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IdTitle * Authors * Abstract * Picture * Thematic fields * RecommenderReviewersSubmission date
11 Aug 2023
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Comparison of enrichment methods for efficient nitrogen fixation on a biocathode

Toward a low-energy bioelectrochemical fixation of N2 via mixed cultures electroactive biofilms

Recommended by ORCID_LOGO based on reviews by 2 anonymous reviewers

Nitrogen fixation and elimination are two key microbial processes that significantly impact the release (and removal) of reactive nitrogen into natural ecosystems. Unlike global change, caused by the emission of greenhouse gasses into our atmosphere, the release of reactive nitrogen into our biosphere only recently (in the last years) received the necessary public attention. Hence, novel techniques for (1) reactive nitrogen recovery, (2) energy-effective removal, and (3) sustainable nitrogen fixation are essential to prevent the nitrogen cycle from spinning out of control without also putting an additional burden on our precious natural resources or increasing the emission of greenhouse gasses.

In this research paper by Rous et al. (2023), the authors investigated the use of a biocathode in a bioelectrochemical system (BES) for sustainable fixation of N2 into NH3, using electricity as a sustainable energy source and CO2 as the only carbon source. A critical element in their study was the enrichment of N2-fixating bacteria, starting from soil samples, in an effort to achieve effective nitrogen fixation. A comparison between the enriched culture and a pure culture of diazotrophic hydrogenotrophic bacteria confirmed comparable results for N2 fixation, indicating that the enrichment process was a viable and successful approach. Although pure culture biotechnological processes have their merits, it is clear that the usage of an enriched microbial culture allows for a more simple, robust, and open microbial process, compared to pure culture systems.

This approach does enable a sustainable way of N2 (and by extension CO2) fixation, as it relies on electricity directly (or indirectly through H2) and CO2 only, but it does suffer from low coulombic efficiencies (<5%). This indicates that, even though the results are promising, there is room for optimization, especially concerning the production of (unwanted) side products, such as acetate and other microbial metabolites. This reflects a key challenge and potential disadvantage of mixed or enriched cultures compared to pure cultures.

It is in that framework that this study provides an interesting, highly relevant view on the potential of bioelectrochemical nitrogen fixation using enriched cultures, yet, it also implies the need to either find a purpose for the byproducts, such as acetate, and/or achieve a more effective enrichment strategy to achieve an increased coulombic efficiency towards sustainable nitrogen fixation.

Reference

Rous A., Santa-Catalina G., Desmond-Le Quéméner E., Eric Trably E. and Nicolas Bernet N. (2023). Comparison of enrichment methods for efficient nitrogen fixation on a biocathode. bioRxiv, 2023.03.02.530809, ver 5, peer-reviewed and recommended by Peer Community in Microbiology. https://doi.org/10.1101/2023.03.02.530809

Comparison of enrichment methods for efficient nitrogen fixation on a biocathodeAxel Rous, Gaëlle Santa-Catalina, Elie Desmond-Le Quéméner, Eric Trably, Nicolas Bernet<p>The production of nitrogen fertilizers in modern agriculture is mostly based on the Haber-Bosch process, representing nearly 2% of the total energy consumed in the world. Low-energy bioelectrochemical fixation of N2 to microbial biomass was pre...Biofilms, microbial mats, Microbial biotechnology, Microbial ecology and environmental microbiologyJo De VriezeAnonymous, Anonymous2023-03-07 08:27:42 View
09 May 2023
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Interactions between Mycoplasma mycoides subsp. mycoides and bovine macrophages under physiological conditions

Interaction of bovine macrophages with Mycoplasma mycoides subsp. mycoides

Recommended by based on reviews by 2 anonymous reviewers

Mycoplasma mycoides subsp. mycoides (Mmm), a pathogenic wall-less bacterium, is the etiological agent of contagious bovine pleuropneumonia (CBPP). This highly contagious respiratory disease may develop in severe pneumonia, with associated high mortality rates in cattle. Mmm can display different immune evasion mechanisms; in addition, a host uncontrolled inflammatory response stands for lung lesions and chronic carrier animals.

Macrophages are among the most important lines of defense against Mmm of the lower respiratory tract. Although their importance in defense and immune response modulation is known, results about their role and mechanisms of action are scarce and sometimes conflicting.

In the present study, Totté et al. (1) aimed to investigate the interaction of bovine macrophages (isolated from cattle peripheral blood mononuclear cells) with Mmm, under in vitro conditions. The authors highlight that the study was performed under physiological conditions (in the presence of complement prepared from the same cell donor).

In their study, using different approaches, the authors provide interesting and original results, proposing a pivotal role of complement in controlling the inflammatory response, which is crucial in the CBPP pathogenesis. 

The authors reported that macrophages did not kill Mmm in the presence of a non-bactericidal concentration of bovine serum. However, Mmm inactivation was observed when antiserum from CBPP convalescent animals was used. They also observed that Mmm induced the production of TNF by macrophages (when a high MOI was assessed). However, complement could even abolish Mmm-induced TNF response when used at bactericidal activity concentrations. This role of complement could be combined with the development of potentially protective antibodies against particular Mmm antigens involved in the interaction with identified macrophage receptors to propose control strategies against CBPP. 

Overall, the study by Totté et al. provides new fundamental insight for the research on preventive or therapeutic strategies for a poorly understood disease that still represents a serious concern for livestock production. 

REFERENCES

1. Totté, P., Bonnefois, T., Manso-Silván, L. Interactions between Mycoplasma mycoides subsp. mycoides and bovine macrophages under physiological conditions. bioRxiv 2022.12.06.519279, ver. 2 peer-reviewed and recommended by Peer Community In Microbiology. https://doi.org/10.1101/2022.12.06.519279

Interactions between *Mycoplasma mycoides* subsp. *mycoides* and bovine macrophages under physiological conditionsPhilippe Totté, Tiffany Bonnefois, Lucia Manso-Silvan<p style="text-align: justify;">Abstract</p> <p>We investigated the interactions of unopsonized and opsonized *Mycoplasma mycoides* subsp. *mycoides* (Mmm) with bovine macrophages *in vitro*. Mmm survived and proliferated extracellularly on bovin...Microbe-microbe and microbe-host interactionsPablo ZuninoAnonymous, Anonymous2022-12-09 15:12:53 View
25 Apr 2023
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Genomic Changes During the Evolution of the Coxiella Genus Along the Parasitism-Mutualism Continuum.

Lifestyle transitions in endosymbiosis

Recommended by based on reviews by Sophie Abby, Adam Ossowicki and 1 anonymous reviewer

Host-microbe symbioses are an essential component of many ecological systems, playing critical roles in the physiology and evolution of all involved partners. In this context, the bacterial family that includes Coxiella burnetii, the causative agent of Q fever, is of particular interest. The Coxiellaceae family is a complex group with members that have adopted a variety of specializations. Closely related lineages to C. burnetii are tick mutualists (Coxiella-like endosymbionts) and aquatic bacteria that may include both free living and symbiotic species. Additionally, four related genera within this family include symbionts of insects and amoebae. Exactly how and when pathogenicity and mutualism evolved in this lineage is not clear, thus remaining a valuable line of enquiry that can help establish general principles on these lifestyle transitions.

A new study by Santos-Garcia and colleagues (2023) places the spotlight on this bacterial group, obtaining new insights through comparative genomics. The authors add two genomes, one of them a circular contig representing a highly reduced (0.9 Mb) chromosome, that increase the resolution of key branches in the Coxiella evolutionary tree. These include a sister group to C. burnetii and the group immediately subtending them, both entirely containing Coxiella-like endosymbionts. By analyzing genetic potential for metabolism, cell dimorphism, virulence and acidophily, the authors find evidence for the ancestrality of genes associated with a pathogenic lifestyle, and support a scenario by which mutualism arose multiple times in a parasitic lineage. In this context shines a pathogenicity island acquired in the common ancestor of this group and subsequently eroded in mutualistic lineages. This scenario highlights the importance of pre-adaptations that facilitate evolutionary specializations, such as the capabilities for B vitamin biosynthesis (key feature in the adaptation to a mutualistic relationship with organisms with B-vitamin-poor diets) and pH homeostasis (harnessed by C. burnetii for infection). 

Microbial groups at the crossroads of parasitism and mutualism help us understand the mechanisms underpinning these evolutionary strategies (see e.g. Drew et al, 2021). Transitions in endosymbiosis, including shifts in the parasitism-mutualism continuum, adaptation to new partners, or switches between free-living and host-associated lifestyles, affect the structure of ecological networks, and understanding them can yield crucial insights into how to manipulate microbial symbioses for health outcomes, sustainable agriculture or ecosystem conservation. The Coxiellaceae, by including a diverse set of mutualistic, parasitic and possibly free-living lineages, are a fantastic model group to tackle these questions. Together with other host-associated bacteria, such as Sodalis (Clayton et al, 2012) or Pantoea (Walterson and Stavrinides, 2015) species, these ecologically diverse microbes are valuable assets in the quest to decipher the molecular basis of lifestyle transitions in endosymbiosis.

REFERENCES

Clayton, A.L., et al (2012). A novel human-infection-derived bacterium provides insights into the evolutionary origins of mutualistic insect–bacterial symbioses. PLoS Genetics, 8: e1002990. https://doi.org/10.1371/journal.pgen.1002990

Drew, G.C., Stevens, E.J., King, K.C. (2021). Microbial evolution and transitions along the parasite-mutualist continuum. Nature Reviews Microbiology, 19: 623-638. https://doi.org/10.1038/s41579-021-00550-7

Santos-Garcia, D., et al. (2023) Genomic changes during the evolution of the Coxiella genus along the parasitism-mutualism continuum. bioRxiv, 2022.10.26.513839, ver. 4 peer-reviewed and recommended by Peer Community In Microbiology. https://doi.org/10.1101/2022.10.26.513839

Walterson, A.M., Stavrinides, J. (2015). Pantoea: insights into a highly versatile and diverse genus within the Enterobacteriaceae. FEMS Microbiology Reviews, 39: 968-984. https://doi.org/10.1093/femsre/fuv027

Genomic Changes During the Evolution of the Coxiella Genus Along the Parasitism-Mutualism Continuum.Diego Santos-Garcia, Olivier Morel, Hélène Henri, Adil El Filali, Marie Buysse, Valérie Noël, Karen D. McCoy, Yuval Gottlieb, Lisa Klasson, Lionel Zenner, Olivier Duron, Fabrice Vavre<p style="text-align: justify;">The Coxiellaceae family is composed of five genera showing lifestyles ranging from free-living to symbiosis. Among them, <em>Coxiella burnetii </em>is a well-known pathogen causing Q fever in humans. This bacterium ...Bioinformatics dedicated to microbial studies, Genomic and evolutionary studies, Microbe-microbe and microbe-host interactions, Microbial symbiosisDaniel Tamarit2022-10-27 12:55:14 View
02 Mar 2023
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Comparative genomics and transcriptomic response to root exudates of six rice root-associated Burkholderia sensu lato species

Burkholderia strains go it alone

Recommended by ORCID_LOGO based on reviews by Vittorio Venturi and 1 anonymous reviewer

The Burkholderia sensu lato group is predominant in the rhizosphere of rice. It includes both plant growth promoting rhizobacteria (typically members of the Paraburkholderia genus) and phytopathogens (typically members of the Burkholderia genus). Better understanding the interaction between Burkholderia sensu lato and their host plant is therefore crucial to advance our knowledge of the ecology of rice, a plant that feeds more than half of the humans on the planet.

The perception of root exudates from their host is key for rhizobacteria. Is the response to root exudates more related to the phylogeny of the bacteria, i.e. genus-dependent, or is it strain-specific? This question is not trivial for the Burkholderia sensu lato group, which has experienced shifting outlines over the last twenty years. During the early stages of rice root colonization, Wallner et al. [1] investigated the transcriptomic regulation of three strains of each Burkholderia and Paraburkholderia genera, in addition to a genomic comparison, in order to better understand their early colonization strategies. 

While these six strains possess a large proportion of gene homologues, their experiment shows their response to root exudates to be strain-specific. In the study, rice root exudates affected several metabolic pathways of interest in most strains, noticeably including i) the Entner-Doudoroff pathway, which had never been reported to be activated in relation to root colonization and ii) the putrescine pathway, which may reflect signaling controlling root colonization. 

The work by Wallner et al. provides new insights on the strain-level response of the transcriptomic regulation of Burkholderia sensu lato in response to root exudates in the early stages of root colonization. Beyond this, the next steps will hopefully shed light on what happens in more complex environments, within a complex bacterial community and during later colonization stages.

 

Reference

Wallner A, Klonowska A, Guigard L, King E, Rimbault I, Ngonkeu E, Nguyen P, Béna G, Moulin L (2022) Comparative genomics and transcriptomic response to root exudates of six rice root-associated Burkholderia sensu lato species. BioRxiv, 2022.10.04.510755, version 2 peer-reviewed and recommended by PCI Microbiol. https://doi.org/10.1101/2022.10.04.510755

Comparative genomics and transcriptomic response to root exudates of six rice root-associated Burkholderia sensu lato speciesAdrian Wallner, Agnieszka Klonowska, Ludivine Guigard, Isabelle Rimbault, Eddy LM Ngonkeu, Phuong V Nguyen, Gilles Bena, Lionel Moulin<p>Beyond being a reliable nutrient provider, some bacteria will perceive the plant as a potential host and undertake root colonization leading to mutualistic or parasitic interactions. Bacteria of the <em>Burkholderia</em> and <em>Paraburkholderi...Microbe-microbe and microbe-host interactions, Microbial symbiosisRomain Barnard Kateryna Zhalnina , Trent Northern , Oscar Kuipers , Cara Haney , Joëlle Schläpfer , Vittorio Venturi, Anonymous, Steffen Kolb, Paulina Estrada-de los Santos 2022-10-06 09:48:59 View