Dr ALEXANDRE DE MENEZES

B.Sc.,PhD

Contact Details

LECTURER BELOW THE BAR
Room ES106, Microbiology
Arts and Science Building
School of Natural Sciences
Ryan Institute
T: -
E: ALEXANDRE.DEMENEZES@nuigalway.ie
 
researcher
 

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 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)