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 and Theoretical Biology
Inorganic sulfur metabolism in members of the Bacteria
(Personnel: Dr Rich Boden (PI), Mr Lee G Hutt (PhD Student), Mr Jack Cowling (Research Assistant). Collaborators: Dr A John Moody (Plymouth), Professor Donovan P Kelly (Warwick); Funding: University of Plymouth 2012 - 2015)
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, polysulfides) 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. We also have interest in the partial Kelly-Trudinger pathway found in chemolithoheterotrophs such as "Thiobacillus trautweinii" and the taxonomy of these organisms.
Impacts of coastal inundation on nitrogen fixation in soils
(Personnel: Dr Mick Hanley (PI), Dr Rich Boden (CoI), Miss Elena Righetti (PhD Student); Collaborators: Dr Joanna Wragg (BGS); Funding: University of Plymouth 2012 - 2015)
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
(Personnel: Dr Rich Boden (CoI), Dr Liz Franklin (PDRA); Collaborators: Dr Mick Hanley (Plymouth); Funding: Seale-Hayne Educational Trust 2013 - 2015)
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.
Microbially mediated mobilisation of As(III) and As(IV) from arsenopyrite in Cornish soils
(Personnel: Dr Rich Boden (PI), Dr Emma Ransome (PDRA); Collaborators: Dr Charlotte Braungardt (Plymouth), Dr Joanna Wragg and Dr Mark Cave (BGS); Funding: Seale-Hayne Educational Trust 2013 - 2015)
Arsenic ions are toxic to most living organisms and pose a risk to human health and to successful farming and management of land. Arsenic ions (As3+ and As5+) mobilise from minerals such as arsenopyrite (AsFeS) found naturally all over the Devon and Cornwall region. In this project, we examine the role of microbial arsenic oxidation reactions and microbial bioleaching of pyrite minerals in the mobilisation and speciation of arsenic ions from arsenopyrite in Cornish soils.
Pathogenicity in Euphydryas editha and Melitaea cinxia and their ethnobotanical responses
(Personnel: Dr Mick Hanley (PI), Dr Rich Boden (CoI), Miss Jessica Alsopp (Summer Student 2013); Collaborators: Prof Mike C Singer and Prof Camille Parmesan (Plymouth and Texas), Dr Richard Billington (Plymouth); Funding: Plymouth 2013)
Microbial pathogenicity in Edith's checkerspot (E. editha) and Glanville fritillary (M. cinxia) butterfly populations kept for scientific research around the world have been observed. This project serves to examine the nature of the infectious agent and to relate this to host-insect interactions with respect to the butterflies' ethnobotanical use of plants to fight the infection.
Applied Research - Biotechnology and Bioremediation
Rare-earth element biorecovery (REECover) and bioextraction (REEMine)
(Personnel: Dr Rich Boden (PI), Mr Ryan Baylis (Research Assistant 2012-13), Miss Megan Kerry (Summer Student 2012), Mr Jack Cowling (Research Assistant), Mr Tom Hathway (Research Assistant); 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 (Sept 2013-March 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.