My current research programme spans physiology, ecology, biochemistry, taxonomy and environmental process, including soil and freshwater geochemistry. My main thrusts of work concern the microbial transformations of metals, metalloids and sulfur in a range of environments.
Active research projects can be split into pure and applied aspects though other smaller projects are on-going. My past interests in "one carbon" or "C1" metabolism and that of methylated sulfur compounds has largely come to a natural close now and my interests instead focus primarily on inorganic ions found in the environment and the minerals from which they derive.
Pure Research - Blue Skies
My central, core research interests concern physiology, biochemistry, taxonomy and systematics of the sulfur Bacteria. Around this area, I am also interested in the associated analytical chemistry (both of biochemicals and of inorganic species), thermodynamics, reaction kinetics, enzyme classification and so on.
My current programme of research is broken into the following broad projects:
Inorganic sulfur metabolism in members of the Bacteria
(Current Personnel: Dr Rich Boden (PI),
Funding: University of Plymouth 2012 - 2015, Royal Society: 2013-2014
Collaborators: Dr Kathleen M Scott, University of South Florida
The microbial oxidation of inorganic sulfur from dissolved ions or insoluble minerals forms a key step in the biogeochemical sulfur cycle, transforming complex polysulfur compounds (polythionates, polysulfanes) into sulfate, which can be used by the Eukarya as a source of sulfur for growth. Our research in this area concerns the underpinning physiology of the Kelly-Trudinger (or "S4I") pathway of inorganic sulfur metabolism in members of the Class Acidithiobacillia, namely the genera Acidithiobacillus and Thermithiobacillus and members of the Betaproteobacteria including Thiobacillus and Annwoodia. We also have interest in the partial Kelly-Trudinger pathway found in chemolithoheterotrophs such as "Thiobacillus trautweinii" (various Pseudomonas and Achromobacter strains).
Former personnel: Dr Lee P Hutt (PhD Student and Postdoctoral Research Fellow, 2012-2015), Mr Jack Cowling (Research Assistant/Intern, 2013-2014).
Taxonomy and systematics of the Bacteria
(Current Personnel: Dr Rich Boden (PI), Dr Kathleen M Scott (University of South Florida, CoI)
Building on the work of Yarza et al. (2014) we have developed and used a series of molecular identity cut-offs to delineate the taxonomic ranks of genus, family, order and class. We have applied these to:
1. Thiobacillus. This resulted in the splitting of the genus creating Annwoodia aquaesulis gen. nov., comb. nov., and resolving the position of the genus relative to the Betaproteobacteria, finding it was in the Nitrosomonadales and not the Hydrogenophilales as previously shown. In the same study we restructured 50% of the class Betaproteobacteria creating new families and transferring the order Hydrogenophilales into a new class Hydrogenophilalia class. nov. Ribosomal mutli-locus sequence typing (rMLST) using 53-ribosomal protein genes was also used in this study.
2. Thiomicrospira sensu lato. The genus of mostly marine chemolithoautotrophs Thiomicrospira and the adjacent genus of similar but alkaliphilic organisms, Thioalkalimicrobium, were examined using methods developed in the above study, merging all members of the latter with Thiomicrospira pelophila (type species) and Thiomicorspira thyasirae as the genus Thiomicrospira sensu stricto. Two other groups of "Thiomicrospira" spp. were 1) split off to create Thiomicrorhabdus gen. nov., and 2) added to the extant genus Hydrogenovibrio.
3. Halothiobacillus. This genus was examined and was split creating Guyparkeria halophila gen. nov., sp. nov. and Guyparkeria hydrothermalis gen. nov., sp. nov., as well as some novel families.
4. Thiothrix. This genus was examined and was split creating Thiofilum gen. nov. and Thiolinea gen. nov. as well as some novel families.
Former personnel: Dr Lee P Hutt (PhD Student and Postdoctoral Research Fellow, 2012-2015), Mr Alex W Rae (Intern 2016/17)
I am also a party in the following collaborations:
Impacts of coastal inundation on nitrogen fixation in soils
(Current Personnel: Dr Mick Hanley (PI), Dr Rich Boden (CoI))
Fixation of nitrogen into ammonium by diazotrophic Bacteria is key to growth of plants in the environment. Our research focusses on the impact of rising sea-levels and increasing inundation of coastal farmlands by seawater during storm surge events. In a bottom-up programme of research, we are assessing the impact of storm surge events on whole ecosystems starting with changes in soil geochemistry and its impact on diazotrophic populations and their subsequent impacts on plant biochemistry and thus ecosystem dynamics.
Impacts of bioenergy crop growth on soil microbiology and geochemistry
(Current Personnel: Dr Mick Hanley (PI), Dr Rich Boden (CoI), Professor Camille Parmesan (CoI); Funding: Seale-Hayne Educational Trust 2013 - 2015, University of Plymouth, 2014-2018)
The environmental impact of cultivation of bioenergy crops such as Miscanthus spp. on UK soils is being assessed through investigation of soil microbial ecology with respect to the sulfur and nitrogen cycles and the underpinning soil geochemistry and metal distributions that are key to the biological activities of microbes, invertebrates and plants.
Former personnel: Dr Liz Franklin (Postdoctoral Research Fellow, 2013); Dr Nicholas Berkley (Ph.D Student, 2014-2018).
Applied Research - Biotechnology and Bioremediation
I have side-interests in the application of microbial communities in mining and metal-related biotechnologies, that ultimately stem from my interests in physiology.
Removal of ions from treated landfill leachates
Personnel: Dr Rich Boden (PI), Dr Dimitri Kaloudis (Postdoctoral Research Associate 2017-2019)
Funding: Innovate UK and Phoenix Engineering Ltd (total c.£150,000)
Landfill systems produce an effluent that is treated in very similar ways to domestic wastewater, using nitrification-denitrification sequencing batch reactors etc to remove ammonium as nitrogen gas. Other systems such as reed beds can be used to remove other constituents but very low level metals can remain. In this project, we are investigating 'polishing' steps to remove low-level metal ions from treated effluents.
Removal of Cd(II) from contaminated groundwater
Personnel: Dr Rich Boden (PI), Dr Charlotte Braungardt (CoI), Mrs Nadia Jebril (Ph.D Student 2015-2019).
Funding: Iraqi Government (2015-2019).
Cadmium (II) ions (Cd(II)) are found in freshwater systems from both the weathering of natural cadmium minerals and from pollution derived from the production and disposal of fine art pigments, batteries etc. In this work, a strain of Brevibacillus agri was used in a lab-scale biotechnology of a continuous-flow immobilised-cell system that could remove Cd(II) ions from artificial groundwaters supplemented to a range of concentrations at and above those commonly found - removal down to below the WHO Water Quality Guidelines was possible.
Former applied research projects:
Development of improved biogas systems
Personnel: Dr Rich Boden (PI), Dr Elisabeth Cazier (Postdoctoral Research Associate)
Funding: Innovate UK and New Generation Biogas Ltd (total c.£200,000) - project terminated owing to bankruptcy of collaborating company
A two-step biogas system had been developed by the collaborating company. Using microbial molecular ecology and radiorespirometry methods, the project's goal was to understand the communities present and their roles and thus to improve upon and stabilise and already extremely rapid technology. Sadly changing tariffs from the government lead to major market changes and resulted in the voluntary administration of our collaborators, terminating the project after 12 months.
Rare-earth element biorecovery (REECover) and bioextraction (REEMine)
(Personnel: Dr Rich Boden (PI), Mr Ryan Baylis (Research Assistant/Intern 2012-13), Miss Megan Kerry (Summer Student 2012), Mr Jack Cowling (Research Assistant/Intern 2013-2014), Mr Tom Hathway (Research Assistant/Intern 2013); Collaborators: BioORE Consortium: Dr Rich Boden (Director), Prof Lynne Macaskie (CoI), Dr Angie Murray (PDRA), Dr Stephanie Handley-Sidhu (PDRA, Birmingham), Prof Richard Pattrick (CoI, Manchester), Dr Joanna Wragg (CoI, BGS); Funding: NERC Security of Supply of Mineral Resources Grant (2013-2014), Plymouth 2012-13, Reinvestment of consultancy profits)
The rare-earth elements (REEs) are increasingly used in electronic goods, medical devices, MRI contrast agents, lasers and a wide range of alloys and ceramics. Owing to the geopolitical implications of relatively few high-grade ore deposits worldwide, efforts have been made to find alternative extraction processes for these elements from low-grade ores found around the world. REEMine and REECover form two elements of these process pipelines and seek to selectively extract and recover REEs from a variety of ores, mine wastes, tailings, run-offs and consumer waste goods.
Coupled biosensors for measurement of organophosphate contamination of freshwater
(Personnel: Dr Rich Boden (PI), Dr Richard Billington (CoI), Dr John Moody (CoI), Mr Hassan Alhammod Alhilli (Visiting PhD Student); Funding: Iraqi Government (Jan 2013 - July 2013).
Organophosphates are commonly used in a variety of agricultural settings and, as such, present a considerable environmental hazard when they are washed off of agricultural land into water courses, where they have ecotoxicological effects on microorganisms, algae and fish. To rapidly monitor organophosphate levels in a range of aquatic settings, we have developed a proven-in-principle diagnostic, quantitative method based on a highly stable microbial alkaline phosphatase that converts organophosphates into phosphate, which is detected with the malachite green-molybdate method widely used for cost-effective, accurate determination of phosphate. We have developed a highly stable, easy to use immobilised preparation of stable alkaline phosphatases that tolerate extremes of heat, light, UV, dessication and cold, enabling a variety of long-term and short-term storage options for both pre-use storage and between-use storage, since the enzyme preparation can be rapidly removed manually after use, washed and stored for re-use. This project has built upon research undertaken by Mr Alhammod Alhilli in Basra and has developed a stable enzyme preparation from Bacillus sp. FH4, which has shown extreme in vitro stability at room temperature, rendering it highly suited to biosensor development. Future work will continue development with the enzyme preparation to develop "dipstick" test methods and a re-usable probe biosensor for industrial use.
Grants & contracts
Innovate UK Development of biotechnologies for the removal of metals from treated landfill liquor. Knowledge Transfer Partnership (KTP) (c. £185,000). Mar 2017 - Present. Industrial Partner: Phoenix Engineering Ltd.
Innovate UK Optimising biogas production using novel technologies. Knowledge Transfer Partnership (KTP) (c. £175,000). Feb 2016 - Jan 2017. Industrial Partner: New Generation Biogas Ltd (entered administration, Jan 2017).
NERC Security of Supply of Mineral Resources Catalyst Grant
"Biogeochemistry, Bioextraction and Biorecovery of Rare Earth Elements (BioORE)". (c
.£125,000) Sept 2013-Mar 2014.
Seale-Hayne Educational Trust "Mobilisation of Arsenic in Cornish Agricultural Soils (MAsC)" for Dr Emma Ransome (c.£4,500) Sept 2013-Sept 2014.
Seale-Hayne Educational Trust "Biogeochemistry, microbiology and their role in underpinning the ecology of bioenergy crop farmland" for Dr Liz Franklin (c.£5,500) June 2013-Sept 2013 (joint with Dr Mick Hanley).
University of Plymouth School of Biomedical & Biological Sciences Undergraduate Summer Studentship "Bioextraction of rare-earth elements (REExtract)" for Mr Jack Cowling (c.£750) July 2013 - August 2013.
University of Plymouth School of Biomedical & Biological Sciences Undergraduate Summer Studentship "Pathogens and Symbionts in Euphydryas editha" for Miss Jessica Alsopp (c.£750) July 2013 - August 2013 (joint with Dr Mick Hanley).
University of Plymouth School of Biomedical & Biological Sciences Ph.D Studentship "Physiology and biochemistry of the Kelly-Trudinger pathway" for Mr Lee Hutt. (c.£68,000) Oct 2012 - Sept 2015.
University of Plymouth School of Biomedical & Biological Sciences Ph.D Studentship "Storm surge events and their impact on soil geochemistry, microbiology and plant ecology of coastal grasslands" for Miss Elena Righetti. (c.£68,000) Oct 2012 - Sept 2015.
University of Plymouth School of Biomedical & Biological Sciences Undergraduate Summer Studentship "Toxicology of rare-earth elements (REETox)" for Miss Megan Kerry (c.£750) July 2012 - Sept 2012.
Undiscolosed "Evaluation of microbial communities in composts" 2015.
Dartmoor Zoological Park "Monitoring of local geochemistry" (pro bono) March 2013.
Imerys Minerals Ltd "Towards molecular diagnostic methods for use in quality control" June 2012 - Sept 2012.