vol 16 (10) ◽

pp. e0258166

Author(s):

A. K. Shukla ◽

S. K. Behera ◽

R. Tripathi ◽

C. Prakash ◽

A. K. Nayak ◽

...

Keyword(s):

Soil Ph ◽

Crop Production ◽

Agricultural Soils ◽

Anthropogenic Activities ◽

Distribution Patterns ◽

Soil Samples ◽

Soil Parameters ◽

Mean Values ◽

Coastal Soils ◽

Spatial Spreading

Understanding the spatial spreading patterns of plant-available sulphur (S) (AS) and plant-available micronutrients (available zinc (AZn), available iron (AFe), available copper (ACu), available manganese (AMn) and available boron (AB)) in soils, especially in coastal agricultural soils subjected to various natural and anthropogenic activities, is vital for sustainable crop production by adopting site-specific nutrient management (SSNM) strategies. We studied the spatial distribution patterns of AS, AZn, AFe, ACu, AMn, and AB in cultivated soils of coastal districts of India using geostatistical approaches. Altogether 39,097 soil samples from surface (0 to 15 cm depth) layers were gathered from farm lands of 68 coastal districts. The analysis of soil samples was carried out for soil pH, electrical conductivity (EC), soil organic carbon (SOC) and AS, AZn, AFe, ACu, AMn, and AB. Soil pH, EC and SOC varied from 3.70 to 9.90, 0.01 to 7.45 dS m-1 and 0.02 to 3.74%, respectively. The concentrations of AS, AZn, AFe, ACu, AMn, and AB varied widely in the study area with their corresponding mean values were 37.4±29.4, 1.50±1.53, 27.9±35.1, 2.14±1.74, 16.9±18.4 and 1.34±1.52 mg kg-1, respectively. The coefficient of variation values of analyzed soil parameters varied from 14.6 to 126%. The concentrations of AS, AZn, AFe, ACu, AMn, and AB were negatively and significantly correlated with soil pH and positively and significantly correlated with SOC. The geostatistical analysis indicated stable, Gaussian and exponential best-fit semivariogram models with moderate to strong spatial dependence for available nutrients. The generated spatial spreading maps revealed different distribution patterns for AS, AZn, AFe, ACu, AMn, and AB. There were variations in spatial spreading patterns of AS, AZn, AFe, ACu, AMn, and AB in east- and west-coastal area. About 62, 35, 12, 0.4, 23 and 45% of the study area had deficiency of AS, AZn, AFe, ACu, AMn, and AB, respectively. The spatial spreading maps will be highly useful for SSNM in the cultivated coastal soils of the country. This study could also be used as a base for assessing spatial spreading patterns of soil parameters in cultivated coastal areas of other parts of the world.

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Expanding the Burkholderia pseudomallei complex with the addition of two novel species: Burkholderia mayonis sp. nov. and Burkholderia savannae sp. nov.

Applied and Environmental Microbiology ◽

10.1128/aem.01583-21 ◽

2021 ◽

Author(s):

Carina M. Hall ◽

Anthony L. Baker ◽

Jason W. Sahl ◽

Mark Mayo ◽

Holger C. Scholz ◽

...

Keyword(s):

Type Strain ◽

Burkholderia Pseudomallei ◽

Novel Species ◽

Phage Type ◽

Distinct Species ◽

Soil Samples ◽

Northern Australia ◽

Coding Regions ◽

Scientific Disciplines ◽

Distinct Cluster

Distinct Burkholderia strains were isolated from soil samples collected in tropical northern Australia (Northern Territory and the Torres Strait Islands, Queensland). Phylogenetic analysis of 16S rRNA and whole genome sequences revealed these strains were distinct from previously described Burkholderia species and assigned them to two novel clades within the B. pseudomallei complex (Bpc). Because average nucleotide identity and digital DNA-DNA hybridization calculations are consistent with these clades representing distinct species, we propose the names Burkholderia mayonis sp. nov. and Burkholderia savannae sp. nov. Strains assigned to B. mayonis sp. nov. include type strain BDU6 T (=TSD-80; LMG 29941; ASM152374v2) and BDU8. Strains assigned to B. savannae sp. nov. include type strain MSMB266 T (=TSD-82; LMG 29940; ASM152444v2), MSMB852, BDU18, and BDU19. Comparative genomics revealed unique coding regions for both putative species, including clusters of orthologous genes associated with phage. Type strains of both B. mayonis sp. nov. and B. savannae sp. nov. yielded biochemical profiles distinct from each other and other species in the Bpc, and profiles also varied among strains within B. mayonis sp. nov. and B. savannae sp. nov. Matrix-assisted laser desorption ionization–time of flight analysis revealed a B. savannae sp. nov. cluster separate from other species, whereas B. mayonis sp. nov. strains did not form a distinct cluster. Neither B. mayonis sp. nov. nor B. savannae sp. nov. caused mortality in mice when delivered via the subcutaneous route. The addition of B. mayonis sp. nov. and B. savannae sp. nov. results in eight species currently in the Bpc. IMPORTANCE Burkholderia species can be important sources of novel natural products and new species are of interest to diverse scientific disciplines. Although many Burkholderia species are saprophytic, Burkholderia pseudomallei is the causative agent of the disease melioidosis. Understanding the genomics and virulence of the closest relatives to B. pseudomallei ( i.e., the other species within the Bpc) is important for identifying robust diagnostic targets specific to B. pseudomallei and understanding evolution of virulence in B. pseudomallei . Two proposed novel species, B. mayonis sp. nov. and B. savannae sp. nov., were isolated from soil samples collected from multiple locations in northern Australia. The two proposed species belong to the Bpc but are phylogenetically distinct from all other members of this complex. The addition of B. mayonis sp. nov. and B. savannae sp. nov. results in a total of eight species within this significant complex of bacteria that are available for future studies.

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Preliminary report on the northern Australian melioidosis environmental surveillance project

Epidemiology and Infection ◽

10.1017/s0950268804002663 ◽

2004 ◽

Vol 132 (5) ◽

pp. 813-820 ◽

Cited By ~ 26

Author(s):

T. J. J. INGLIS ◽

N. F. FOSTER ◽

D. GAL ◽

K. POWELL ◽

M. MAYO ◽

...

Keyword(s):

Burkholderia Pseudomallei ◽

Northern Territory ◽

Soil Samples ◽

Environmental Surveillance ◽

Free Living ◽

Water Supplies ◽

Surveillance Programme ◽

Outbreak Investigations ◽

Water And Soil Samples ◽

Culture Positive

An environmental surveillance programme was developed to determine whether water supplies could be a source of Burkholderia pseudomallei as noted during previous melioidosis outbreak investigations. Water supplies to communities in the three northern Australian jurisdictions (Western Australia, Northern Territory and Queensland) were sampled periodically during 2001 and 2002. Water and soil samples were collected from communities known to have had recent culture-positive melioidosis cases and nearby communities where no cases had been diagnosed. Clinical isolates of B. pseudomallei obtained from northern Australian patients during 2001 and 2002 were compared with the environmental B. pseudomallei isolates by ribotyping and pulsed-field gel electrophoresis. B. pseudomallei was isolated from 11 distinct locations, all in the Northern Territory, seven of which were associated with culture-positive melioidosis cases (>1 case at three locations). Water was implicated as a possible environmental source of melioidosis in six locations. A variety of free-living amoebae including Acanthamoeba and Hartmannella spp. that are potential hosts to B. pseudomallei were recovered from environmental specimens. Culturable B. pseudomallei was not found to be widely dispersed in the environments sampled.

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Mapping the probability of detecting Burkholderia pseudomallei in rural rice paddy soil based on indicator kriging and spatial soil factor analysis

Transactions of the Royal Society of Tropical Medicine and Hygiene ◽

10.1093/trstmh/traa029 ◽

2020 ◽

Vol 114 (7) ◽

pp. 521-530

Author(s):

Wacharapong Saengnill ◽

Kitsanai Charoenjit ◽

Karnjana Hrimpeng ◽

Jutharat Jittimanee

Keyword(s):

Infectious Disease ◽

Paddy Soil ◽

Burkholderia Pseudomallei ◽

Rice Paddy ◽

Latex Agglutination ◽

Indicator Kriging ◽

Soil Samples ◽

Soil Factors ◽

Semivariogram Model ◽

Gram Staining

Abstract Background Melioidosis is an infectious disease commonly found in Thailand. This infectious disease is caused by Burkholderia pseudomallei in soil. This study aims to analyze the association between spatial soil factors and B. pseudomallei detection, as well as to map the probability of B. pseudomallei contamination based on indicator kriging in paddy soil. Methods Seventy-eight soil samples were collected randomly on 22 April 2018 in various paddy fields. Oxidase, Gram staining and monoclonal antibody-based latex agglutination assays were performed to confirm the presence of B. pseudomallei in soil samples. The association between B. pseudomallei detection and spatial soil factors including soil temperature, soil pH, soil texture and soil drainage were analyzed by the Mann–Whitney U test and χ2 test. Subsequently, a semivariogram model and indicator kriging were used to map the probability of B. pseudomallei contamination. Results Of the 78 samples, B. pseudomallei was detected in 32 (41.03%). The presence or absence of B. pseudomallei was not significantly associated with spatial soil factors. The semivariogram model showed that the lag distance between positive B. pseudomallei samples was 90.51 m. Conclusion The empirical semivariogram and indicator kriging are an alternative option for predicting the spatial distribution of B. pseudomallei in soil.

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