Microenvironmental Conditions Drive the Differential Cyanobacterial Community Composition of Biocrusts from the Sahara Desert

The Sahara Desert is characterized by extreme environmental conditions, which are a unique challenge for life. Cyanobacteria are key players in the colonization of bare soils and form assemblages with other microorganisms in the top millimetres, establishing biological soil crusts (biocrusts) that cover most soil surfaces in deserts, which have important roles in the functioning of drylands. However, knowledge of biocrusts from these extreme environments is limited. Therefore, to study cyanobacterial community composition in biocrusts from the Sahara Desert, we utilized a combination of methodologies in which taxonomic assignation, for next-generation sequencing of soil samples, was based on phylogenetic analysis (16S rRNA gene) in parallel with morphological identification of cyanobacteria in natural samples and isolates from certain locations. Two close locations that differed in microenvironmental conditions were analysed. One was a dry salt lake (a “chott”), and the other was an extension of sandy, slightly saline soil. Differences in cyanobacterial composition between the sites were found, with a clear dominance of Microcoleus spp. in the less saline site, while the chott presented a high abundance of heterocystous cyanobacteria as well as the filamentous non-heterocystous Pseudophormidium sp. and the unicellular cf. Acaryochloris. The cyanobacteria found in our study area, such as Microcoleus steenstrupii, Microcoleus vaginatus, Scytonema hyalinum, Tolypothrix distorta, and Calothrix sp., are also widely distributed in other geographic locations around the world, where the conditions are less severe. Our results, therefore, indicated that some cyanobacteria can cope with polyextreme conditions, as confirmed by bioassays, and can be considered extremotolerant, being able to live in a wide range of conditions.

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Morphological and molecular characterisation of several Paratylenchus Micoletzky, 1922 (Tylenchida: Paratylenchidae) species from South Africa and USA, together with some taxonomic notes

Nematology ◽

10.1163/15685411-00002769 ◽

2014 ◽

Vol 16 (3) ◽

pp. 323-358 ◽

Cited By ~ 17

Author(s):

Esther Van den Berg ◽

Louwrens R. Tiedt ◽

Esther Van den Berg ◽

Louwrens R. Tiedt ◽

...

Keyword(s):

South Africa ◽

Rrna Genes ◽

Morphological Identification ◽

Rrna Gene ◽

28S Rrna ◽

Molecular Characterisation ◽

Electron Microscopic ◽

Wide Range ◽

Its Rrna Gene ◽

Its Rrna

Pin nematodes of the genus Paratylenchus are widely distributed across the world and associated with many plant species. Morphological identification of Paratylenchus species is a difficult task because it relies on many characters with a wide range of intraspecific variation. In this study we provide morphological and molecular characterisation of several pin nematodes: Paratylenchus aquaticus, P. dianthus, P. hamatus, P. nanus and P. straeleni, collected in different states of the USA and South Africa. Paratylenchus aquaticus is reported from South Africa and Hawaii and P. nanus is found from South Africa for the first time. Morphological descriptions, morphometrics, light and scanning electron microscopic photos and drawings are given for these species. Molecular characterisation of nematodes using the D2-D3 of 28S rRNA and ITS rRNA gene sequence revealed that samples morphologically identified as P. aquaticus, P. hamatus and P. nanus indeed represent species complexes containing several species. Sequences of the rRNA genes are also provided for several unidentified Paratylenchus. Phylogenetic relationships within the genus Paratylenchus are given as inferred from the analyses of the D2-D3 of 28S rRNA and ITS rRNA gene sequences. We present here the most complete phylogenetic analysis of the genus.

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Natrinema altunense sp. nov., an extremely halophilic archaeon isolated from a salt lake in Altun Mountain in Xinjiang, China

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.63622-0 ◽

2005 ◽

Vol 55 (3) ◽

pp. 1311-1314 ◽

Cited By ~ 40

Author(s):

Xue-Wei Xu ◽

Pei-Gen Ren ◽

Shuang-Jiang Liu ◽

Min Wu ◽

Pei-Jin Zhou

Keyword(s):

Dna Hybridization ◽

Gene Sequence ◽

Nature Reserve ◽

Salt Lake ◽

Rrna Gene ◽

Physiological Properties ◽

Gene Sequence Analysis ◽

Wide Range ◽

Extremely Halophilic Archaeon ◽

Derivatives Of

A novel extremely halophilic strain, AJ2T, was isolated from Ayakekum salt lake located in the Altun Mountain National Nature Reserve in Xinjiang, China. This isolate was neutrophilic, motile and grew in a wide range of MgCl2 concentrations (0·005–1·0 M). The major polar lipids of the isolate were C20C20 and C20C25 derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol sulfate. A comprehensive 16S rRNA gene sequence analysis revealed that the isolate shared 96·6–97·7 % sequence identity with Natrinema species. The isolate, however, could be genetically differentiated from these species by DNA–DNA hybridization analysis and on the basis of its physiological properties. On the basis of the polyphasic evidence, strain AJ2T (=AS 1.3731T=JCM 12890T) represents the type strain of a novel species, for which the name Natrinema altunense sp. nov. is proposed.

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First Detection of Ditylenchus destructor Parasitizing Maize in Northeast China

Life ◽

10.3390/life11121303 ◽

2021 ◽

Vol 11 (12) ◽

pp. 1303

Author(s):

Fengjuan Pan ◽

Feng Li ◽

Yanzhi Mao ◽

Dan Liu ◽

Aoshuang Chen ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Economic Losses ◽

Morphological Identification ◽

Rrna Gene ◽

Heilongjiang Province ◽

Maize Seedlings ◽

Wide Range ◽

Its Rrna ◽

Ditylenchus Destructor ◽

Plant Parasitic

Maize is one of the most important crops in the world. Heilongjiang province has the largest maize area in China. Plant-parasitic nematodes are important agricultural pests, which cause huge economic losses every year and have attracted global attention. Potato rot nematode Ditylenchus destructor is a plant-parasitic nematode with a wide range of hosts and strong survival ability in different environments, which brings risks to agricultural production. In 2020, D. destructor was detected in seven maize fields in Heilongjiang province. Morphological identification and molecular approach were used to characterize the isolated D. destructor. The observed morphological and morphometric characteristics were highly similar and consistent with the existing description. The DNA sequencing on the D2/D3 region of the ribosomal DNA 28S and the phylogenetic analysis showed that D. destructor population obtained from maize and other isolates infesting carrot, sweet potato, and potato were in subclade I supported by a 96% bootstrap value. Additionally, the phylogenetic analysis of the ITS rRNA gene sequence further indicated that this D. destructor population from maize clustered in a clade I group and belonged to ITS rRNA haplotype C. An inoculation experiment revealed that D. destructor was pathogenic on the maize seedlings in pots and caused the disease symptoms in the stem base of maize seedlings. This is the first report of D. destructor causing stem rot of maize in Heilongjiang province, and contributes additional information on disease control and safe production of maize in the region.

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Benchmarking laboratory processes to characterise low-biomass respiratory microbiota

Scientific Reports ◽

10.1038/s41598-021-96556-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Raiza Hasrat ◽

Jolanda Kool ◽

Wouter A. A. de Steenhuijsen Piters ◽

Mei Ling J. N. Chu ◽

Sjoerd Kuiling ◽

...

Keyword(s):

Microbial Community ◽

Community Composition ◽

Microbial Community Composition ◽

Positive Control ◽

Rrna Gene ◽

Elution Buffer ◽

Community Profile ◽

Microbial Community Profile ◽

Microbial Dna ◽

Pcr Conditions

AbstractThe low biomass of respiratory samples makes it difficult to accurately characterise the microbial community composition. PCR conditions and contaminating microbial DNA can alter the biological profile. The objective of this study was to benchmark the currently available laboratory protocols to accurately analyse the microbial community of low biomass samples. To study the effect of PCR conditions on the microbial community profile, we amplified the 16S rRNA gene of respiratory samples using various bacterial loads and different number of PCR cycles. Libraries were purified by gel electrophoresis or AMPure XP and sequenced by V2 or V3 MiSeq reagent kits by Illumina sequencing. The positive control was diluted in different solvents. PCR conditions had no significant influence on the microbial community profile of low biomass samples. Purification methods and MiSeq reagent kits provided nearly similar microbiota profiles (paired Bray–Curtis dissimilarity median: 0.03 and 0.05, respectively). While profiles of positive controls were significantly influenced by the type of dilution solvent, the theoretical profile of the Zymo mock was most accurately analysed when the Zymo mock was diluted in elution buffer (difference compared to the theoretical Zymo mock: 21.6% for elution buffer, 29.2% for Milli-Q, and 79.6% for DNA/RNA shield). Microbiota profiles of DNA blanks formed a distinct cluster compared to low biomass samples, demonstrating that low biomass samples can accurately be distinguished from DNA blanks. In summary, to accurately characterise the microbial community composition we recommend 1. amplification of the obtained microbial DNA with 30 PCR cycles, 2. purifying amplicon pools by two consecutive AMPure XP steps and 3. sequence the pooled amplicons by V3 MiSeq reagent kit. The benchmarked standardized laboratory workflow presented here ensures comparability of results within and between low biomass microbiome studies.

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Impact of Diagnosed and Undiagnosed Respiratory Pseudomonas on VAP and VAE During Long-Term Acute Care

Infection Control and Hospital Epidemiology ◽

10.1017/ice.2020.823 ◽

2020 ◽

Vol 41 (S1) ◽

pp. s258-s259

Author(s):

James Harrigan ◽

Ebbing Lautenbach ◽

Emily Reesey ◽

Magda Wernovsky ◽

Pam Tolomeo ◽

...

Keyword(s):

Bacterial Community ◽

Acute Care ◽

Statistical Significance ◽

Rrna Gene ◽

Care Hospital ◽

16S Sequencing ◽

Increased Risk ◽

Wide Range ◽

The Impact

Background: Clinically diagnosed ventilator-associated pneumonia (VAP) is common in the long-term acute-care hospital (LTACH) setting and may contribute to adverse ventilator-associated events (VAEs). Pseudomonas aeruginosa is a common causative organism of VAP. We evaluated the impact of respiratory P. aeruginosa colonization and bacterial community dominance, both diagnosed and undiagnosed, on subsequent P. aeruginosa VAP and VAE events during long-term acute care. Methods: We enrolled 83 patients on LTACH admission for ventilator weaning, performed longitudinal sampling of endotracheal aspirates followed by 16S rRNA gene sequencing (Illumina HiSeq), and bacterial community profiling (QIIME2). Statistical analysis was performed with R and Stan; mixed-effects models were fit to relate the abundance of respiratory Psa on admission to clinically diagnosed VAP and VAE events. Results: Of the 83 patients included, 12 were diagnosed with P. aeruginosa pneumonia during the 14 days prior to LTACH admission (known P. aeruginosa), and 22 additional patients received anti–P. aeruginosa antibiotics within 48 hours of admission (suspected P. aeruginosa); 49 patients had no known or suspected P. aeruginosa (unknown P. aeruginosa). Among the known P. aeruginosa group, all 12 patients had P. aeruginosa detectable by 16S sequencing, with elevated admission P. aeruginosa proportional abundance (median, 0.97; IQR, 0.33–1). Among the suspected P. aeruginosa group, all 22 patients had P. aeruginosa detectable by 16S sequencing, with a wide range of admission P. aeruginosa proportional abundance (median, 0.0088; IQR, 0.00012–0.31). Of the 49 patients in the unknown group, 47 also had detectable respiratory Psa, and many had high P. aeruginosa proportional abundance at admission (median, 0.014; IQR, 0.00025–0.52). Incident P. aeruginosa VAP was observed within 30 days in 4 of the known P. aeruginosa patients (33.3%), 5 of the suspected P. aeruginosa patients (22.7%), and 8 of the unknown P. aeruginosa patients (16.3%). VAE was observed within 30 days in 1 of the known P. aeruginosa patients (8.3%), 2 of the suspected P. aeruginosa patients (9.1%), and 1 of the unknown P. aeruginosa patients (2%). Admission P. aeruginosa abundance was positively associated with VAP and VAE risk in all groups, but the association only achieved statistical significance in the unknown group (type S error <0.002 for 30-day VAP and <0.011 for 30-day VAE). Conclusions: We identified a high prevalence of unrecognized respiratory P. aeruginosa colonization among patients admitted to LTACH for weaning from mechanical ventilation. The admission P. aeruginosa proportional abundance was strongly associated with increased risk of incident P. aeruginosa VAP among these patients.Funding: NoneDisclosures: None

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Do initial concentration and activated sludge seasonality affect pharmaceutical biotransformation rate constants?

Applied Microbiology and Biotechnology ◽

10.1007/s00253-021-11475-9 ◽

2021 ◽

Author(s):

Tamara J. H. M. van Bergen ◽

Ana B. Rios-Miguel ◽

Tom M. Nolte ◽

Ad M. J. Ragas ◽

Rosalie van Zelm ◽

...

Keyword(s):

Microbial Community ◽

Activated Sludge ◽

Community Composition ◽

Rate Constants ◽

Wastewater Treatment Plants ◽

Microbial Community Composition ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Initial Concentration ◽

Different Seasons

Abstract Pharmaceuticals find their way to the aquatic environment via wastewater treatment plants (WWTPs). Biotransformation plays an important role in mitigating environmental risks; however, a mechanistic understanding of involved processes is limited. The aim of this study was to evaluate potential relationships between first-order biotransformation rate constants (kb) of nine pharmaceuticals and initial concentration of the selected compounds, and sampling season of the used activated sludge inocula. Four-day bottle experiments were performed with activated sludge from WWTP Groesbeek (The Netherlands) of two different seasons, summer and winter, spiked with two environmentally relevant concentrations (3 and 30 nM) of pharmaceuticals. Concentrations of the compounds were measured by LC–MS/MS, microbial community composition was assessed by 16S rRNA gene amplicon sequencing, and kb values were calculated. The biodegradable pharmaceuticals were acetaminophen, metformin, metoprolol, terbutaline, and phenazone (ranked from high to low biotransformation rates). Carbamazepine, diatrizoic acid, diclofenac, and fluoxetine were not converted. Summer and winter inocula did not show significant differences in microbial community composition, but resulted in a slightly different kb for some pharmaceuticals. Likely microbial activity was responsible instead of community composition. In the same inoculum, different kb values were measured, depending on initial concentration. In general, biodegradable compounds had a higher kb when the initial concentration was higher. This demonstrates that Michealis-Menten kinetic theory has shortcomings for some pharmaceuticals at low, environmentally relevant concentrations and that the pharmaceutical concentration should be taken into account when measuring the kb in order to reliably predict the fate of pharmaceuticals in the WWTP. Key points • Biotransformation and sorption of pharmaceuticals were assessed in activated sludge. • Higher initial concentrations resulted in higher biotransformation rate constants for biodegradable pharmaceuticals. • Summer and winter inocula produced slightly different biotransformation rate constants although microbial community composition did not significantly change. Graphical abstract

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Biodiversity of Secondary Metabolites Compounds Isolated from Phylum Actinobacteria and Its Therapeutic Applications

Molecules ◽

10.3390/molecules26154504 ◽

2021 ◽

Vol 26 (15) ◽

pp. 4504

Author(s):

Muhanna Al-shaibani ◽

Radin Maya Saphira Radin Mohamed ◽

Nik Sidik ◽

Hesham Enshasy ◽

Adel Al-Gheethi ◽

...

Keyword(s):

Secondary Metabolites ◽

Bioactive Compounds ◽

Extreme Environments ◽

Software Tool ◽

Gene Clusters ◽

Well Being ◽

Bioactive Substances ◽

Diverse Range ◽

Wide Range ◽

Potential Applications

The current review aims to summarise the biodiversity and biosynthesis of novel secondary metabolites compounds, of the phylum Actinobacteria and the diverse range of secondary metabolites produced that vary depending on its ecological environments they inhabit. Actinobacteria creates a wide range of bioactive substances that can be of great value to public health and the pharmaceutical industry. The literature analysis process for this review was conducted using the VOSviewer software tool to visualise the bibliometric networks of the most relevant databases from the Scopus database in the period between 2010 and 22 March 2021. Screening and exploring the available literature relating to the extreme environments and ecosystems that Actinobacteria inhabit aims to identify new strains of this major microorganism class, producing unique novel bioactive compounds. The knowledge gained from these studies is intended to encourage scientists in the natural product discovery field to identify and characterise novel strains containing various bioactive gene clusters with potential clinical applications. It is evident that Actinobacteria adapted to survive in extreme environments represent an important source of a wide range of bioactive compounds. Actinobacteria have a large number of secondary metabolite biosynthetic gene clusters. They can synthesise thousands of subordinate metabolites with different biological actions such as anti-bacterial, anti-parasitic, anti-fungal, anti-virus, anti-cancer and growth-promoting compounds. These are highly significant economically due to their potential applications in the food, nutrition and health industries and thus support our communities’ well-being.

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Exploring protocol bias in airway microbiome studies: one versus two PCR steps and 16S rRNA gene region V3 V4 versus V4

BMC Genomics ◽

10.1186/s12864-020-07252-z ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Christine Drengenes ◽

Tomas M. L. Eagan ◽

Ingvild Haaland ◽

Harald G. Wiker ◽

Rune Nielsen

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Bacterial Load ◽

Marker Gene ◽

Gene Region ◽

Lower Airway ◽

Rrna Gene ◽

Wide Range ◽

Airway Microbiome ◽

The Impact

Abstract Background Studies on the airway microbiome have been performed using a wide range of laboratory protocols for high-throughput sequencing of the bacterial 16S ribosomal RNA (16S rRNA) gene. We sought to determine the impact of number of polymerase chain reaction (PCR) steps (1- or 2- steps) and choice of target marker gene region (V3 V4 and V4) on the presentation of the upper and lower airway microbiome. Our analyses included lllumina MiSeq sequencing following three setups: Setup 1 (2-step PCR; V3 V4 region), Setup 2 (2-step PCR; V4 region), Setup 3 (1-step PCR; V4 region). Samples included oral wash, protected specimen brushes and protected bronchoalveolar lavage (healthy and obstructive lung disease), and negative controls. Results The number of sequences and amplicon sequence variants (ASV) decreased in order setup1 > setup2 > setup3. This trend appeared to be associated with an increased taxonomic resolution when sequencing the V3 V4 region (setup 1) and an increased number of small ASVs in setups 1 and 2. The latter was considered a result of contamination in the two-step PCR protocols as well as sequencing across multiple runs (setup 1). Although genera Streptococcus, Prevotella, Veillonella and Rothia dominated, differences in relative abundance were observed across all setups. Analyses of beta-diversity revealed that while oral wash samples (high biomass) clustered together regardless of number of PCR steps, samples from the lungs (low biomass) separated. The removal of contaminants identified using the Decontam package in R, did not resolve differences in results between sequencing setups. Conclusions Differences in number of PCR steps will have an impact of final bacterial community descriptions, and more so for samples of low bacterial load. Our findings could not be explained by differences in contamination levels alone, and more research is needed to understand how variations in PCR-setups and reagents may be contributing to the observed protocol bias.

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Species-specific duplex PCR for the detection of Pratylenchus penetrans

Nematology ◽

10.1163/156854109x428016 ◽

2009 ◽

Vol 11 (6) ◽

pp. 847-857 ◽

Cited By ~ 21

Author(s):

Lieven Waeyenberge ◽

Nicole Viaene ◽

Maurice Moens

Keyword(s):

Internal Control ◽

Dna Sequences ◽

Rrna Gene ◽

Duplex Pcr ◽

Specific Primers ◽

5.8S Rrna Gene ◽

5.8S Rrna ◽

Wide Range ◽

Pcr Products ◽

Species Specific

Abstract ITS1, the 5.8S rRNA gene and ITS2 of the rDNA region were sequenced from 20 different Pratylenchus species. Additionally, the same region was sequenced from seven populations of P. penetrans. After purifying, cloning and sequencing the PCR products, all sequences were aligned in order to find unique sites suitable for the design of species-specific primers for P. penetrans. Since ITS regions showed variability between and even within populations of P. penetrans, only three small DNA sequences were suitable for the construction of three potentially useful species-specific primers. New species-specific primers were paired with existing universal ITS primers and tested in all possible primer combinations. The best performing primer set, supplemented with a universal 28S rDNA primer set that served as an internal control, was tested in duplex PCR. The ideal annealing temperature, Mg2+ concentration and primer ratios were then determined for the most promising primer set. The optimised duplex PCR was subsequently tested on a wide range of different Pratylenchus spp. and 25 P. penetrans populations originating from all over the world. To test the sensitivity, the duplex PCR was conducted on DNA extracted from a single P. penetrans nematode mixed with varying amounts of nematodes belonging to another Pratylenchus species. Results showed that a reliable and sensitive P. penetrans species-specific duplex PCR was constructed.

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The bacterial community of the lone star tick (Amblyomma americanum)

Parasites & Vectors ◽

10.1186/s13071-020-04550-z ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

L. Paulina Maldonado-Ruiz ◽

Saraswoti Neupane ◽

Yoonseong Park ◽

Ludek Zurek

Keyword(s):

Bacterial Community ◽

Amblyomma Americanum ◽

Rrna Gene ◽

Culturable Bacteria ◽

Core Microbiome ◽

Lone Star Tick ◽

Animal Pathogens ◽

Wide Range ◽

Culture Independent ◽

Culture Dependent

Abstract Background The lone star tick (Amblyomma americanum), an important vector of a wide range of human and animal pathogens, is very common throughout the East and Midwest of the USA. Ticks are known to carry non-pathogenic bacteria that may play a role in their vector competence for pathogens. Several previous studies using the high throughput sequencing (HTS) technologies reported the commensal bacteria in a tick midgut as abundant and diverse. In contrast, in our preliminary survey of the field collected adult lone star ticks, we found the number of culturable/viable bacteria very low. Methods We aimed to analyze the bacterial community of A. americanum by a parallel culture-dependent and a culture-independent approach applied to individual ticks. Results We analyzed 94 adult females collected in eastern Kansas and found that 60.8% of ticks had no culturable bacteria and the remaining ticks carried only 67.7 ± 42.8 colony-forming units (CFUs)/tick representing 26 genera. HTS of the 16S rRNA gene resulted in a total of 32 operational taxonomic units (OTUs) with the dominant endosymbiotic genera Coxiella and Rickettsia (> 95%). Remaining OTUs with very low abundance were typical soil bacterial taxa indicating their environmental origin. Conclusions No correlation was found between the CFU abundance and the relative abundance from the culture-independent approach. This suggests that many culturable taxa detected by HTS but not by culture-dependent method were not viable or were not in their culturable state. Overall, our HTS results show that the midgut bacterial community of A. americanum is very poor without a core microbiome and the majority of bacteria are endosymbiotic.

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