Draft Whole-Genome Sequence of the Alkaliphilic Alishewanella aestuarii Strain HH-ZS, Isolated from Historical Lime Kiln Waste-Contaminated Soil

Salah, Zohier B.; Rout, Simon P.; Humphreys, Paul

doi:10.1128/genomea.01447-16

Cited by 2 publications

(3 citation statements)

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“…Of the environmental taxa, the identified genera include Alishewanella , Aminivibrio , Bacillus , Cloacibacterium , Okibacterium , Paenibacillus , Pseudomonas , and Streptococcus . Alishewanella , a member of the core microbiome, was identified in all 10 pine nut brands at proportional abundances of 0.6–5.3%, with the greatest abundances observed in brands H and I. Alishewanella is a relatively new bacterial taxon and since its discovery in 1992 has been isolated from water and landfill soil [ 25 , 26 ]. Alishewanella is thought to play a role in the bioremediation process of chromate and sulfate [ 25 ] which provides insight into its existence in landfill and waste soil.…”

Section: Resultsmentioning

confidence: 99%

Microbiomes of commercially-available pine nuts and sesame seeds

et al. 2021

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Metagenomic analysis of food is becoming more routine and can provide important information pertaining to the shelf life potential and the safety of these products. However, less information is available on the microbiomes associated with low water activity foods. Pine nuts and sesame seeds, and food products which contain these ingredients, have been associated with recalls due to contamination with bacterial foodborne pathogens. The objective of this study was to identify the microbial community of pine nuts and sesame seeds using targeted 16S rRNA sequencing technology. Ten different brands of each seed type were assessed, and core microbiomes were determined. A total of 21 and 16 unique taxa with proportional abundances >1% in at least one brand were identified in the pine nuts and sesame seeds, respectively. Members of the core pine nut microbiome included the genera Alishewanella, Aminivibrio, Mycoplasma, Streptococcus, and unassigned OTUs in the families of Desulfobacteraceae and Xanthomonadaceae. For sesame seeds, the core microbiome included Aminivibrio, Chryseolina, Okibacterium, and unassigned OTUs in the family Flavobacteriaceae. The microbiomes of these seeds revealed that these products are dominated by environmental bacterial genera commonly isolated from soil, water, and plants; bacterial genera containing species known as commensal organisms were also identified. Understanding these microbiomes can aid in the risk assessment of these products by identifying food spoilage potential and community members which may co-enrich with foodborne bacterial pathogens.

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Section: Resultsmentioning

confidence: 99%

Microbiomes of commercially-available pine nuts and sesame seeds

et al. 2021

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“…6 and 7). Some of the microbial phyla (Cyanobacteria, Chloroflexi, Chlamydiae and Euryarchaeota) indigenous to deep subsurface environments (Puente-Sánchez et al, 2014, 2018Fullerton and Moyer, 2016;Rempfert et al, 2017) were only observed in the core OTUs of lower depths (DF4 onwards). The microbial families (Carnobacteriaceae, Rhodobacteraceae, Clostridiaceae 1, Cellulomonadaceae, Erysipelotrichaceae, Cyclobacteriaceae, Opitutaceae, Bradyrhizobiaceae and Desulfovibrionaceae) detected in the core OTUs of DF were different from the microbial families (Idiomarinaceae, Moraxellaceae, Methylophilaceae, Nocardioidaceae, Nitrosomonadaceae, Enterobacteriaceae, Comamonadaceae, Chitinophagaceae) detected in granitic core OTUs at higher depths (1500 m b.s.)…”

Section: Discussionmentioning

confidence: 99%

“…The sequence reads obtained were submitted to the sequence read archive (SRA) under SRA accession: SRP155468. It can be accessed from the following link: https: //www.ncbi.nlm.nih.gov/bioproject/PRJNA482760/ (Sar, 2018).…”

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Microbial diversity of drilling fluids from 3000 m deep Koyna pilot borehole provides insights into the deep biosphere of continental earth crust

et al. 2020

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Abstract. Scientific deep drilling of the Koyna pilot borehole into the continental crust up to a depth of 3000 m below the surface at the Deccan Traps, India, provided a unique opportunity to explore microbial life within the deep granitic bedrock of the Archaean Eon. Microbial communities of the returned drilling fluid (fluid returned to the mud tank from the underground during the drilling operation; designated here as DF) sampled during the drilling operation of the Koyna pilot borehole at a depth range of 1681–2908 metres below the surface (m b.s.) were explored to gain a glimpse of the deep biosphere underneath the continental crust. Change of pH to alkalinity, reduced abundance of Si and Al, but enrichment of Fe, Ca and SO42- in the samples from deeper horizons suggested a gradual infusion of elements or ions from the crystalline bedrock, leading to an observed geochemical shift in the DF. Microbial communities of the DFs from deeper horizons showed progressively increased abundance of Firmicutes, Gammaproteobacteria and Actinobacteria as bacterial taxa and members of Euryarchaeota as the major archaeal taxa. Microbial families, well known to strive in strictly anaerobic and extremophilic environments, (e.g. Thermoanaerobacteraceae, Clostridiaceae, Bacillaceae, Carnobacteriaceae, Ruminococcaceae), increased in the samples obtained at a depth range of 2000 to 2908 m b.s. Phylogenetic analysis of common and unique operational taxonomic units (OTUs) of DF samples indicated signatures of extremophilic and deep subsurface relevant bacterial genera (Mongoliitalea, Hydrogenophaga, Marinilactibacillus, Anoxybacillus, Symbiobacterium, Geosporobacter, Thermoanaerobacter). Thermophilic, obligatory anaerobic sulfate-reducing bacterial taxa known to inhabit the deep subsurface were enriched from DF samples using sulfate as a terminal electron acceptor. This report on the geomicrobiology of the DF obtained during drilling of the deep subsurface of the Deccan Traps showed new opportunities to investigate deep life from terrestrial, granite-rock-hosted habitats.

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Draft Whole-Genome Sequence of the Alkaliphilic Alishewanella aestuarii Strain HH-ZS, Isolated from Historical Lime Kiln Waste-Contaminated Soil

Abstract: Here, we present the whole-genome sequence of an environmental Gram-negative Alishewanella aestuarii strain (HH-ZS), isolated from the hyperalkaline contaminated soil of a historical lime kiln in Buxton, United Kingdom.

Cited by 2 publications

References 14 publications

Microbiomes of commercially-available pine nuts and sesame seeds

Microbiomes of commercially-available pine nuts and sesame seeds

Microbial diversity of drilling fluids from 3000 m deep Koyna pilot borehole provides insights into the deep biosphere of continental earth crust

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