Scientific-Technical Publications or Documents in BOOKS or BOOK CHAPTERS

2025

Bargiela R, Méndez-García C, Martínez-Martínez M, Ferrer M. Metagenomic protocols and strategies. Book chapter. In: Muniyandi Nagarajan Ed, Metagenomics: Perspectives, Methods, and Applications, 2nd edition. Elsevier Inc 2025

2023

Molina-Espeja P, Fernandez-Lopez L, Golyshin P, Ferrer M. Metagenomics and new enzymes for the bioeconomy to 2030. In: Brahmachari G eds. Biotechnology of Microbial Enzymes Production, Biocatalysis, and Industrial Applications 2nd Edition, ElSevier 2023. Paperback ISBN: 9780443190599; eBook ISBN: 9780443190605

Molina-Espeja, Patricia, Fernandez-Lopez L, Golyshin Peter, Ferrer M. Assigning Functions of Unknown Enzymes by High-Throughput Enzyme Characterization.  In: Streit, W.R., Daniel, R. (eds) Metagenomics. Methods in Molecular Biology, vol 2555. Humana, New York, NY, 2023.

2019

Ferrer M, Méndez-García C. Del gen a la función: metatranscriptómica, metaproteómica y metabolómica microbiana. In: “ómicas en el estudio de probióticos y microbiota”. Publisher: Amazing Books  (ed. Abelardo Margolles), 2019.

Violeta-Zubeldia E, Raczkowska BA, Ferrer M, Perez-Gordo M, Rojo D.Techniques for Phenotyping the Gut Microbiota Metabolome. In Microbiome and Metabolome in Diagnosis, Therapy, and other Strategic Applications. Copyright © 2019 Elsevier Inc.

2018

Golyshin P, Jaeger K, Toshchakov S, Golyshina O, Chernikova T, Yakimov M, Manuel M. Aerobic Hydrocarbon-degrading Gammaproteobacteria – Oleiphilaceae and Relatives. In: Aerobic Hydrocarbon-Degrading Gammaproteobacteria: Oleiphilaceae and Relatives. In: McGenity T. (eds) Taxonomy, Genomics and Ecophysiology of Hydrocarbon-Degrading Microbes. Handbook of Hydrocarbon and Lipid Microbiology. Springer, Cham, 2018.
https://doi.org/10.1007/978-3-319-60053-6_23-1

Reyes-Duarte D, Coscolín C, Martínez-Martínez M, Ferrer M, García-Arellano H. Functional-Based Screening Methods for Detecting Esterase and Lipase Activity Against Multiple Substrates.
Methods in Molecular Biology 2018, 1835:109-117.
https://doi.org/10.1007/978-1-4939-8672-9_4

Coscolín C, Bargiela R, Martínez-Martínez M, Alonso S, Chernikova TN, Hai T, Golyshina OV, Yakimov MM, Golyshin PN, Ferrer M. Hydrocarbon-degrading Microbes as Sources of New Biocatalysts. In: Hydrocarbon-Degrading Microbes as Sources of New Biocatalysts. In: McGenity T. (eds) Taxonomy, Genomics and Ecophysiology of Hydrocarbon-Degrading Microbes. Handbook of Hydrocarbon and Lipid Microbiology. Springer, Cham, 2018
https://doi.org/10.1007/978-3-319-60053-6_13-1

2017

Méndez-García C, Bargiela R, Martínez-Martínez M, Ferrer M. Metagenomic protocols and strategies. In: Metagenomics: Perspectives, Methods and Applications (Elsevier; ed. Muniyandi Nagarajan). Academic Press (ISBN 978-0-08-102268-9), 2017, pp. 15-54.

https://doi.org/10.1016/B978-0-08-102268-9.00002-1

2016

Alarcón Cavero T, D’Auria G, Delgado Palacio S, del Campo Moreno R, Ferrer Martínez M. 59. 59. MICROBIOTA. 2016. del Campo Moreno, R. (coordinator). In: Procedimientos en Microbiología Clínica. Cercenado Mansilla E, Cantón Moreno R (eds). Sociedad EspYearla de Enfermedades Infecciosas y Microbiología Clínica (SEIMC). 2016, 43 páginas.

ISBN: 978-84-617-7001-4

https://seimc.org/contenidos/documentoscientificos/procedimientosmicrobiologia/seimc-procedimientomicrobiologia59.pd.

Bargiela R, Yakimov MM, Golyshin PN, Ferrer M. Distribution of Hydrocarbon Degradation Pathways in the Sea. In: Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Production of Fuels and Chemicals, Publisher: Springer International Publishing (eds. Terry J. McGenity, Kenneth N. Timmis and Balbina Nogales), 2017, pp. 1-23.

https://doi.org/10.1007/978-3-319-31421-1_383-1

http://link.springer.com/referenceworkentry/10.1007/978-3-319-31421-1_383-1

Distaso MA, Tran H, Ferrer M, Golyshin PN. Metagenomic Mining of Enzyme Diversity. In: Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Production of Fuels and Chemicals, Publisher: Springer International Publishing, 2017, pp.1-25 (eds. Terry J. McGenity, Kenneth N. Timmis and Balbina Nogales).

https://doi.org/10.1007/978-3-319-31421-1_216-1

Martínez-Martínez M, Bargiela R, Coscolín R, Navarro J, Golyshin PN, Ferrer M. Functionalization and Modification of Hydrocarbon-like Molecules Guided by Metagenomics: Esterases and Lipases from the α/β-Hydrolase Fold Superfamily and Transaminases as Study Cases. In: Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Production of Fuels and Chemicals, Publisher: Springer International Publishing (eds. Terry J. McGenity, Kenneth N. Timmis and Balbina Nogales) (978-3-319-31421-1), 2017, pp-1-21.

https://doi.org/10.1007/978-3-319-31421-1_211-1

Antunes A, Ferrer M, Yarza P. Halorhabdus. In: Bergey’s Manual of Systematics of Archaea and Bacterias (Online © 2015 Bergey’s Manual Trust. This article is © 2016 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust; Ed. W. Aharon Oren).

https://doi.org/10.1002/9781118960608.gbm01349

Bargiela R, Ferrer M. Degradation newtowork reconstruction guided by metagenomic data

“In: Metagenomics: methods and protocols (Ed. W. Streit y R. Daniel), HumanaPress”, 2017, pp. 145-157.

https://doi.org/10.1007/978-1-4939-6682-0_8

https://www.ncbi.nlm.nih.gov/pubmed/27900688

Golyshina OV, Ferrer M, Golyshin PN. Diversity and Physiologies of Acidophilic Archaea. In the Part III   Diversity of acidophilic organisms. In: Acidophiles: Life in Extremely Acidic Environments (Edited by: Raquel Quatrini and D. Barrie Johnson). Caister Academic Press, U.K., 2016, pp. 93-106.

http://www.horizonpress.com/acidophiles

2015

Martínez-Martínez M, Bargiela R, Ferrer M. Metagenomics and the search for industrial enzymes

In: Biotechnology of Microbial Enzymes, 1st Edition, Production, Biocatalysis and Industrial Applications (G. Brahmachari, ed.; Academic Press), 2015, pp. 167-184.

eBook ISBN: 9780128037461

https://doi.org/10.1016/B978-0-12-803725-6.00007-8

Martínez-Martínez M, Ferrer M. Screening of metagenomic libraries: enzymes acting on greasy molecules as study case. In: Hydrocarbon and Lipid Microbiology Protocols (Springer Protocols Handbooks) (Ed. Terry J. McGenity, Kenneth N. Timmis and Balbina Nogales), 2015, pp.1-24.

http://dx.doi.org/10.1007/8623_2015_104

http://link.springer.com/protocol/10.1007%2F8623_2015_104

2014

Del Pozo MV, Martínez-Martínez M, Ferrer. Protein extraction from contaminated soils and sediments. In: Hydrocarbon and Lipid Microbiology Protocols (Springer Protocols Handbooks) (Ed. Terry J. McGenity, Kenneth N. Timmis and Balbina Nogales), 2014, pp. 1-17).  http://dx.doi.org/10.1007/8623_2014_45
http://link.springer.com/protocol/10.1007%2F8623_2014_45

Nechitaylo T, Ferrer M, Golyshin PN. Terrestrial invertebrate animal metagenomics, Lumbrididae
In: Encyclopedia of Metagenomics (Springer Science+Business Media New York), 2014.
https://doi.org/10.1007/978-1-4614-6418-1_21-1
Web: http://link.springer.com/referenceworkentry/10.1007/978-1-4614-6418-1_21-1

2013

Yakimov MM, La Cono V, Ferrer M, Golyshin PN, Giuliano L. Metagenomics of Deep Hypersaline Anoxic Basins. In: Encyclopedia of Metagenomics (Springer Science+Business Media New York), 2013.

https://doi.org/10.1007/978-1-4614-6418-1_36-1

http://link.springer.com/referenceworkentry/10.1007/978-1-4614-6418-1_36-1

2012

Reyes-Duarte D, Ferrer M, García-Arellano H. Functional-based screening methods for lipases, esterases, and phospholipases in metagenomic libraries. Methods in Molecular Biology 2012, 861:101-113.

https://doi.org/10.1007/978-1-61779-600-5_6

2011

Guazzaroni ME, Fernández-Arrojo L, López-Cortés N, Ferrer M. Era post-genómica para el desarrollo de nuevos biocatalizadores. In: Monografía XXXV: Biocatálisis aplicada a la obtención de fármacos y productos de alto valor añadido (eds José María Sánchez Montero, Fidel Ortega Ortiz Apocada y Antonio Doadrio Villarejo). Monografías de la Real Academia Nacional de Farmacia (Madrid, España), 2011.

ISBN: 978-84-938172-7-5)

http://www.analesranf.com/index.php/mono/article/view/1321

Guazzaroni ME, Fernández-Arrojo L, López-Cortés N, Ferrer M. The role of new (meta-) metabolomic technologies in medical systems microbiology. In: ebook “The Role of New Technologies in Medical Microbiological Research and Diagnosis (eds John P. Hays and W.B. van Leeuwen). Bentham ebook, The Netherlands, 2011.

eISBN: 978-1-60805-316-2

https://doi.org/10.2174/978160805316211201010072

http://ebooks.benthamscience.com/book/9781608053162/

Cowan DA, Kirby BB, Meiring TL, Ferrer M, Guazzaroni ME, Golyshina OV, Golyshin PN. Enzymes from Extreme Environments. In: Enzymes from Extreme Environments, Ch. 4. In Manual of Industrial Microbiology and Biotechnology, 3rd Edition, Baltz, RH, Davies, JE, Demain, AL, Eds. ASM Press, 2011

ISBN: 978-1-55581-512-7

http://www.asmscience.org/content/book/10.1128/9781555816827.ch04.

Guazzaroni ME, Ferrer M. (Meta) genomics in System biology. Chapter 54. In: Handbook of Molecular Microbial Ecology, Volume I: Metagenomics and Complementary Approaches, First Edition (ed Frans J. de Bruijn). Wiley-Blackwell, John Wiley & Sons, Inc-2, 2011, pp. 475-489.

http://eu.wiley.com/WileyCDA/WileyTitle/productCd-0470644796.html

2010

Ferrer M, Beloqui A, Golyshin PN. Screening metagenomic libraries for laccase activity. In: Metagenomics: methods and protocols (ed W. Streit y R. Daniel), HumanaPress, 2010, pp. 189-202.

ISBN: 978-1-4939-8274-5

Vieites JM, Guazzaroni ME, Beloqui A, Golyshin PN, Ferrer M. Molecular methods to study complex microbial communities. In: Metagenomics: methods and protocols (ed W. Streit y R. Daniel), HumanaPress, 2010, pp. 1-38.

ISBN: 978-1-4939-8274-5

Golyshin PN, Ferrer M, Chernikova TN, Golyshina OV, Yakimov MM. Oleispira. In: Handbook of Microbiology of Hydrocarbons, Oils, Lipids, and Derived Compounds (ed. Kenneth N. Timmis), Springer, pp. 1775-1763, 2010.

ISBN: 978–3–540–77584–3

https://link.springer.com/referencework/10.1007/978-3-540-77587-4

Golyshin PN, Lündsdorf H, Ferrer M, Yakimov MM. Thermoleophilum: a gram positive hydrocarboclastic thermophilic bacterium. In: Handbook of Microbiology of Hydrocarbons, Oils, Lipids, and Derived Compounds (ed. Kenneth N. Timmis), Springer, pp. 1881-1886, 2010.

ISBN: 978–3–540–77584–3

https://link.springer.com/referencework/10.1007/978-3-540-77587-4

Beloqui A, Guazzaroni ME, Ferrer M. Procedures for Protein Isolation in Pure Culture and Microbial Communities. In: Handbook of Microbiology of Hydrocarbons, Oils, Lipids, and Derived Compounds (ed. Kenneth N. Timmis), Springer, pp. 4183-4194, 2010.

ISBN: 978–3–540–77584–3

https://link.springer.com/referencework/10.1007/978-3-540-77587-4

Guazzaroni ME, Beloqui A, Vieites JM, Al-Ramahi Y, López-Cortés N, Ghazi A, Golyshin PN, Ferrer M. Metagenomic mining of enzyme diversity. In: Handbook of Microbiology of Hydrocarbons, Oils, Lipids, and Derived Compounds (ed. Kenneth N. Timmis), Springer, pp. 4183-4194, 2010.

ISBN: 978–3–540–77584–3

https://link.springer.com/referencework/10.1007/978-3-540-77587-4

López-Cortés N, Beloqui A, Gazhi A, Ferrer M. Enzymatic functionalization of hydrocarbon-like molecules. In: Handbook of Microbiology of Hydrocarbons, Oils, Lipids, and Derived Compounds (ed. Kenneth N. Timmis), Springer, pp. 4183-4194, 2010.

ISBN: 978–3–540–77584–3

https://link.springer.com/referencework/10.1007/978-3-540-77587-4

Guazzaroni ME, Golyshin PN, Ferrer M. Analysis of complex microbial communities through metagenomic survey. In: Metagenomics: theory, methods and applications (ed. D. Marco), Caister Academic Press, pp. 55-77, 2010.

ISBN: 978-1-904455-54-7

https://doi.org/10.21775/9781912530120

López-Cortés N, Beloqui A, Gazhi A, Ferrer M. Enzymatic functionalization of hydrocarbon-like molecules. In: Handbook of Microbiology of Hydrocarbons, Oils, Lipids, and Derived Compounds (Ed. Kenneth N. Timmis), Springer, pp. 2841-2858, 2010.

https://doi.org/10.1007/978-3-540-77587-4_211

Ferrer M, Beloqui A, Golyshin PN.  Screening metagenomic libraries for laccase activities.

Methods in Molecular Biology 2010, 668:189-202.

https://doi.org/10.1007/978-1-60761-823-2_13

Vieites JM, Guazzaroni ME, Beloqui A, Golyshin PN, Ferrer M. Molecular methods to study complex microbial communities. Methods in Molecular Biology 2010, 668:1-37.

https://doi.org/10.1007/978-1-60761-823-2_1

2009

Ferrer M, Beloqui A, Zumárraga M, Alcalde M, Golyshin PN. Microbes and enzymes: recent trends and new directions to explore protein diversity space. In: Protein Engineering Handbook (ed. S. Lutz y U.T. Bornscheuer), Wiley-VCH Verlag GmbH & Co. KGaA, pp. 233-264, 2009.

Ferrer M, Golyshin PN. Rare metabolic conversions: harvesting diversity through nature. In: Handbook for Metabolic Pathway Engineering (ed. C. Smolke), Vol. 1, CRC Press, Boca Raton (FL), pp. 5-11, 2009.

2006

Ballesteros A, Plou FJ, Alcalde M, Ferrer M, García-Arellano H, Reyes-Duarte D, Ghazi I. Enzymatic synthesis of sugar esters and oligosaccharides from renewable resources. In: Biocatalysis in the Pharmaceutical and Biotechnology Industries (ed. R.N. Patel, Marcel Dekker), 2006.
ISBN ebook 9780429115462

2003

Plou FJ, Ferrer M, Ballesteros A. Transesterification with biological catalysts. In: Encyclopedia of Catalysis (ed István Horváth), John Wiley & Sons, Inc, New York. Vol 6, Wiley Interscience, New York,pp. 483-506, 2003.

1998

Plou FJ, Calvo MV, Ferrer M, Ballesteros A. Stabilization of hydrolases by chemical modification with fatty acids or poliethylene glycol. In: Stability and Stabilization of Biocatalysts. Eds.: Ballesteros A, Plou FJ, Iborra JL, Halling P. Elsevier, Amsterdam, pp. 535-540, 1998.
ISBN 0-444 82970-9

1996

Plou FJ, Ferrer M, Nuero OM, Calvo MV, Alcalde M, Reyes F, Ballesteros A. Esterasic/lipasic character of Tween 80 as a substrate to measure enzymatic activity. In: Comunicaciones del III Congress Hispano-Luso de Biotecnología. Eds: Fernández-Polanco F, García-Encina PA, González-Benito G, Peña-Miranda MP. Servicio de Publicaciones de la University de Valladolid, pp. 569-570, 1996.
ISBN 84-7762-649-9