EAM highlights in FEMS 2023: from the Petri dish to planet Earth

Abstract On 9–13 July 2023, the 10th FEMS Congress took place in Hamburg, Germany. As part of this major event in European microbiology, the European Academy of Microbiology (EAM) organized two full sessions. One of these sessions aimed to highlight the research of four recently elected EAM fellows and saw presentations on bacterial group behaviours and development of resistance to antibiotics, as well as on new RNA viruses including bacteriophages and giant viruses of amoebae. The other session included five frontline environmental microbiologists who showcased real-world examples of how human activities have disrupted the balance in microbial ecosystems, not just to assess the current situation but also to explore fresh approaches for coping with external disturbances. Both sessions were very well attended, and no doubt helped to gain the EAM and its fellows more visibility.

The European Academy of Microbiology (EAM) was founded by the Feder ation of Eur opean Micr obiological Societies (FEMS) and consists of a distinguished panel of esteemed experts in the field of microbiology.One major element of the EAM's mission is to enhance the visibility and prominence of microbiology itself, as well as of the leading European researchers in this field.This overarching goal is centred on advancing excellence in microbiology across both the European landscape and the global stage.To fulfil this mission, the EAM employs targeted programms and initiatives designed to push the boundaries of the discipline, while also ensuring effective communication of these endeavours to scientists , stakeholders , and the public.
At the 10th FEMS Congress of European Microbiologists (FEMS2023), the EAM organized and held two sessions, one organized and c hair ed by EAM Pr esident Jör g Vogel (Würzbur g, Germany), the other by EAM Executive Board member Victor de Lorenzo (Madrid, Spain).

Session with highlights from the EAM
The EAM curr entl y is 160 fellows str ong.Ne w fellows ar e elected e v ery other year, through a structured process that involves external nomination and a v ote b y all fellows .T he purpose of the first session, 2 hours long, was to highlight the breadth of r esearc h of r ecentl y elected fellows.To this end, EAM President Jörg Vogel, invited fellows from four different countries to present an overview of their recent and ongoing research, that is, Ines Mandic-Mulec (Slovenia, elected 2022), Uri Gophna (Israel, 2017), Chantal Abergel (France, 2017), and Csaba Pal (Hungary, 2017) (Fig. 1 ).
The session was kicked off by Ines Mandic-Mulec, who is a Professor of Microbiology and currently serves as the Vice-dean of the Department of Microbiology at the Biotechnical Faculty of the University of Ljubljana, Slovenia.Her laboratory has had a strong interest in molecular mechanisms , consequences , and evolution of bacterial group beha viours .In her presentation, she focused on kinship-dependent social behaviours as observed with the model soil-dwelling bacterium, Bacillus subtilis , which nicely illustrated that and how microbes can be social organisms.One of her experimental a ppr oac hes is to look for kinship-dependent differential behaviours within the same species, using bacteria that were isolated from soil patches only a few meters apart.It was fascinating to see examples of v ery differ ent s warming beha viour: closely r elated swarms mer ge, in contr ast, less r elated swarms form a boundary at which killing occurs (Stefanic et al. 2015, Kraigher et al. 2022 ).She also pr esented r ecent r esults to suggest that swarm combat promotes horizontal gene transfer with a potential involvement of these bacteria's ability to respond to envelope stress (Stefanic et al. 2021 ).Lastl y, she discussed the r ole of so-called exploiters and whether kin discrimination occurs because it limits the spread of exploiters in evolved populations.
The second talk of the session was given by Uri Gophna, who is a Professor of Microbiology at the Faculty of Life Science, Tel Avi v Uni v ersity, Isr ael.While he br oadl y r esearc hes into micr oorganisms from all domains of life, he has r ecentl y made a big splash in the discovery of viruses of bacteria and archaea.In Hambur g, he pr esented two recent stories, the first of which is based on a large metatranscriptome study that has led to a multifold expansion of the microbial RNA virosphere (Neri 2022 ).Compared with their DN A counterparts, RN A viruses are much less understood with respect to their diversity and role in micr obial ecosystems, whic h is partl y due to a discov ery bias.Mining se v er al thousands of metatr anscriptomes fr om v arious envir onments, an international collabor ation led by Gophna established an extensive catalogue of RNA virus genomes .T his catalogue produced two new phyla, including one with new RNA phages .T he many newly predicted genes present not only exciting opportunities to better understand virus-host interactions but also potential new molecular tools for biotechnology.In his other story, yet unpublished, he showed fascinating observations with a lemon-shaped archaeal virus that infects Haloferax species and influences mating behaviour.Using RNA-seq, the laboratory is seeking to le v er a ge tr anscriptome-deriv ed information to understand how this virus alters the behaviour of virus-infected strains.
The third talk of the session continued on the theme of virus and was given by Chantal Abergel, who is a cofounder of the Structural and Genomic Information (IGS) laboratory at CNRS Marseille , France .Her laboratory combines bioinformatics with experimental biology.Here, she spoke about genome organization in giant viruses infecting Acanthamoeba.Starting with the original discovery of the giant mimivirus, whose genome turned out to be three times the size of the known large Chlorella virus (Raoult 2004 ), she sho w ed ho w the isolation of man y mor e envir onmental DNA viruses later produced more of a continuum such that ther e ar e man y eukaryotic viruses that possess genomes se v er al hundreds of kilobases and up to > 2.8 megabase in size .T he mimivirus virion is more like a Russian doll, with particles of highl y complex structur e in whic h genomic fibr e is interspersed with molecules of RNA pol ymer ase; an elegant supr amolecular or-ganization that ensures that the genome can be safely packaged but viral transcription can jump-start upon unwinding of these genomic fibres in the host cytoplasm (Fig. 2 ).This fine-grained pictur e has emer ged fr om the integr ation of div erse high-r esolution structural data, running the gamut from traditional X-ray crystallogr a phy to cryogenic electr on micr oscopy (cryoEM) and electron cryotomogr a phy (cryoET) (Villalta 2022 ).Puzzling observ ations r emain, for example the GMC oxidoreductase composing the genomic fibre is not essential its formation.Abergel concluded her talk by asking the pr ovocativ e question of why giant viruses such as the mimiviruses e volv ed in the first place.Is their gigantism just a consequence of an increasing functional redundancy in the viral world?
The session concluded with a talk by Csaba Pal, whose laboratory belongs to the Synthetic and Systems Biology Unit at the Biological Researc h Centr e in Szeged, Hungary.He ask ed k e y questions about the mechanisms and evolutionary path of resistance de v elopment for futur e antibiotics that ar e just being de v eloped.This is not a small question, as it takes a company > 20 years to make a profit from a new antibiotic.If resistance develops early after the start of use in the clinics, this will kill the ov er all inv estment, whic h can easily be in the range of a billion US dollars.Because studying antimicrobial resistance in the lab is a complex task, Pal has built a po w erful pipeline to assess resistance development (Apjok et al. 2023, Nyerges et al. 2018, Spohn et al. 2019 ), with a focus on Gr am-negativ e bacteria suc h as the concerning bugs Esc heric hia coli , Klebsiella spp., Pseudomonas aeruginosa , and Acinetobacter baumannii .Using his pipeline, he has discov er ed a substantial ov erla p in the molecular mec hanisms of r esistance a gainst clinically used and new antibiotics .T hese data will be important to come up with new combinations of antibiotics that will con-F igure 2. F rom left to right: Laura Zucconi, Rebecca Bärhle, Itzhak Mizrahi, Nicole Adam-Beyer, and Victor de Lorenzo.
tinue to work in the future and argue for more narrow-spectrum ther a py.He concluded his presentation by showing data on how resistance might change bacterial virulence, using the example of SPR206, a promising peptide antibiotics.Alarmingly, it appears that SPR206-resistant Klebsiella bacteria, which emerge rapidly after tr eatment, ar e also m uc h mor e virulent, pr esumabl y due to changes in their envelope stress pathwa y.T hus , resistance ma y select for hypervirulent bacteria, a situation that must be avoided in the clinics.

EAM symposium: microbial responses to envir onmental threa ts
The second scientific e v ent or ganized b y EAM w as the Symposium entitled Microbial Responses to Environmental Threats , with chair Victor de Lorenzo and speakers from four different countries (Fig. 2 ).The rationale and motivation behind the sequence of talks of this session were the presentation of several exemplary instances wher e anthr opogenic activities hav e had a serious impact on the homeostasis of existing microbial ecosystems-whether marine, terrestrial, or animal-associated.To this end, the expectation was not only a mere stocktaking of the state of affairs, but also gathering some insights on the metrics and technologies for monitoring micr obial comm unities, their composition and their variations upon external perturbations .Furthermore , the issue at stake was not only engaging in descriptions of the current picture (grim as they may look at the moment) but also entertaining forw ar dlooking prescriptions fuelled by contemporary Systems and Synthetic Biology.
The Symposium was opened by short talks of two early career scientists of the GEOMAR-Helmholtz Center for Ocean Research in Kiel, Germany.The first of them, Nicole Adam-Beyer, discussed the dynamics of microbial communities under seasonal hypoxia.This is an important issue, as human activities are modifying the oceanic environment rapidly and are causing ocean warming and deoxygenation, affecting biodiv ersity, pr oductivity, and biogeochemical cycling.She presented studies on the seasonally dynamic Boknis Eck time series station (SW Baltic Sea), where bottom waters annually fall hypoxic or anoxic after the summer months.Geoc hemical and micr obiological (16S rRNA-based) analyses of sediments were used to extrapolate how the benthic micr obial comm unities and the associated metabolic activities reflect rising temper atur es and deoxygenation.Based on these data, the localization of the microbial populations catalyzing sulphide and methane metabolisms seems to change to shallo w er sediment horizons following hypoxic e v ents and a shift from a primaril y or ganotr ophic to an (autotrophic) sulphide oxidizing regime w as observed (P erner et al. 2022 ).Continuous sampling campaigns will be used to further c har acterize the effects of hypoxic e v ents and enhanced microbial sulphide production in the Baltic Sea.
The second GEOMAR speaker, Rebecca Bährle, explained ongoing strategies for finding new carbon monoxide dehydrogenases (CODHs).These are superinteresting enzymes as the catalyze the reaction between carbon monoxide (CO) with water to carbon dioxide (CO 2 ) protons and two electrons-and therefore, these enzymes can help to convert the greenhouse gas CO 2 into valuable commodities.Bährle shared her strategies for detecting such activity in metagenomic libraries by means of a colorimetric scr eening a ppr oac h that detects oxidation of CO to CO 2 .Anoxic marine sediments appear to be a good hunting ground of bacteria carrying new catalysts of this sort.An interesting debate follo w ed on ho w suc h impr ov ed enzymesonce identified, cloned, and so on-could be deliv er ed at lar ge scale in either an industrial setting or a large environmental scenario.
These two starting pr esentations wer e followed by an amazing talk by Laura Zucconi from the University of Tuscia, Viterbo, Italy, on her long-time monitoring of soil communities in polar and alpine ecosystems hit by global warming.Remarkably, suc h envir onments ar e among the most endanger ed fr om climate change, making them hotspots for studies on the effects on soil ecosystems.Although heat-induced upw ar d plant migration has been well-documented in high altitude regions, the responses of the associated soil microbial communities has been ov erlooked.Of consider able inter est is the observ ation that at lo w er altitude, shrubland had the highest proportion of fungi, whic h was corr elated with higher amounts of enzymes for degrading biomass and recalcitrant plant biopolymers.Shrub encr oac hment may acceler ate higher r ecalcitr ant C decomposition and reduce total ecosystem C storage, increasing the efflux of CO 2 to the atmosphere with a positive feedback to w arming.Ho we v er differ ent studies in differ ent envir onments ar e pr oviding differ ent pictur es, ther efor e m ultidisciplinary studies, integr ating differ ent warming-sim ulation a ppr oac hes, ar e needed to giv e a clear picture of the responses of these ecosystems (D'Alò et al. 2021(D'Alò et al. , 2022 ) ).Instead, in Antarctica, the prediction is that climate change will lead to extinction of unique highly adapted taxa.The str ong corr elation of the comm unities' div ersity and composition with soil abiotic properties is of particular concern in the light of possible shifts of environmental conditions (Severgnini et al. 2021 ).
The issue of superfunctionalities of micr obial comm unities initiated by Laura was a perfect prologue of the presentation by Itzhak Mizr ahi fr om the Ben Gurion Univ ersity, Bershee v a, Israel.In an entirely different context, the subject in this case was unveiling the microbiome-metabolome interplay in a system as extr emel y complex as the rumen a distinct compartment in the bovine digestive tract.The rumen microbiome is responsible for the production of one of the most potent greenhouse gases , methane , and contributes about 18% of its total anthropogenic emissions.In this case, unlike soil and marine ecosystems, the physical container of the community is itself a contained, living scenario with its own properties and dynamics .T his adds one more screw turn to the technical challenge of solving metabolic interactions among all partners not just in terms of composition and biochemical transactions but also as influenced by the 3D organization of the bacterial consortia involv ed.In this r espect, the link between taxonomy and cellular/comm unity arc hitectur e, has been r ecentl y tac kled with cryoelectr on micr oscopy and tomogr a phy, enabling to decipher micr obial inter actions and phenotypes at the nanoscale r esolution (Tatli et al. 2022 ).These methods promise to become a phenomenal tool for addressing similar questions in other complex microbiomes.
Finall y, to tr ansition the Symposium's focus from description to prescription, Víctor de Lorenzo concluded the session by sharing his recent endeavours in the National Center of Biotechnology CSIC in Madrid.He highlighted ongoing efforts to harness the latest advancements in strain and community engineering, made possible by Synthetic Biology, for the purpose of extensive envir onmental bior emediation.He delv ed into the explor ation of an optimal bacterial c hassis, whic h could serve as the preferred plat-form for crafting designer live agents (de Lorenzo 2022 ).These agents would effectively and safely execute synthetically primed environmental activities on a large scale.As an example, he elaborated on the concept of ectopically expressing camel antibodies (nanobodies) on the surface of environmental bacteria, such as Pseudomonas putida.This a ppr oac h facilitates the formation of microbial skins on solid surfaces (Fraile et al. 2021 ) and the creation of more proficient catalytic communities.Ho w ever, realizing these a ppr oac hes at a lar ge scale necessitates addressing numerous knowledge gaps, developing robust dispersion models, and initiating a r ene wed societal and r egulatory discourse r egarding the contr olled r elease of engineer ed catal ysts into the environment.

Conclusion
Natur all y, eac h pr esentation of either Symposia w as succeeded b y a liv el y discussion among the participants, poised to yield fresh collaborations and experiments.In essence, each of the two EAM e v ents serv ed as a testament to some of the most interesting scientific questions of our time as well as a display of the top concerns of our era, while providing compelling evidence regarding the role and potential of microorganisms .T hese function as sensitive indicators of environmental shifts while also serving-by themselves of with some rational priming-as agents capable of dealing with the impacts of human activities on global health.