Biological and Chemical Sciences

Dr Alexandre De Menezes

B.Sc.,PhD

Contact Details

Lecturer Above The Bar
E: ALEXANDRE.DEMENEZES@nuigalway.ie

Biography

Dr. Alexandre Barretto de Menezes (ABM) joined NUI Galway as a lecturer in soil microbiology in January 2017. Dr. de Menezes is specialised in molecular microbial ecology, metagenomics and has expertise in multivariate statistical analyses and correlation network analysis. After obtaining a Ph.D. at the University of Liverpool, ABM worked as a postdoc at University of College Dublin, where he used next-generation sequencing to characterise the gut microbiome of dairy cows undergoing methane mitigation experiments and the metatranscriptome of soils exposed to pollutants. Subsequently, ABM worked as a postdoc at CSIRO in Canberra, Australia, where he used molecular, biogeochemical and environmental sensor data to study variability in soil microbial ecosystem function. At CSIRO, ABM worked on a range of topics in microbial ecology, including molecular analysis of cellulose degradation genes, fungal-bacterial associations in soil, the effects of invasive earthworms on soil microbial communities and the impacts of wildfire on soil microbes. Prior to his current position, ABM worked as a Research Fellow at the University of Salford, UK, where he developed research in the relationships between gut microbiome and parasite loads of wild mice and metagenomic sequencing of viral communities in rivers.

Research Interests

My research interest is in determining the drivers of microbial ecosystem function, particularly in the soil environment but also in the mammalian rumen. I have experience in next generation sequencing, bacterial 16S rRNA sequence analysis, metagenomics and metatranscriptomics. I work with a range of topics, including climate change, bioremediation, land use change and sustainable agriculture. I also have a long-standing interest in working with microbial glycoside hydrolase genes, their diversity and role in the environment as well as potential applications.

Peer Reviewed Journals

	Year	Publication
	(2020)	'Towards solving a scientific controversy – The effects of ionising radiation on the environment' Beresford, N.A.; Horemans, N.; Copplestone, D.; Raines, K.E.; Orizaola, G.; Wood, M.D.; Laanen, P.; Whitehead, H.C.; Burrows, J.E.; Tinsley, M.C.; Smith, J.T.; Bonzom, J.-M.; Gagnaire, B.; Adam-Guillermin, C.; Gashchak, S.; Jha, A.N.; de Menezes, A.; Willey, N.; Spurgeon, D. (2020) 'Towards solving a scientific controversy – The effects of ionising radiation on the environment'. Journal Of Environmental Radioactivity, 211 (August) [DOI] [Details]
	(2019)	'Geographical location influences the composition of the gut microbiota in wild house mice (Mus musculus domesticus) at a fine spatial scale' Goertz S;de Menezes AB;Birtles RJ;Fenn J;Lowe AE;MacColl ADC;Poulin B;Young S;Bradley JE;Taylor CH; (2019) 'Geographical location influences the composition of the gut microbiota in wild house mice (Mus musculus domesticus) at a fine spatial scale'. Plos One, 14 (9) [DOI] [ARAN Link] [Details]
	(2018)	'Opportunistic Bacteria Dominate the Soil Microbiome Response to Phenanthrene in a Microcosm-Based Study' Storey, S,Ashaari, MM,Clipson, N,Doyle, E,de Menezes, AB (2018) 'Opportunistic Bacteria Dominate the Soil Microbiome Response to Phenanthrene in a Microcosm-Based Study'. Frontiers In Microbiology, 9 [DOI] [ARAN Link] [Details]
	(2018)	'Earthworm-induced shifts in microbial diversity in soils with rare versus established invasive earthworm populations' de Menezes, AB,Prendergast-Miller, MT,Macdonald, LM,Toscas, P,Baker, G,Farrell, M,Wark, T,Richardson, AE,Thrall, PH (2018) 'Earthworm-induced shifts in microbial diversity in soils with rare versus established invasive earthworm populations'. Fems Microbiology Ecology, 94 [DOI] [Details]
	(2018)	'Organic phosphorus in the terrestrial environment: a perspective on the state of the art and future priorities' George, TS;Giles, CD;Menezes-Blackburn, D;Condron, LM;Gama-Rodrigues, AC;Jaisi, D;Lang, F;Neal, AL;Stutter, MI;Almeida, DS;Bol, R;Cabugao, KG;Celi, L;Cotner, JB;Feng, G;Goll, DS;Hallama, M;Krueger, J;Plassard, C;Rosling, A;Darch, T;Fraser, T;Giesler, R;Richardson, AE;Tamburini, F;Shand, CA;Lumsdon, DG;Zhang, H;Blackwell, MSA;Wearing, C;Mezeli, MM;Almas, AR;Audette, Y;Bertrand, I;Beyhaut, E;Boitt, G;Bradshaw, N;Brearley, CA;Bruulsema, TW;Ciais, P;Cozzolino, V;Duran, PC;Mora, ML;de Menezes, AB;Dodd, RJ;Dunfield, K;Engl, C;Frazao, JJ;Garland, G;Jimenez, JLG;Graca, J;Granger, SJ;Harrison, AF;Heuck, C;Hou, EQ;Johnes, PJ;Kaiser, K;Kjaer, HA;Klumpp, E;Lamb, AL;Macintosh, KA;Mackay, EB;McGrath, J;McIntyre, C;McLaren, T;Meszaros, E;Missong, A;Mooshammer, M;Negron, CP;Nelson, LA;Pfahler, V;Poblete-Grant, P;Randall, M;Seguel, A;Seth, K;Smith, AC;Smits, MM;Sobarzo, JA;Spohn, M;Tawaraya, K;Tibbett, M;Voroney, P;Wallander, H;Wang, L;Wasaki, J;Haygarth, PM (2018) 'Organic phosphorus in the terrestrial environment: a perspective on the state of the art and future priorities'. Plant And Soil, 427 :191-208 [DOI] [Details]
	(2017)	'Wildfire impact: Natural experiment reveals differential short-term changes in soil microbial communities' Prendergast-Miller, MT;de Menezes, AB;Macdonald, LM;Toscas, P;Bissett, A;Baker, G;Farrell, M;Richardson, AE;Wark, T;Thrall, PH (2017) 'Wildfire impact: Natural experiment reveals differential short-term changes in soil microbial communities'. Soil Biology & Biochemistry, 109 :1-13 [DOI] [Details]
	(2017)	'Linking fungal–bacterial co-occurrences to soil ecosystem function' Alexandre B. de Menezes, Alan E. Richardson, Peter H. Thrall (2017) 'Linking fungal–bacterial co-occurrences to soil ecosystem function'. [Details]
	(2017)	'Fifty important research questions in microbial ecology' Antwis RE;Griffiths SM;Harrison XA;Aranega-Bou P;Arce A;Bettridge AS;Brailsford FL;de Menezes A;Devaynes A;Forbes KM;Fry EL;Goodhead I;Haskell E;Heys C;James C;Johnston SR;Lewis GR;Lewis Z;Macey MC;McCarthy A;McDonald JE;Mejia-Florez NL;O'Brien D;Orland C;Pautasso M;Reid WDK;Robinson HA;Wilson K;Sutherland WJ; (2017) 'Fifty important research questions in microbial ecology'. Fems Microbiology Ecology, 93 (5) [DOI] [Details]
	(2016)	'The soil microbiome at the Gi-FACE experiment responds to a moisture gradient but not to CO2 enrichment' de Menezes, AB;Muller, C;Clipson, N;Doyle, E (2016) 'The soil microbiome at the Gi-FACE experiment responds to a moisture gradient but not to CO2 enrichment'. Microbiology, 162 :1572-1582 [DOI] [Details]
	(2015)	'Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range' Henderson, G;Cox, F;Ganesh, S;Jonker, A;Young, W;Janssen, PH (2015) 'Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range'. Scientific Reports, 5 [DOI] [Details]
	(2015)	'C/N Ratio Drives Soil Actinobacterial Cellobiohydrolase Gene Diversity' de Menezes, AB;Prendergast-Miller, MT;Poonpatana, P;Farrell, M;Bissett, A;Macdonald, LM;Toscas, P;Richardson, AE;Thrall, PH (2015) 'C/N Ratio Drives Soil Actinobacterial Cellobiohydrolase Gene Diversity'. Applied And Environmental Microbiology, 81 :3016-3028 [DOI] [Details]
	(2015)	'Network analysis reveals that bacteria and fungi form modules that correlate independently with soil parameters' de Menezes, AB;Prendergast-Miller, MT;Richardson, AE;Toscas, P;Farrell, M;Macdonald, LM;Baker, G;Wark, T;Thrall, PH (2015) 'Network analysis reveals that bacteria and fungi form modules that correlate independently with soil parameters'. Environmental Microbiology, 17 :2677-2689 [DOI] [Details]
	(2015)	'Microbial community structure mediates response of soil C decomposition to litter addition and warming' Creamer, CA;de Menezes, AB;Krull, ES;Sanderman, J;Newton-Walters, R;Farrell, M (2015) 'Microbial community structure mediates response of soil C decomposition to litter addition and warming'. Soil Biology & Biochemistry, 80 :175-188 [DOI] [Details]
	(2015)	'Soil nitrogen pools and turnover in native woodland and managed pasture soils' Prendergast-Miller, MT;de Menezes, AB;Farrell, M;Macdonald, LM;Richardson, AE;Bissett, A;Toscas, P;Baker, G;Wark, T;Thrall, PH (2015) 'Soil nitrogen pools and turnover in native woodland and managed pasture soils'. Soil Biology & Biochemistry, 85 :63-71 [DOI] [Details]
	(2012)	'Importance of Micromonospora spp. as Colonizers of Cellulose in Freshwater Lakes as Demonstrated by Quantitative Reverse Transcriptase PCR of 16S rRNA' de Menezes, AB;McDonald, JE;Allison, HE;McCarthy, AJ (2012) 'Importance of Micromonospora spp. as Colonizers of Cellulose in Freshwater Lakes as Demonstrated by Quantitative Reverse Transcriptase PCR of 16S rRNA'. Applied And Environmental Microbiology, 78 :3495-3499 [DOI] [Details]
	(2012)	'Comparative metatranscriptomics reveals widespread community responses during phenanthrene degradation in soil' de Menezes, A;Clipson, N;Doyle, E (2012) 'Comparative metatranscriptomics reveals widespread community responses during phenanthrene degradation in soil'. Environmental Microbiology, 14 :2577-2588 [DOI] [Details]
	(2011)	'Microbiome analysis of dairy cows fed pasture or total mixed ration diets' de Menezes, AB;Lewis, E;O'Donovan, M;O'Neill, BF;Clipson, N;Doyle, EM (2011) 'Microbiome analysis of dairy cows fed pasture or total mixed ration diets'. Fems Microbiology Ecology, 78 :256-265 [DOI] [Details]
	(2009)	'Molecular Biological Detection and Quantification of Novel Fibrobacter Populations in Freshwater Lakes' McDonald, JE;de Menezes, AB;Allison, HE;McCarthy, AJ (2009) 'Molecular Biological Detection and Quantification of Novel Fibrobacter Populations in Freshwater Lakes'. Applied And Environmental Microbiology, 75 :5148-5152 [DOI] [Details]
	(2008)	'Microbial dynamics during the decline of a spring diatom bloom in the Northeast Atlantic' Llewellyn, CA;Tarran, GA;Galliene, CP;Cummings, DG;De Menezes, A;Rees, AP;Dixon, JL;Widdicombe, CE;Fileman, ES;Wilson, WH (2008) 'Microbial dynamics during the decline of a spring diatom bloom in the Northeast Atlantic'. Journal Of Plankton Research, 30 :261-273 [DOI] [Details]
	(2008)	'Cellulose Degradation by Micromonosporas Recovered from Freshwater Lakes and Classification of These Actinomycetes by DNA Gyrase B Gene Sequencing' de Menezes, AB;Lockhart, RJ;Cox, MJ;Allison, HE;McCarthy, AJ (2008) 'Cellulose Degradation by Micromonosporas Recovered from Freshwater Lakes and Classification of These Actinomycetes by DNA Gyrase B Gene Sequencing'. Applied And Environmental Microbiology, 74 :7080-7084 [DOI] [Details]

Professional Associations

Association	Function	From / To
International Society for Microbial Ecology (ISME)	Full member	29-MAY-07 /
UK-Ireland Microbiological Society	Full memmber	31-JAN-06 /
Society for Applied Microbiology	Full memmber	01-MAY-06 /

Committees

Committee	Function	From / To
Microbiology Discipline Health and Safety Committee	Member	18-DEC-19 /
SNS Athena Swan Self-Assessment Team	Member of working group 4	30-OCT-19 /
Research and Ethics Committee	Member of committee for ethics application assessments	08-APR-19 /
Postgraduate Teaching Committee	Representative for the MSc in Biotechnlogy	15-AUG-18 /
EuroXanth COST action WP1 management committee	Member of the manangement committee for work package 1 of the COST action	05-FEB-18 /

Employment

Employer	Position	From / To
Commonwealth Scientific and Industrial Research Organisation - CSIRO - Australia	Postdoctoral Fellow	02-APR-12 / 03-APR-15
University of Salford, UK	Research Fellow in Microbiome Genomics	06-APR-15 / 31-DEC-16
University College Dublin	Postdoctoral Research Assistant	06-JUL-09 / 31-MAR-12
Plymouth Marine Laboratory, UK	Research Assistant	01-OCT-02 / 31-AUG-04
National University of Ireland Galway	Lecturer Above the Bar in Soil Microbiology	23-JAN-17 /
Plymouth Marine Laboratory, UK	Junior Scientist	01-SEP-04 / 31-AUG-05

Education

	Year	Institution	Qualification	Subject
	2002	Universidade Federal de Sao Carlos, Brazil	BACHELOR OF SCIENCE	Biological Sciences
	2009	University of Liverpool, UK	PhD	Biological Sciences

Consultancy

	Client	Description
	Applied Genomics	I am a scientific advisor for Applied Genomics, a UK company providing environmental consultancy work using genomics

Community Engagement

Title	Type	From / To
Outreach	Interview with Galway Bay FM	20-DEC-17 / 20-DEC-17
Outreach	Organiser of Microbiology Science Experience Workshop	/
Outreach	Participation in Flirt FM radio program	19-SEP-19 /
Outreach	Representative of the MSc in Biotechnology in NUIG PG open days	/
Outreach	News article on the NUIG website	30-NOV-17 /
Outreach	Microbiology representatve in NUIG UG open days	/

Reviews

	Journal	Role
	Scientific Reports	Reviewer
	International Journal Of Environmental Research And Public Health	Editoral Board
	Soil Biology & Biochemistry	Reviewer
	Mbio	Reviewer
	Biotechnology For Biofuels	Reviewer
	Fems Microbiology Ecology	Reviewer
	Environmental Pollution	Reviewer
	Archives of Agronomy and Soil Science	Reviewer
	The ISME journal	Reviewer
	Fems Microbiology Letters	Reviewer
	Microbiology-Uk	Reviewer
	Plos One	Reviewer
	Microbiologyopen	Reviewer
	Global Change Biology	Reviewer
	Molecular Ecology	Reviewer
	Soil Science Society Of America Journal	Reviewer
	Biology And Environment-Proceedings Of The Royal Irish Academy	Reviewer
	Sustainability	Reviewer
	Evolutionary Applications	Reviewer
	Reviews In Environmental Science And Bio/Technology	Reviewer
	Journal Of Medical Microbiology	Reviewer
	Plant And Soil	Reviewer
	Acta Oecologica-International Journal Of Ecology	Reviewer

Other Activities

	Description
	2019 - Reviewer of Research grant for FONDECYT (Chile)
	2018-2019 - Reviewed research grant application for the European REsearch Council (ERC Advanced Grants).
	2014 - Reviewed grant for FAPESP (Brazil)
	2016 - Reviewed grant for FAPESP (Brazil)