none4openErijman L.; Campanaro S.; Etchebehere C.; Varesche M.B.A.Erijman, L.; Campanaro, S.; Etchebehere, C.; Varesche, M. B. A

Amancio Varesche, Maria Bernadete

Campanaro, Stefano

Erijman, Leonardo

Etchebehere, Claudia

Frontiers in Microbiology

Anaerobic digestion is an established process for the stabilization of organic matter and production of renewable energy that has a central role in sustainable development and circular economy. It is currently being used worldwide for fuel generation and the production of a stabilized fertilizer from livestock manures and crop residues. High-rate anaerobic technologies can be applied to treat wastewater from virtually any industrial process, and novel strategies open avenues for obtaining products of biotechnological interest, including alternative energy carriers, such as methane and hydrogen, and valuable end-products with industrial application, such as organic acids.Fil: Erijman, Leonardo. Universidad de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Campanaro, Stefano. Università di Padova; ItaliaFil: Etchebehere, Claudia. Instituto de Investigaciones Biológicas "Clemente Estable"; UruguayFil: Amancio Varesche, Maria Bernadete. Universidade de Sao Paulo; Brasi

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EDITORIALpublished: 07 May 2021doi: 10.3389/fmicb.2021.664716Frontiers in Microbiology | www.frontiersin.org 1 May 2021 | Volume 12 | Article 664716Edited by:Ashwani Kumar,Dr. Harisingh Gour CentralUniversity, IndiaReviewed by:Micol Bellucci,Politecnico di Milano, ItalyMarc Strous,University of Calgary, Canada*Correspondence:Leonardo Erijmanerijman@dna.uba.arSpecialty section:This article was submitted toMicrobiotechnology,a section of the journalFrontiers in MicrobiologyReceived: 05 February 2021Accepted: 12 April 2021Published: 07 May 2021Citation:Erijman L, Campanaro S,Etchebehere C and Varesche MBA(2021) Editorial: Meta-omicApproaches to the ComplexAnaerobic Communities inWastewater Treatment Plants andDigesters.Front. Microbiol. 12:664716.doi: 10.3389/fmicb.2021.664716Editorial: Meta-omic Approaches tothe Complex Anaerobic Communitiesin Wastewater Treatment Plants andDigestersLeonardo Erijman 1,2*, Stefano Campanaro 3,4, Claudia Etchebehere 5 andMaria Bernadete Amancio Varesche 61 Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr Héctor N. Torres” (INGEBI-CONICET),Buenos Aires, Argentina, 2Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas yNaturales, Universidad de Buenos Aires, Buenos Aires, Argentina, 3Department of Biology, University of Padua, Padua, Italy,4Centro di Ricerca Interdipartimentale per le Biotecnologie Innovative (CRIBI), University of Padua, Padua, Italy, 5 Instituto deInvestigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay, 6 Laboratório de Processos Biológicos,Departamento de Hidráulica e Saneamento, Escola de Engenharia de São Carlos, Universidade de São Paulo, São Paulo,BrazilKeywords: anaerobic digestion, biogas microbiome, metagenomics, metaproteomics, environmentalbiotechnologyEditorial on the Research TopicMeta-omic Approaches to the Complex Anaerobic Communities in Wastewater TreatmentPlants and DigestersAnaerobic digestion is an established process for the stabilization of organic matter and productionof renewable energy that has a central role in sustainable development and circular economy. Itis currently being used worldwide for fuel generation and the production of a stabilized fertilizerfrom livestock manures and crop residues. High-rate anaerobic technologies can be applied to treatwastewater from virtually any industrial process, and novel strategies open avenues for obtainingproducts of biotechnological interest, including alternative energy carriers, such as methane andhydrogen, and valuable end-products with industrial application, such as organic acids.The anaerobic digestion process is driven by a complex network of specialized microbialguilds. Environmental and operational factors, as well as immigration and stochastic events,determine the microbial community structure of anaerobic digesters. These communities consist ofhundreds of different species of bacteria and archaea, together making up the “biogas microbiome”(Campanaro et al., 2020; Nierychlo et al., 2020). Only a minor fraction of the microbiome isaccessible by cultivation-based approaches, which are additionally unable to capture complexinteractions. Therefore, meta-omic techniques are key to gain deeper understanding of thefunctional importance of specific organisms and to elucidate microbial interactions such asmetabolic cross-feeding.The five articles in this Research Topic asked relevant questions about the roles of individualor defined populations of microbes in the anaerobic digestion process and used metagenomic andmetatranscriptomic tools to address those questions.Mei et al. revealed the role of previously uncharacterized Bacteroidales populations as keyplayers for amino-acid fermentation. The authors combined short-term enrichment cultureswith genome-centric metagenomic and metatranscriptomic resolution to unravel the pathway ofelectron transfer and energy conservation in this group of microbes. By mapping the sequencesof the metagenome-assembled genomes to public metagenomic and metatranscriptomic datasets,Erijman et al. Editorial: Meta-omics of Anaerobic Digester MicrobiotaMei et al. found that members of the proposed new family ofBacteroidales appear to be abundant and widespread amino aciddegraders in full-scale anaerobic digesters.Chloroflexi are prominent members of the biogasmicrobiome. Based on the high abundance of members ofChloroflexi in anaerobic digesters, it is assumed that membersof this phylum contribute significantly to the overall function ofAD systems, presumably as primary fermenters (Petriglieri et al.,2018). Bovio-Winkler et al. compared reactors fed with eitherwastewater or solid waste in a meta-analysis of 62 full-scalemethanogenic reactors and concluded that members of theclass Anaerolineae predominate in anaerobic bioreactors. Thesemicroorganisms may have a structural role as their filamentousmorphology would assist in maintaining granule structure. Thiswork is a good example showing the potential of using sequencedata deposited in databases to answer important questions aboutAD microbiomes.The centrality of lactate cross-feeding in well-performinghydrogen producing reactors was illustrated by Detman et al.in the digestion of sugar-beet molasses in packed bed reactors.Optimal hydrogen production required a balance betweenhydrogen-producing bacteria (HPB), namely Clostridium,Ruminococcus and Prevotella and lactic acid bacteria (LAB), suchas Lactobacillus, Bifidobacterium, Leuconostoc, Streptococcus,and Lactococcus. Surveys of the ratio between HPB and LABreported in other hydrogen-producing microbial communitiesvalidated this conclusion. Intriguingly, Detman et al. found astrong correlation between Caproiciproducens and hydrogenproduction. Caproiciproducens, which was present at relativelyhigh abundance, includes species involved in caproic acidbiosynthesis from several electron donors, including lactate(Contreras-Dávila et al., 2020).The growth and activity of specific microorganisms as wellas the interaction between different microbial guilds may beseverely affected by the occurrence of antimicrobials in anaerobicdigesters. In their review article, Xiao et al. analyzed the impact ofantibiotics on fermentative bacteria and methanogenic archaeareporting both negative and positive effects at different levelsof the anaerobic digestion food chain. Authors reported therole of a range of antibiotics including macrolides, tetracyclines,β-lactams, and they also considered the impact of antibioticmixtures. Analysis of scientific literature allowed the authorsto summarize the influence of antibiotics on the anaerobicdigestion process and to delineate some general “rules” about theshort/long term effects, the duration of the bacteriostatic activityand the role of environmental factors in increasing or decreasingtheir impact.Kim et al. evaluated the effects of inoculum heat shock,pH, temperature and solids retention time (SRT) on anaerobicdigestion of waste activated sludge (WAS). They inferred the roleof individual microbial populations from the net growth ratesestimated using amass balance, which considered 16S rRNA geneabundance in the influent and effluent. A major strength of theapproach is that it could help discriminate populations that growactively and those that are introduced by immigration with thefeed sludge.We still lack a complete understanding of communityassembly that would allow us to move into the design offully active synthetic communities. It is conceivable that speciesdiversity and functional redundancy are critical to maintainstable process functioning. Meta-omic approaches are startingto uncover the numerous direct and indirect interactions thatoperate through networks of metabolic pathways. The newknowledge afforded by the articles in this topic represents anotherstep forward in the understanding of the role of key microbialplayers on performance, stability, and versatility of the anaerobicdigestion process.AUTHOR CONTRIBUTIONSAll authors contributed to the preparation of this editorial.ACKNOWLEDGMENTSWe would like to thank all authors for their valuablecontributions, and the reviewers for assuring the quality of thepapers in this Topic.REFERENCESCampanaro, S., Treu, L., Rodriguez, R., L. M., Kovalovszki, A., Ziels, R.M., Maus, I., et al. (2020). New insights from the biogas microbiomeby comprehensive genome-resolved metagenomics of nearly 1600 speciesoriginating from multiple anaerobic digesters. Biotechnol. Biofuels 13:25.doi: 10.1186/s13068-020-01679-yContreras-Dávila, C. A., Carrión, V. J., Vonk, V. R., Buisman, C. N., and Strik,D. P. (2020). Consecutive lactate formation and chain elongation to reduceexogenous chemicals input in repeated-batch food waste fermentation. WaterRes. 169:115215. doi: 10.1016/j.watres.2019.115215Nierychlo, M., Andersen, K. S., Xu, Y., Green, N., Jiang, C., Albertsen,M., et al. (2020). MiDAS 3: An ecosystem-specific reference database,taxonomy and knowledge platform for activated sludge and anaerobic digestersreveals species-level microbiome composition of activated sludge. Water Res.182:115955. doi: 10.1016/j.watres.2020.115955Petriglieri, F., Nierychlo, M., Nielsen, P. H., and McIlroy, S. J. (2018). In situvisualisation of the abundant Chloroflexi populations in full-scale anaerobicdigesters and the fate of immigrating species. PLoS ONE 13:e0206255.doi: 10.1371/journal.pone.0206255Conflict of Interest: The authors declare that the research was conducted in theabsence of any commercial or financial relationships that could be construed as apotential conflict of interest.Copyright © 2021 Erijman, Campanaro, Etchebehere and Varesche. This is an open-access article distributed under the terms of the Creative Commons AttributionLicense (CC BY). The use, distribution or reproduction in other forums is permitted,provided the original author(s) and the copyright owner(s) are credited and that theoriginal publication in this journal is cited, in accordance with accepted academicpractice. No use, distribution or reproduction is permitted which does not complywith these terms.Frontiers in Microbiology | www.frontiersin.org 2 May 2021 | Volume 12 | Article 664716

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Editorial: Meta-omic approaches to the complex anaerobic communities in wastewater treatment plants and digesters

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Erijman L.

Campanaro S.

Etchebehere C.

Varesche M. B. A.

Archivio istituzionale della ricerca - Università di Padova

Editorial: Meta-omic Approaches to the Complex Anaerobic Communities in Wastewater Treatment Plants and Digesters

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Editorial: Meta-omic Approaches to the Complex Anaerobic Communities in Wastewater Treatment Plants and Digesters

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