Background and Aims The combination of rising sea levels and increased storm frequency and intens... more Background and Aims The combination of rising sea levels and increased storm frequency and intensity is predicted to increase the severity of oceanic storm surge events and the impact of flooding on coastal ecosystems globally. Understanding how plant communities respond to this threat necessitates experiments involving plant immersion in saline water, but logistical issues and natural variation in seawater composition mean that pure NaCl solutions or marine aquarium salts (MS) are widely used. Nonetheless, their comparative impact on plant ecophysiology, and thus relevance to understanding real-world flooding scenarios, is unknown. Methods In the first of two experiments, we examined how six ecophysiological responses in white clover (Trifolium repens) varied when plants were subjected to five different inundation treatments: deionized water, natural seawater, an MS solution and two NaCl solutions. In a second experiment, we examined how immersion in deionized water, MS solution an...
More harmful response to Escherichia coli in the presence of nanomaterials during anaerobic ferme... more More harmful response to Escherichia coli in the presence of nanomaterials during anaerobic fermentation as compared to aerobic respiration.
A novel moderately haloalkaliphilic methylotrophic bacterium (strain MPL T), possessing the ribul... more A novel moderately haloalkaliphilic methylotrophic bacterium (strain MPL T), possessing the ribulose monophosphate pathway for carbon assimilation, was isolated from two week old Lonar Lake sediment microcosms that were actively oxidizing methane. The ...
IOP Conference Series: Earth and Environmental Science
Cadmium-resistant bacteria that are used to remove cadmium (Cd) are becoming increasingly of the ... more Cadmium-resistant bacteria that are used to remove cadmium (Cd) are becoming increasingly of the most important and hygienic method. Resistant mechanisms are involved in different ways, and some of them which can be used in cadmium removal techniques based on their molecular mechanisms and minimum inhibitory concentration (MIC). This review summarises recent improvements in understanding the mechanisms by which bacteria are either intrinsically resistant or acquire resistance to cadmium to be used as a way for cadmium removal.
International Journal of Systematic and Evolutionary Microbiology, 2022
Two sulphur-oxidizing, chemolithoautotrophic aerobes were isolated from the chemocline of an anch... more Two sulphur-oxidizing, chemolithoautotrophic aerobes were isolated from the chemocline of an anchialine sinkhole located within the Weeki Wachee River of Florida. Gram-stain-negative cells of both strains were motile, chemotactic rods. Phylogenetic analysis of the 16S rRNA gene and predicted amino acid sequences of ribosomal proteins, average nucleotide identities, and alignment fractions suggest the strains HH1T and HH3T represent novel species belonging to the genus Thiomicrorhabdus . The genome G+C fraction of HH1T is 47.8 mol% with a genome length of 2.61 Mb, whereas HH3T has a G+C fraction of 52.4 mol% and 2.49 Mb genome length. Major fatty acids of the two strains included C16 : 1, C18 : 1 and C16 : 0, with the addition of C10:0 3-OH in HH1T and C12 : 0 in HH3T. Chemolithoautotrophic growth of both strains was supported by elemental sulphur, sulphide, tetrathionate, and thiosulphate, and HH1T was also able to use molecular hydrogen. Neither strain was capable of heterotrophic ...
Eight Cd-resistant bacteria were isolated from the soil. Based on the resistance and specific gro... more Eight Cd-resistant bacteria were isolated from the soil. Based on the resistance and specific growth rate, one isolate from these was chosen. The 16S rRNA (rrs) gene sequence was used to assert this isolate belongs to the genus of Brevibacillus and closely related to Brevibacillus agri (B.agri) DSM 6348T (AB112716). The isolate was termed B.agri C15. The specific growth yields and the Cd-dependent fall in specific growth yield of B.agri C15 was determined under different concentrations of Cd. The current study provides a basis for isolation Cd resistant bacteria with maximum tolerable concentration (MTC) 15 mM Cd from a contaminated soil 490±50 μmolal Cd that could be suitable for a new Cd-bioremediation process; therefore, further studies are needed to investigate this possibility.
Thermithiobacillus tepidarius DSM 3134 was originally isolated (1983) from the waters of a sulfid... more Thermithiobacillus tepidarius DSM 3134 was originally isolated (1983) from the waters of a sulfidic spring entering the Roman Baths (Temple of Sulis-Minerva) at Bath, United Kingdom and is an obligate chemolithoautotroph growing at the expense of reduced sulfur species. This strain has a genome size of 2,958,498 bp. Here we report the genome sequence, annotation and characteristics. The genome comprises 2,902 protein coding and 66 RNA coding genes. Genes responsible for the transaldolase variant of the Calvin-Benson-Bassham cycle were identified along with a biosynthetic horseshoe in lieu of Krebs’ cycle sensu stricto. Terminal oxidases were identified, viz. cytochrome c oxidase (cbb3, EC 1.9.3.1) and ubiquinol oxidase (bd, EC 1.10.3.10). Metalloresistance genes involved in pathways of arsenic and cadmium resistance were found. Evidence of horizontal gene transfer accounting for 5.9 % of the protein-coding genes was found, including transfer from Thiobacillus spp. and Methylococcus ...
Here we show the application of R-SIP for detecting isotopically-labelled substrate incorporation... more Here we show the application of R-SIP for detecting isotopically-labelled substrate incorporation into microbial cells in the lab, expanding the range of previously used stable isotopes.
Methylomonas methanica MC09 is a mesophilic, halotolerant, aerobic, methanotrophic member of the ... more Methylomonas methanica MC09 is a mesophilic, halotolerant, aerobic, methanotrophic member of the Gammaproteobacteria , isolated from coastal seawater. Here we present the complete genome sequence of this strain, the first available from an aerobic marine methanotroph.
Methylophaga thiooxydans is a mesophilic, obligately halophilic bacterium that is capable of meth... more Methylophaga thiooxydans is a mesophilic, obligately halophilic bacterium that is capable of methylotrophic growth on a range of one-carbon compounds as well as chemolithoheterotrophic growth at the expense of thiosulfate. Here we present the draft genome sequence of Methylophaga thiooxydans DMS010 (DSM 22068 T , VKM B2586 T ), the type strain of the species, which has allowed prediction of the genes involved in one-carbon metabolism, nitrogen metabolism, and other aspects of central metabolism.
Background and Aims The combination of rising sea levels and increased storm frequency and intens... more Background and Aims The combination of rising sea levels and increased storm frequency and intensity is predicted to increase the severity of oceanic storm surge events and the impact of flooding on coastal ecosystems globally. Understanding how plant communities respond to this threat necessitates experiments involving plant immersion in saline water, but logistical issues and natural variation in seawater composition mean that pure NaCl solutions or marine aquarium salts (MS) are widely used. Nonetheless, their comparative impact on plant ecophysiology, and thus relevance to understanding real-world flooding scenarios, is unknown. Methods In the first of two experiments, we examined how six ecophysiological responses in white clover (Trifolium repens) varied when plants were subjected to five different inundation treatments: deionized water, natural seawater, an MS solution and two NaCl solutions. In a second experiment, we examined how immersion in deionized water, MS solution an...
More harmful response to Escherichia coli in the presence of nanomaterials during anaerobic ferme... more More harmful response to Escherichia coli in the presence of nanomaterials during anaerobic fermentation as compared to aerobic respiration.
A novel moderately haloalkaliphilic methylotrophic bacterium (strain MPL T), possessing the ribul... more A novel moderately haloalkaliphilic methylotrophic bacterium (strain MPL T), possessing the ribulose monophosphate pathway for carbon assimilation, was isolated from two week old Lonar Lake sediment microcosms that were actively oxidizing methane. The ...
IOP Conference Series: Earth and Environmental Science
Cadmium-resistant bacteria that are used to remove cadmium (Cd) are becoming increasingly of the ... more Cadmium-resistant bacteria that are used to remove cadmium (Cd) are becoming increasingly of the most important and hygienic method. Resistant mechanisms are involved in different ways, and some of them which can be used in cadmium removal techniques based on their molecular mechanisms and minimum inhibitory concentration (MIC). This review summarises recent improvements in understanding the mechanisms by which bacteria are either intrinsically resistant or acquire resistance to cadmium to be used as a way for cadmium removal.
International Journal of Systematic and Evolutionary Microbiology, 2022
Two sulphur-oxidizing, chemolithoautotrophic aerobes were isolated from the chemocline of an anch... more Two sulphur-oxidizing, chemolithoautotrophic aerobes were isolated from the chemocline of an anchialine sinkhole located within the Weeki Wachee River of Florida. Gram-stain-negative cells of both strains were motile, chemotactic rods. Phylogenetic analysis of the 16S rRNA gene and predicted amino acid sequences of ribosomal proteins, average nucleotide identities, and alignment fractions suggest the strains HH1T and HH3T represent novel species belonging to the genus Thiomicrorhabdus . The genome G+C fraction of HH1T is 47.8 mol% with a genome length of 2.61 Mb, whereas HH3T has a G+C fraction of 52.4 mol% and 2.49 Mb genome length. Major fatty acids of the two strains included C16 : 1, C18 : 1 and C16 : 0, with the addition of C10:0 3-OH in HH1T and C12 : 0 in HH3T. Chemolithoautotrophic growth of both strains was supported by elemental sulphur, sulphide, tetrathionate, and thiosulphate, and HH1T was also able to use molecular hydrogen. Neither strain was capable of heterotrophic ...
Eight Cd-resistant bacteria were isolated from the soil. Based on the resistance and specific gro... more Eight Cd-resistant bacteria were isolated from the soil. Based on the resistance and specific growth rate, one isolate from these was chosen. The 16S rRNA (rrs) gene sequence was used to assert this isolate belongs to the genus of Brevibacillus and closely related to Brevibacillus agri (B.agri) DSM 6348T (AB112716). The isolate was termed B.agri C15. The specific growth yields and the Cd-dependent fall in specific growth yield of B.agri C15 was determined under different concentrations of Cd. The current study provides a basis for isolation Cd resistant bacteria with maximum tolerable concentration (MTC) 15 mM Cd from a contaminated soil 490±50 μmolal Cd that could be suitable for a new Cd-bioremediation process; therefore, further studies are needed to investigate this possibility.
Thermithiobacillus tepidarius DSM 3134 was originally isolated (1983) from the waters of a sulfid... more Thermithiobacillus tepidarius DSM 3134 was originally isolated (1983) from the waters of a sulfidic spring entering the Roman Baths (Temple of Sulis-Minerva) at Bath, United Kingdom and is an obligate chemolithoautotroph growing at the expense of reduced sulfur species. This strain has a genome size of 2,958,498 bp. Here we report the genome sequence, annotation and characteristics. The genome comprises 2,902 protein coding and 66 RNA coding genes. Genes responsible for the transaldolase variant of the Calvin-Benson-Bassham cycle were identified along with a biosynthetic horseshoe in lieu of Krebs’ cycle sensu stricto. Terminal oxidases were identified, viz. cytochrome c oxidase (cbb3, EC 1.9.3.1) and ubiquinol oxidase (bd, EC 1.10.3.10). Metalloresistance genes involved in pathways of arsenic and cadmium resistance were found. Evidence of horizontal gene transfer accounting for 5.9 % of the protein-coding genes was found, including transfer from Thiobacillus spp. and Methylococcus ...
Here we show the application of R-SIP for detecting isotopically-labelled substrate incorporation... more Here we show the application of R-SIP for detecting isotopically-labelled substrate incorporation into microbial cells in the lab, expanding the range of previously used stable isotopes.
Methylomonas methanica MC09 is a mesophilic, halotolerant, aerobic, methanotrophic member of the ... more Methylomonas methanica MC09 is a mesophilic, halotolerant, aerobic, methanotrophic member of the Gammaproteobacteria , isolated from coastal seawater. Here we present the complete genome sequence of this strain, the first available from an aerobic marine methanotroph.
Methylophaga thiooxydans is a mesophilic, obligately halophilic bacterium that is capable of meth... more Methylophaga thiooxydans is a mesophilic, obligately halophilic bacterium that is capable of methylotrophic growth on a range of one-carbon compounds as well as chemolithoheterotrophic growth at the expense of thiosulfate. Here we present the draft genome sequence of Methylophaga thiooxydans DMS010 (DSM 22068 T , VKM B2586 T ), the type strain of the species, which has allowed prediction of the genes involved in one-carbon metabolism, nitrogen metabolism, and other aspects of central metabolism.
Uploads
Papers by Rich Boden