Ecology and Environmental Microbiology Group

This fully funded PhD studentship will achieve new insights into animal bio-acoustic signalling and potential industrial applications, using new development and applications of machine learning, including attentional AI.

We welcome applicants with a 1st class or 2:1 BSc (or equivalent) in biology, computer science or any related field. The project will require strong skills in programming (e.g. Python), machine learning and data analysis, including recent machine learning techniques and computer simulation.

This PhD is based at the University of Essex, but the successful candidate will also undertake a fully funded, 1.5 year placement in Japan with Cross Labs, an AI research institute within the company Cross Compass Ltd.

Title: Learning from animal signals: new machine learning applications and development inspired by bioacoustics

Based in: School of Life Sciences

Deadline: 28th February 2023

This fully funded PhD studentship, will explore the benefits of protection and recovery of key Mediterranean marine habitats – from shallow subtidal seagrasses to coralligenous reefs with a focus on biodiversity and fishery enhancement and the role these habitats play in the Blue Carbon economy of the Aegean sea.

The project is largely field-based in the Mediterranean working closely with Archipelagos with opportunity for many days at sea. In addition to funding covering a stipend and Home fees, Archipelagos will provide basic accommodation and board in the Aegean sea field sites.

Title: Ecosystem function of key marine habitats in the Mediterranean: shallow seagrasses to deep coralligenous reefs

Based in: School of Life Sciences

Deadline: 6th March 2023

• Sing Wong, Amy and Vrontos, Spyridon and Taylor, Michelle (2022) 'An assessment of people living by coral reefs over space and time.' Global Change Biology. ISSN 1354-1013
• Bohmann, Kristine and Elbrecht, Vasco and Carøe, Christian and Bista, Iliana and Leese, Florian and Bunce, Michael and Yu, Douglas W and Seymour, Mathew and Dumbrell, Alex J and Creer, Simon (2022) 'Strategies for sample labelling and library preparation in DNA metabarcoding studies.' Molecular Ecology Resources, 22 (4). pp. 1231-1246. ISSN 1471-8278
• Clark, Dave R and McKew, Boyd A and Binley, Andrew and Heppell, Catherine M and Whitby, Corinne and Trimmer, Mark (2022) 'Hydrological properties predict the composition of microbial communities cycling methane and nitrogen in rivers.' ISME Communications, 2 (1). ISSN 2730-6151
• Ellis, Matthew B and Cameron, Tom C (2022) 'An initial assessment of the sustainability of waterbird harvest in the United Kingdom.' Journal of Applied Ecology. ISSN 0021-8901
• Gregson, Benjamin H and Bani, Alessia and Steinfield, Laurel and Holt, Diane and Whitby, Corinne (2022) 'Anaerobes and methanogens dominate the microbial communities in water harvesting ponds used by Kenyan rural smallholder farmers.' Science of the Total Environment, 819. p. 153040. ISSN 0048-9697
• Hoyal Cuthill, Jennifer (2022) 'Ediacaran survivors in the Cambrian: suspicions, denials and a smoking gun.' Geological Magazine, 159 (7). pp. 1210-1219. ISSN 0016-7568
• Kratina, Pavel and Rosenbaum, Benjamin and Gallo, Bruno and Horas, Elena L and O'Gorman, Eoin J (2022) 'The Combined Effects of Warming and Body Size on the Stability of Predator-Prey Interactions.' Frontiers in Ecology and Evolution, 9. ISSN 2296-701X
• López-López, Lucía and Genner, Martin J and Tarling, Geraint A and Saunders, Ryan A and O'Gorman, Eoin J (2022) 'Ecological Networks in the Scotia Sea: Structural Changes Across Latitude and Depth.' Ecosystems, 25 (2). pp. 457-470. ISSN 1432-9840
• Maxwell, Jamie and Taboada, Sergi and Taylor, Michelle L (2022) 'Gorgoniapolynoe caeciliae revisited: The discovery of new species and molecular connectivity in deep-sea commensal polynoids from the Central Atlantic.' Deep Sea Research Part I: Oceanographic Research Papers, 185. p. 103804. ISSN 0967-0637
• McKenzie, Morwenna and England, Judy and Foster, Ian and Wilkes, Martin (2022) 'Evaluating the performance of taxonomic and trait-based biomonitoring approaches for fine sediment in the UK.' Ecological Indicators, 134. p. 108502. ISSN 1470-160X
• McLean, Dianne L and Ferreira, Luciana C and Benthuysen, Jessica A and Miller, Karen J and Schläppy, Marie-Lise and Ajemian, Matthew J and Berry, Oliver and Birchenough, Silvana NR and Bond, Todd and Boschetti, Fabio and Bull, Ann S and Claisse, Jeremy T and Condie, Scott A and Consoli, Pierpaolo and Coolen, Joop WP and Elliott, Michael and Fortune, Irene S and Fowler, Ashley M and Gillanders, Bronwyn M and Harrison, Hugo B and Hart, Kristen M and Henry, Lea-Anne and Hewitt, Chad L and Hicks, Natalie and Hock, Karlo and Hyder, Kieran and Love, Milton and Macreadie, Peter I and Miller, Robert J and Montevecchi, William A and Nishimoto, Mary M and Page, Henry M and Paterson, David M and Pattiaratchi, Charitha B and Pecl, Gretta T and Porter, Joanne S and Reeves, David B and Riginos, Cynthia and Rouse, Sally and Russell, Debbie JF and Sherman, Craig DH and Teilmann, Jonas and Todd, Victoria LG and Treml, Eric A and Williamson, David H and Thums, Michele (2022) 'Influence of offshore oil and gas structures on seascape ecological connectivity.' Global Change Biology, 28 (11). pp. 3515-3536. ISSN 1354-1013
• Robinson, Sinikka I and O'Gorman, Eoin J and Frey, Beat and Hagner, Marleena and Mikola, Juha (2022) 'Soil organic matter, rather than temperature, determines the structure and functioning of subarctic decomposer communities.' Global Change Biology, 28 (12). pp. 3929-3943. ISSN 1354-1013
• Su, Min and Dell'Orto, Marta and D'Imporzano, Giuliana and Bani, Alessia and Dumbrell, Alex J and Adani, Fabrizio (2022) 'The structure and diversity of microalgae-microbial consortia isolated from various local organic wastes.' Bioresource Technology, 347. p. 126416. ISSN 0960-8524
• Underwood, Graham JC and Dumbrell, Alex J and McGenity, Terry J and McKew, Boyd A and Whitby, Corinne (2022) 'The Microbiome of Coastal Sediments.' In: Stal, Lucas J and Cretoiu, Mariana Silvia, (eds.) The Marine Microbiome. The Microbiomes of Humans, Animals, Plants, and the Environment, 3 . Springer International Publishing, pp. 479-534.
• Uttarotai, Toungporn and Sutheeworapong, Sawannee and Crombie, Andrew T and Murrell, J Colin and Mhuantong, Wuttichai and Noirungsee, Nuttapol and Wangkarn, Sunanta and Bovonsombut, Sakunnee and McGenity, Terry J and Chitov, Thararat (2022) 'Genome Characterisation of an Isoprene-Degrading Alcaligenes sp. Isolated from a Tropical Restored Forest.' Biology, 11 (4). p. 519. ISSN 2079-7737
• Whitworth, Paul and Aldred, Nick and Reynolds, Kevin J and Plummer, Joseph and Duke, Phillip W and Clare, Anthony S (2022) 'Importance of Duration, Duty-Cycling and Thresholds for the Implementation of Ultraviolet C in Marine Biofouling Control.' Frontiers in Marine Science, 8. ISSN 2296-7745

• Cordoleani, F and Phillis, CC and Sturrock, AM and FitzGerald, AM and Malkassian, A and Whitman, GE and Weber, PK and Johnson, RC (2021) 'Threatened salmon rely on a rare life history strategy in a warming landscape.' Nature Climate Change, 11 (11). pp. 982-988. ISSN 1758-678X
• Fell, Sarah C and Carrivick, Jonathan L and Cauvy-Fraunié, Sophie and Crespo-Pérez, Verónica and Hood, Eran and Randall, Kate C and Nicholass, Kirsty J Matthews and Tiegs, Scott D and Dumbrell, Alex J and Brown, Lee E (2021) 'Fungal decomposition of river organic matter accelerated by decreasing glacier cover.' Nature Climate Change, 11 (4). pp. 349-353. ISSN 1758-678X
• Clark, Dave R and Underwood, Graham JC and McGenity, Terry J and Dumbrell, Alex J (2021) 'What drives study-dependent differences in distance–decay relationships of microbial communities?' Global Ecology and Biogeography, 30 (4). pp. 811-825. ISSN 1466-822X
• Davey, Peter A and Power, Anne Marie and Santos, Romana and Bertemes, Philip and Ladurner, Peter and Palmowski, Pawel and Clarke, Jessica and Flammang, Patrick and Lengerer, Birgit and Hennebert, Elise and Rothbächer, Ute and Pjeta, Robert and Wunderer, Julia and Zurovec, Michal and Aldred, Nick (2021) 'Omics‐based molecular analyses of adhesion by aquatic invertebrates.' Biological Reviews, 96 (3). pp. 1051-1075. ISSN 1464-7931
• Ferguson, Robert MW and Neath, Charlotte EE and Nasir, Zaheer A and Garcia-Alcega, Sonia and Tyrrel, Sean and Coulon, Frederic and Dumbrell, Alex J and Colbeck, Ian and Whitby, Corinne (2021) 'Size fractionation of bioaerosol emissions from green-waste composting.' Environment International, 147. p. 106327. ISSN 0160-4120
• Ferguson, Robert MW and O'Gorman, Eoin J and McElroy, David J and McKew, Boyd A and Coleman, Ross A and Emmerson, Mark C and Dumbrell, Alex J (2021) 'The Ecological Impacts of Multiple Environmental Stressors on Coastal Biofilm Bacteria.' Global Change Biology, 27 (13). pp. 3166-3178. ISSN 1354-1013
• Gregson, Benjamin H and McKew, Boyd A and Holland, Robert D and Nedwed, Timothy J and Prince, Roger C and McGenity, Terry J (2021) 'Marine Oil Snow, a Microbial Perspective.' Frontiers in Marine Science, 8. ISSN 2296-7745
• Grydaki, Nikoletta and Colbeck, Ian and Mendes, Luis and Eleftheriadis, Konstantinos and Whitby, Corinne (2021) 'Bioaerosols in the Athens Metro: Metagenetic insights into the PM₁₀ microbiome in a naturally ventilated subway station.' Environment International, 146. p. 106186. ISSN 0160-4120
• McGenity, Terry J and McKew, Boyd A and Lea-Smith, David J (2021) 'Cryptic microbial hydrocarbon cycling.' Nature Microbiology, 6 (4). pp. 419-420. ISSN 2058-5276
• Rogers, Alex D and Baco, Amy and Escobar-Briones, Elva and Gjerde, Kristina and Gobin, Judith and Jaspars, Marcel and Levin, Lisa and Linse, Katrin and Rabone, Muriel and Ramirez-Llodra, Eva and Sellanes, Javier and Shank, Timothy M and Sink, Kerry and Snelgrove, Paul VR and Taylor, Michelle L and Wagner, Daniel and Harden-Davies, Harriet (2021) 'Marine Genetic Resources in Areas Beyond National Jurisdiction: Promoting Marine Scientific Research and Enabling Equitable Benefit Sharing.' Frontiers in Marine Science, 8. ISSN 2296-7745
• Scarlett, Kelly and Denman, Sandra and Clark, David R and Forster, Jack and Vanguelova, Elena and Brown, N and Whitby, Corinne (2021) 'Relationships between nitrogen cycling microbial community abundance and composition reveal the indirect effect of soil pH on oak decline.' The ISME Journal, 15 (3). pp. 623-635. ISSN 1751-7362
• Sohlström, Esra H and Archer, Louise C and Gallo, Bruno and Jochum, Malte and Kordas, Rebecca L and Rall, Björn C and Rosenbaum, Benjamin and O'Gorman, Eoin J (2021) 'Thermal acclimation increases the stability of a predator-prey interaction in warmer environments.' Global Change Biology, 27 (16). pp. 3765-3778. ISSN 1354-1013

• King praises our students helping coastal defence project

• Louder than Words Podcast - Good Bugs Bad Bugs Terry McGenity and Corinne Whitby join  Jules Pretty (@JulesPretty1) to discuss the worlds of microbes in oceans, soils and air, and how they can be deployed in new ways to clean up pollution and improve the environment.

• As part of an EU Horizon-funded project, Dr Robert Ferguson will be working with local schools to assess the air quality children are exposed to, both in the classroom and on their journeys to and from school.
• Dr Michael Steinke will be part of an interdisciplinary Essex team attending COP27 to talk about their work on climate change, coastal erosion and the impact on Essex's oyster population.
• We're working to improve diversity through the Environmental Science Summer School, funded by the Natural Environment Research Council (NERC).
• Researchers from our group showcased their research at the Royal Society Summer Science Exhibition 2022, presenting Ocean Travellers to the public during this week-long event. You can also watch our Ocean Travellers video on Vimeo or Youtube.
• We are collaborating with the UK Government’s Centre for Environment, Fisheries and Aquaculture Science (Cefas) on training and research linked to aquatic ecosystems.
• Endurance: Shackleton's lost ship is found in Antarctic - Dr Michelle Taylor is quoted in this BBC news article on the discovery of Ernest Shackleton's lost ship Endurance. Michelle herself took part in an expedition to the Weddell Sea, including looking for the Endurance, in 2019.
• Essex ecologist to showcase shipwreck research to MPs
• Tom's work on restoring native oysters showcased by Nature - We're so pleased to see the great work by Dr Tom Cameron working with local oyster growers to restore native oysters in their natural habitat has been showcased on the Nature website.
• Podcast focuses on saving our seas - The latest episode of our Louder Than Words Podcast focuses on the threats to our seas and features Dr Michelle Taylor and Dr Natalie Hicks plus BBC presenter writer and BBC presenter Tom Heap. You can also read a blog by Dr Taylor and Dr Hicks.
• Dr Michelle Taylor is new President of Deep-Sea Biology Society
• Microplastics affect individual fish differently, study finds
• Salmon eyes may hold secrets of their survival … and decline
• Essex part of world’s largest coral restoration programme

• "It is vital that climate action involves the ocean"
• Louder than Words: Saving the Seas (podcast)
• The Time For Action Q&A: Emeritus Professor Ian Colbeck discusses air pollution
• Can pollution face masks really protect us from exposure to toxic particles?
• Conservation is all about the people