Search

To study the role of exoelectrogens within the trophic network of deep-sea hydrothermal vents, we performed successive subcultures of a hyperthermophilic community from a hydrothermal chimney sample on a mix of electron donors in a microbial fuel cell system. Electrode (the electron acceptor) was swapped every week to enable fresh development from spent media as inoculum. The MFC at 80 °C yielded maximum current production increasing from 159 to 247 mA m−2 over the subcultures. The experiments demonstrated direct production of electric current from acetate, pyruvate, and H2 and indirect production from yeast extract and peptone through the production of H2 and acetate from fermentation. The microorganisms found in on-electrode communities were mainly affiliated to exoelectrogenic Archaeoglobales and Thermococcales species, whereas in liquid media, the communities were mainly affiliated to fermentative Bacillales and Thermococcales species. The work shows interactions between fermentative microorganisms degrading complex organic matter into fermentation products that are then used by exoelectrogenic microorganisms oxidizing these reduced compounds while respiring on a conductive support. The results confirmed that with carbon cycling, the syntrophic relations between fermentative microorganisms and exoelectrogens could enable some microbes to survive as biofilm in extremely unstable conditions. [ABSTRACT FROM AUTHOR]

Bacteria often live in spatially structured groups such as biofilms. In these groups, cells can collectively generate gradients through the uptake and release of compounds. In turn, individual cells adapt their activities to the environment shaped by the whole group. Here, we studied how these processes can generate phenotypic variation in clonal populations and how this variation contributes to the resilience of the population to antibiotics. We grew two-dimensional populations of Escherichia coli in microfluidic chambers where limiting amounts of glucose were supplied from one side. We found that the collective metabolic activity of cells created microscale gradients where nutrient concentration varied over a few cell lengths. As a result, growth rates and gene expression levels varied strongly between neighbouring cells. Furthermore, we found evidence for a metabolic cross-feeding interaction between glucose-fermenting and acetate-respiring subpopulations. Finally, we found that subpopulations of cells were able to survive an antibiotic pulse that was lethal in well-mixed conditions, likely due to the presence of a slow-growing subpopulation. Our work shows that emergent metabolic gradients can have important consequences for the functionality of bacterial populations as they create opportunities for metabolic interactions and increase the populations' tolerance to environmental stressors. This article is part of a discussion meeting issue 'Single cell ecology'. [ABSTRACT FROM AUTHOR]

Oral supra- and subgingival biofilms are complex communities in which hundreds of bacteria, viruses, and fungi reside and interact. In these social environments, microbes compete and cooperate for resources, such as living space and nutrients. The metabolic activities of bacteria can transform their microenvironment and dynamically influence the fitness and growth of cohabitating organisms. Biofilm communities are temporally and spatially organized largely due to cell-to-cell communication, which promotes synergistic interactions. Metabolic interactions maintain biofilm homeostasis through mutualistic cross-feeding, metabolic syntrophy, and cross-respiration. These interactions include reciprocal metabolite exchanges that promote the growth of physiologically compatible bacteria, processive catabolism of complex substrates, and unidirectional interactions that are globally important for the polymicrobial community. Additionally, oral bacterial interactions can lead to detoxification of oxidative compounds, which will provide protection to the community at large. It has also been established that specific organisms provide terminal electron acceptors to partner species that result in a shift from fermentation to respiration, thus increasing ATP yields and improving fitness. Indeed, many interspecies relationships are multidimensional, and the net outcome can be spatially and temporally dependent. Cross-kingdom interactions also occur as oral yeast are antagonistic to some oral bacteria, while numerous mutualistic interactions contribute to yeast-bacterial colonization, fitness in the oral community, and the pathogenesis of caries. Consideration of this social environment reveals behaviors and phenotypes that are not apparent through the study of microbes in isolation. Here, we provide a comprehensive overview of the metabolic interactions that shape the oral microbial community. [ABSTRACT FROM AUTHOR]

Bacterial consortia are among the most basic units in the biodegradation of environmental pollutants. Pollutant-degrading strains frequently encounter different types of environmental stresses and must be able to survive with other bacteria present in the polluted environments. In this study, we proposed a noncontact interaction mode between a tetrahydrofuran (THF)-degrading strain, Rhodococcus ruber YYL, and a non-THF-degrading strain, Bacillus cereus MLY1. The metabolic interaction mechanism between strains YYL and MLY1 was explored through physiological and molecular studies and was further supported by the metabolic response profile of strain YYL, both monocultured and cocultured with strain MLY1 at the optimal pH (pH 8.3) and under pH stress (pH 7.0), through a liquid chromatographymass spectrometry-based metabolomic analysis. The results suggested that the coculture system resists pH stress in three ways: (i) strain MLY1 utilized acid metabolites and impacted the proportion of glutamine, resulting in an elevated intracellular pH of the system; (ii) strain MLY1 had the ability to degrade intermediates, thus alleviating the product inhibition of strain YYL; and (iii) strain MLY1 produced some essential micronutrients for strain YYL to aid the growth of this strain under pH stress, while strain YYL produced THF degradation intermediates for strain MLY1 as major nutrients. In addition, a metabolite cross-feeding interaction with respect to pollutant biodegradation is discussed. [ABSTRACT FROM AUTHOR]

Summary: Propionate is an important intermediate in the anaerobic mineralization of organic matter. In methanogenic environments, its degradation relies on syntrophic associations between syntrophic propionate‐oxidizing bacteria (SPOB) and Archaea. However, only 10 isolated species have been identified as SPOB so far. We report syntrophic propionate oxidation in thermophilic enrichments of Candidatus Syntrophosphaera thermopropionivorans, a novel representative of the candidate phylum Cloacimonetes. In enrichment culture, methane was produced from propionate, while Ca. S. thermopropionivorans contributed 63% to total bacterial cells. The draft genome of Ca. S. thermopropionivorans encodes genes for propionate oxidation via methymalonyl‐CoA. Phylogenetically, Ca. S. thermopropionivorans affiliates with the uncultured Cloacimonadaceae W5 and is more distantly related (86.4% 16S rRNA gene identity) to Ca. Cloacimonas acidaminovorans. Although Ca. S. thermopropionivorans was enriched from a thermophilic biogas reactor, Ca. Syntrophosphaera was in particular associated with mesophilic anaerobic digestion systems. 16S rRNA gene amplicon sequencng and a novel genus‐specific quantitative PCR assay consistently identified Ca. Syntrophosphaera/Cloacimonadaceae W5 in 9 of 12 tested full‐scale biogas reactors thereby outnumbering other SPOB such as Pelotomaculum, Smithella and Syntrophobacter. Taken together the ubiquity and abundance of Ca. Syntrophosphaera, those SPOB might be key players for syntrophic propionate metabolism that have been overlooked before. [ABSTRACT FROM AUTHOR]

An integrative pattern-process-mechanism approach is revealing the roles of biotic interactions in microbiome assembly. Patterns of microbiome diversity observed in metagenomic studies can be partly explained by interaction processes (e.g. competition, facilitation) and underlying molecular or genetic mechanisms (e.g. antibiotic production, nutrient cross-feeding). Exciting opportunities remain to fully understand the significance and generalizability of biotic interactions within microbiomes. Many microbial interactions have been studied by chasing easily quantifiable phenotypes including changes in growth or pigmentation, but it is likely that diverse cryptic interactions occur without obvious growth changes or macroscopic phenotypes. A narrow phylogenetic breadth of well-studied microbes limits our understanding of whether there are conserved genetic or molecular mechanisms of microbial interactions. Biotic interactions can impose strong selective pressures that could shape rates and modes of microbial evolution, but few studies have examined the evolutionary consequences of interactions within microbiomes. Continued exploration of the chemical and genetic mechanisms underlying biotic interactions may provide novel tools to manipulate and manage microbiomes. [ABSTRACT FROM AUTHOR]

Microbial electrosynthesis (MES) has been gaining considerable interest as the next step in the evolution of microbial electrochemical technologies. Understanding the niche biocathode environment and microbial community is critical for further developing this technology as the biocathode is key to product formation and efficiency. MES is generally operated to enrich a specific functional group (e.g., methanogens or homoacetogens) from a mixed-culture inoculum. However, due to differences in H2 and CO2 availability across the cathode surface, competition and syntrophy may lead to overall variability and significant beta-diversity within and between replicate reactors, which can affect performance reproducibility. Therefore, this study aimed to investigate the distribution and potential spatial variability of the microbial communities in MES methanogenic biocathodes. Triplicate methanogenic biocathodes were enriched in microbial electrolysis cells for 5 months at an applied voltage of 0.7 V. They were then transferred to triplicate dual-chambered MES reactors and operated at -1.0 V vs. Ag/AgCl for six batches. At the end of the experiment, triplicate samples were taken at different positions (top, center, bottom) from each biocathode for a total of nine samples for total biomass protein analysis and 16S rRNA gene amplicon sequencing. Microbial community analyses showed that the biocathodes were highly enriched with methanogens, especially the hydrogenotrophic methanogen family Methanobacteriaceae, Methanobacterium sp., and the mixotrophic Methanosarcina sp., with an overall core community representing > 97% of sequence reads in all samples. There was no statistically significant spatial variability (p > 0.05) observed in the distribution of these communities within and between the reactors. These results suggest deterministic community assembly and indicate the reproducibility of electromethanogenic biocathode communities, with implications for larger-scale reactors. [ABSTRACT FROM AUTHOR]

Syntrophy allows a microbial community as a whole to survive in an environment, even though individual microbes cannot. The metabolic interdependence typical of syntrophy is thought to arise from the accumulation of degenerative mutations during the sustained co-evolution of initially self-sufficient organisms. An alternative and underexplored possibility is that syntrophy can emerge spontaneously in communities of organisms that did not co-evolve. Here, we study this de novo origin of syntrophy using experimentally validated computational techniques to predict an organism’s viability from its metabolic reactions. We show that pairs of metabolisms that are randomly sampled from a large space of possible metabolism and viable on specific primary carbon sources often become viable on new carbon sources by exchanging metabolites. The same biochemical reactions that are required for viability on primary carbon sources also confer viability on novel carbon sources. Our observations highlight a new and important avenue for the emergence of metabolic adaptations and novel ecological interactions. [ABSTRACT FROM AUTHOR]

Beyond being simply positive or negative, beneficial or inhibitory, microbial interactions can involve a diverse set of mechanisms, dependencies and dynamical properties. These more nuanced features have been described in great detail for some specific types of interactions, (e.g. pairwise metabolic cross-feeding, quorum sensing or antibiotic killing), often with the use of quantitative measurements and insight derived from modeling. With a growing understanding of the composition and dynamics of complex microbial communities for human health and other applications, we face the challenge of integrating information about these different interactions into comprehensive quantitative frameworks. Here, we review the literature on a wide set of microbial interactions, and explore the potential value of a formal categorization based on multidimensional vectors of attributes. We propose that such an encoding can facilitate systematic, direct comparisons of interaction mechanisms and dependencies, and we discuss the relevance of an atlas of interactions for future modeling and rational design efforts. [ABSTRACT FROM AUTHOR]

Highlights • Resource allocation affects evolution of cooperation within microbial communities. • Presence of cheaters negatively impact the emergence of cooperation. • Cooperative behavioral differences emerge between passive and active transport system. Abstract Microbial communities that implement mutual cross-feeding are commonly observed in nature and with synthetic constructs in laboratory experiments. A mathematical model of competition in a chemostat is developed to investigate the role that resource allocation and transport of metabolites play in cooperation. The model contains four cell types that differ by whether they produce two, one, or none of two essential metabolites. Producing cell types may export these resources into the environment, and those that do not produce both metabolites must import the missing resource. The contribution to the emergence of a collaborative consortium of single resource producers from the transport rate of these metabolites and the type of transport used by the cell (active vs. passive) is studied. Multiple instances of bi-stability and tri-stability are observed, and the effect of the initial concentration of a non-cooperative cheater cell type on the final outcome of the competition is examined. When the cost of producing metabolites is introduced into the model, significant changes to the outcome of the competition are observed, including coexistence of multiple cell types. [ABSTRACT FROM AUTHOR]

Summary: Bacteria frequently engage in cross‐feeding interactions that involve an exchange of metabolites with other micro‐ or macroorganisms. The often obligate nature of these associations, however, hampers manipulative experiments, thus limiting our mechanistic understanding of the ecophysiological consequences that result for the organisms involved. Here we address this issue by taking advantage of a well‐characterized experimental model system, in which auxotrophic genotypes of E. coli derive essential amino acids from prototrophic donor cells using intercellular nanotubes. Surprisingly, donor–recipient cocultures revealed that the mere presence of auxotrophic genotypes was sufficient to increase amino acid production levels of several prototrophic donor genotypes. Our work is consistent with a scenario, in which interconnected auxotrophs withdraw amino acids from the cytoplasm of donor cells, which delays feedback inhibition of the corresponding amino acid biosynthetic pathway and, in this way, increases amino acid production levels. Our findings indicate that in newly established mutualistic associations, an intercellular regulation of exchanged metabolites can simply emerge from the architecture of the underlying biosynthetic pathways, rather than requiring the evolution of new regulatory mechanisms. [ABSTRACT FROM AUTHOR]

Highlights • Resource competition theory is used to examine the coexistence of species. • The mutualists can coexist through cross-feeding, without external nutrient supplies. • Cross-feeding allows the inferior macronutrient competitor to coexist with the superior one. • The cheater may trigger collapse of the system if it is uniformly superior on all resources. Abstract Mutualism, interspecific cooperation that yields reciprocal benefits, can promote species coexistence, enhancing biodiversity. As a specific form of mutualism, cross-feeding, where each of two mutualists produces a resource the other one needs, has been broadly studied. However, few theoretical studies have examined competition between cross-feeding mutualists and cheaters, who do not synthesize resources themselves. In this paper we study a model with two mutualists, a cheater, two micronutrients that are synthesized and exchanged by the mutualists, and one macronutrient that is only from external supply. We investigate the coexistence of the species in the framework of resource competition theory. In particular, we examine the effect of the mutualists' synthesis rates on their coexistence. In the absence of cheaters, multiple stable states occur if the synthesis rates are high, and higher synthesis rates increase the possibility that mutualists coexist. However, when the cheater is present, higher synthesis rates promote invasion by the cheater: If the cheater is superior on all three resources, it will either persist with at most one mutualist or even trigger extinction of all three species; if the cheater is only superior on the macronutrient, both mutualists may still coexist with the cheater. Our results provide a framework for further study on more complex mutualistic networks and real microbial communities. [ABSTRACT FROM AUTHOR]

Syntrophic microbial partnerships are found in many environments and play critical roles in wastewater treatment, global nutrient cycles, and gut systems. An important type of syntrophy for the anaerobic conversion of carboxylic acids is H2 syntrophy. In this type of microbial partnership, dissolved H2 is produced by a bacterium and rapidly consumed by an archeon (methanogen), resulting in methane gas. This is referred to as interspecies H2 transfer, and some conversions rely on this mechanism to become thermodynamically feasible. For this reason, syntrophic partners are often not possible to separate in the lab, which hampers the full understanding of their physiology. Bioelectrochemical systems (BESs) may show promise to ultimately separate and study the behavior of the syntrophic bacterium by employing an abiotic H2 oxidation reaction at the anode, actively removing dissolved H2. Here, we performed a proof-of-concept study to ascertain whether an H2-removing anode can: (1) provide a growth advantage for the syntrophic bacterium; and (2) compete with the methanogenic partner. A mathematical model was developed to design a BES to perform competition experiments. Indeed, the operated BES demonstrated the ability to provide a growth advantage to the syntrophic bacterium Syntrophus aciditrophicus compared to its methanogenic partner Methanospirillum hungatei when grown in co-culture. Further, the BES provided the never-before isolated Syntrophomonas zehnderi with a growth advantage compared to Methanobacterium formicicum. Our results demonstrate a potential to use this BES to enrich H2-sensitive syntrophic bacteria, and gives prospects for the development of an effective method for the separation of obligate syntrophs. [ABSTRACT FROM AUTHOR]

Plants nourish rhizospheric microbes via provision of carbon substrates, and the composition of the microbiome is strongly influenced by metabolic phenomena such as niche differentiation, competitive exclusion, and cross-feeding. Despite intensive investigations of the taxonomic structure in root microbiomes, there is relatively little biochemical knowledge of the metabolic niches occupied by microbial strains in the rhizosphere. Here, we review new tools and approaches that are boosting our knowledge of the metabolic mechanisms that shape the composition of the root microbiome. New studies have elucidated biochemical pathways that mediate root colonisation and pathogen suppression, and synthetic communities are emerging as a powerful tool to understand microbe–microbe interactions. Knowledge of root exudate composition is being advanced by new metabolomics methodologies, which have highlighted that specific exudate components can inhibit pathogen growth, and that certain metabolites can recruit mutualistic strains according to substrate uptake preferences. Microbial genomics is rapidly advancing, with large collections of isolated rhizosphere strains and mutant libraries giving new insights into the metabolic mechanisms of root colonisation. Exometabolomics is emerging as a powerful methodology for directly observing microbial uptake of root metabolites, and also for profiling microbial cross-feeding. Integrative studies using these resources should enable rapid advances, particularly when applied to standardised experimental set-ups and model synthetic communities. [ABSTRACT FROM AUTHOR]

Summary: Species interactions and coexistence are often dependent upon environmental conditions. When two cross‐feeding bacteria exchange essential nutrients, the addition of a cross‐fed nutrient to the environment can release one species from its dependence on the other. Previous studies suggest that continued coexistence depends on relative growth rates: coexistence is maintained if the slower‐growing species is released from its dependence on the other, but if the faster‐growing species is released, the slower‐growing species will be lost (a hypothesis that we call 'feed the faster grower' or FFG). Using invasion‐from‐rare experiments with two reciprocally cross‐feeding bacteria, genome‐scale metabolic modelling and classical ecological models, we explored the potential for coexistence when one cross‐feeder became independent. We found that whether nutrient addition shifted an interaction from mutualism to commensalism or parasitism depended on whether the nutrient that limited total growth was required by one or both species. Parasitism resulted when both species required the growth‐limiting resource. Importantly, coexistence was only lost when the interaction became parasitism, and the obligate species had a slower growth rate. Under these restricted conditions, the FFG hypothesis applied. Our results contribute to a mechanistic understanding of how resources can be manipulated to alter interactions and coexistence in microbial communities. [ABSTRACT FROM AUTHOR]

Anaerobic digestion (AD) is a biological process that employs anaerobic microorganisms to degrade organic material, yielding biogas and biofertilizers. Understanding quorum sensing (QS) signaling in mixed microbial systems provides valuable insights into microbial behavior and functions. This review aims to examine recent studies on the roles of QS and QQ in the AD processes. A QS signal molecule, N -acyl homoserine lactone (AHL), induce the production of extraceluller polymers, promoting biofilm formation and bacterial aggregation, thereby the efficiency of AD process. QS-assisted granule formation fosters syntrophy between acetogens and methanogens, leading to increased organic removal and methane production. Specific AHLs were shown to be correlated with the abundance of hydrolytic bacteria and acidogens, further benefiting methane production. QQ was shown to effectively control membrane fouling in anaerobic membrane bioreactors, yet its impact on methane productivity remains unclear. This review shed lights on the existing literature gaps regarding the mechanisms of QS and QQ in AD systems, which will play a vital role in advancing AD applications in the future. [ABSTRACT FROM AUTHOR]

Microbial interactions play an important role in regulating the metabolic function of fermented food communities, especially the production of key flavor compounds. However, little is known about specific molecular mechanisms that regulate the production of key flavor compounds through microbial interactions. Here, we designed a synthetic consortium containing Debaryomyces hansenii D1, Staphylococcus xylosus S1, and Pediococcus pentosaceus PP1 to explore the mechanism of the microbial interactions underlying the branched-chain aldehydes production. In this consortium, firstly, D. hansenii secreted amino acids that promoted the growth of P. pentosaceus and S. xylosus. Specifically, D. hansenii D1 secreted alanine, aspartate, glutamate, glutamine, glycine, phenylalanine, serine, and threonine, which were the primary nutrients for bacterial growth. P. pentosaceus PP1 utilized all these eight amino acids through cross-feeding, whereas S. xylosus S1 did not utilize aspartate and serine. Furthermore, D. hansenii D1 promoted the production of branched-chain aldehydes from S. xylosus and P. pentosaceus through cross-feeding of α-keto acids (intermediate metabolites). Thus, the accumulation of 2-methyl-butanal was promoted in all co-culture. Overall, this work revealed the mechanism by which D. hansenii and bacteria cross-feed to produce branched-chain aldehydes in fermented sausages. • There is cross-feeding of amino acids and α-keto acids between S. xylosus S1 and P. pentosaceus PP1 with D. hansenii D1. • The amino acids provided by D. hansenii D1 are the primary growth-promoting nutrients of bacterial growth. • The co-culture of D. hansenii D1 and bacteria enhanced branched chain aldehydes production by α-keto acids cross-feeding. • D. hansenii D1 could convert branched-chain aldehydes, especially 3-methyl-butanal, to the corresponding alcohols. [ABSTRACT FROM AUTHOR]

Although partial denitrification coupled with the anammox process has received considerable attention, the partial denitrification function of companion bacteria in mixotrophic anammox systems remains experimentally investigated. Herein, a partial denitrification process was realized in mixotrophic anammox systems with a COD/TN ratio of 0.75. Furthermore, the experimental verification results revealed that nitrate and ammonia were eliminated concurrently, showing that partial denitrifying bacteria were present in the mixotrophic anammox systems. Denitratisoma and Norank Xanthobacteraceae were the dominant genera of companion bacteria containing functional genes related to partial denitrification. Especially, Denitratisoma was a companion bifunctional bacterium for Candidatus Kuenenia shifted between complete and partial denitrification at different COD/TN ratios. Moreover, nir gene abundance in the mixotrophic anammox system increased by 135.4 % compared to that in the autotrophic anammox system. In contrast, nor gene abundance decreased by 28.00 %, indicating that NO might be used as a medium for cross-feeding anammox and partial denitrification. This study provides a more thorough understanding of companion bacteria in mixotrophic anammox systems. [Display omitted] • Companion partial denitrifying bacteria existed in mixotrophic anammox systems. • Removal efficiency of TN was 98.91 ± 0.60 % with a COD/TN ratio of 0.75. • Norank Xanthobacteraceae was a dominant genus related to partial denitrification. • Denitratisoma was a companion bifunctional bacterium for Candidatus Kuenenia. • Partial denitrifying bacteria exhibited NO cross-feeding with anammox bacteria. [ABSTRACT FROM AUTHOR]

[Display omitted] • Reactor performance was independent of the relative abundance of anammox bacteria. • The overall migration of microbes from flocs to biofilm was verified. • Microbial interactions were vital to sludge proliferation and biofilm formation. • Acetate and glycogen produced by AnAOB act as key substrates for cross-feeding. Two mature anaerobic ammonium oxidation (anammox) consortia with high/low relative abundance of anammox bacteria were inoculated for the rapid sludge proliferation and biofilm formation in this study, named up-flow anaerobic sludge blanket reactor (UASB1) (high) and UASB2 (low), respectively. Results showed that the nitrogen removal efficiency of UASB2 reached 90.94% after the 120-day operation, which was 13% higher than that of UASB1. Moreover, its biomass amounts were 22.18% (biofilm) and 40.96% (flocs) higher than that of UASB1, respectively. Ca. Kuenenia possessed relative abundances of 29.32% (flocs), 27.42% (biofilm) and 31.56% (flocs), 35.20% (biofilm) in the UASB1 and UASB2, respectively. The relative abundances of genes involved in anammox transformation (hzs , nir) and carbon metabolism (fdh , lgA/B/C , acs) were higher in the UASB2, indicating that Ca. Kuenenia might produce acetate and glycogen to enhance microbial interactions. These findings emphasized the importance of microbial interactions in anammox sludge proliferation and biofilm formation. [ABSTRACT FROM AUTHOR]

A model for competition between bacterial strains in a chemostat is studied using a model reduction argument and phase portrait analysis for the specific case of trophic chain. The first strain feeds on glucose but secretes a metabolic intermediate (acetate), which the second strain consumes. However, the metabolic intermediate imposes a cost to growth to both strains. The geometric and asymptotic analysis of the reduced model allows a rigourous treatment of the role of this assumption in the emergence of coexistence (cross‐feeding) equilibria. Conditions for non‐existence of cross‐feeding equilibria are given for certain parameter ranges. In the case of trophic chains, existence of cross‐feeding equilibria does not rely only on the presence of the acetate specialist scavenging for the intermediate metabolite inside the resource‐limited chemostat environment. The glucose specialist must, in addition, possess a certain degree of tolerance to the metabolic intermediate. Relaxing the assumption of the cost of growth helps establish a cross‐feeding equilibrium. [ABSTRACT FROM AUTHOR]

Mutualisms are essential for life, yet it is unclear how they arise. A two-stage process has been proposed for the evolution of mutualisms that involve exchanges of two costly resources. First, costly provisioning by one species may be selected for if that species gains a benefit from costless byproducts generated by a second species, and cooperators get disproportionate access to byproducts. Selection could then drive the second species to provide costly resources in return. Previously, a synthetic consortium evolved the first stage of this scenario: Salmonella enterica evolved costly production of methionine in exchange for costless carbon byproducts generated by an auxotrophic Escherichia coli. Growth on agar plates localized the benefits of cooperation around methionine-secreting S. enterica. Here, we report that further evolution of these partners on plates led to hypercooperative E. coli that secrete the sugar galactose. Sugar secretion arose repeatedly across replicate communities and is costly to E. coli producers, but enhances the growth of S. enterica. The tradeoff between individual costs and group benefits led to maintenance of both cooperative and efficient E. coli genotypes in this spatially structured environment. This study provides an experimental example of de novo, bidirectional costly mutualism evolving from byproduct consumption. The results validate the plausibility of costly cooperation emerging from initially costless exchange, a scenario widely used to explain the origin of the mutualistic species interactions that are central to life on Earth. [ABSTRACT FROM AUTHOR]

Bicarbonate (HCO 3 − ) has been extensively researched as a buffer in anaerobic digestion. The effect of HCO 3 − concentration on syntrophic butyrate oxidation process was evaluated by batch culturing of anaerobic activated sludge, and the mechanism was further revealed by the changes of Gibbs free energy (Δ G ) and the interspecies transfers of electron and proton. The results showed that butyrate degradation rate was enhanced by 32.07% when the supplement of HCO 3 − increased from 0 to 0.20 mol/L. However, methane production and acetate degradation were strongly inhibited by HCO 3 − more than 0.10 mol/L. More function of HCO 3 − was found as 1) decreasing the Δ G of syntrophic methanogenesis of butyrate while increasing the Δ G of methanogenesis of acetate, 2) enriching M. harundinacea and M. concilii , 3) increasing the diffusion rate of protons between the syntrophic consortia. This work would increase the anaerobic digestion efficiency by enhancing the interaction of the syntrophic consortia. [ABSTRACT FROM AUTHOR]

Cooperative cross-feeding, a resource-exchange mutualism between microbes, is ubiquitous; however, models suggest it should be susceptible to cheating. Recent work suggested two novel mechanisms that could allow cross-feeders to exclude cheaters, even in the absence of tight coupling between cooperative organisms. The first is pattern formation, where cross-feeders form regular patterns so that their resources are separated and cheaters cannot obtain both. The second mechanism is neighbor uncertainty, where demographic stochasticity separates resources so cheaters cannot obtain both. Here we use a stochastic spatial model to test whether those mechanisms are evolutionarily stable, or whether they will collapse under gradual evolution towards reduced resource production. The answer depends on whether a microbe can make the resource for itself without sharing it. If it cannot (i.e. if producing more of a resource means sharing more of a resource), then both mechanisms continue to function. In this case, resource production directly benefits the individual, and cooperation is a byproduct. If microbes can make the resource without sharing it (i.e. if production is an altruistic trait), then neighbor uncertainty completely fails, and pattern formation is weakened. In this case, the costly trait has no direct benefit to the individual, and can only persist if cooperative organisms become associated with their partner. Thus, the novel mechanisms, which operate without tight associations, falter. These results have implications for synthetic ecology, as they suggest that how cross-feeding is engineered will impact its evolutionary stability. [ABSTRACT FROM AUTHOR]

Abstract In this study, we have investigated for the first time the metabolism of E. coli grown on agar using 13C metabolic flux analysis (13C-MFA). To date, all 13C-MFA studies on microbes have been performed with cells grown in liquid culture. Here, we extend the scope of 13C-MFA to biological systems where cells are grown in dense microbial colonies. First, we identified new optimal 13C tracers to quantify fluxes in systems where the acetate yield cannot be easily measured. We determined that three parallel labeling experiments with the tracers [1,2–13C]glucose, [1,6–13C]glucose, and [4,5,6–13C]glucose permit precise estimation of not only intracellular fluxes, but also of the amount of acetate produced from glucose. Parallel labeling experiments were then performed with wild-type E. coli and E. coli Δ ackA grown in liquid culture and on agar plates. Initial attempts to fit the labeling data from wild-type E. coli grown on agar did not produce a statistically acceptable fit. To resolve this issue, we employed the recently developed co-culture 13C-MFA approach, where two E. coli subpopulations were defined in the model that engaged in metabolite cross-feeding. The flux results identified two distinct E. coli cell populations, a dominant cell population (92% of cells) that metabolized glucose via conventional metabolic pathways and secreted a large amount of acetate (~40% of maximum theoretical yield), and a second smaller cell population (8% of cells) that consumed the secreted acetate without any glucose influx. These experimental results are in good agreement with recent theoretical simulations. Importantly, this study provides a solid foundation for future investigations of a wide range of problems involving microbial biofilms that are of great interest in biotechnology, ecology and medicine, where metabolite cross-feeding between cell populations is a core feature of the communities. Graphical abstract fx1 Highlights • Metabolism of E. coli grown on agar was investigated using 13C metabolic flux analysis. • Optimal tracers for 13C-MFA are [1,2–13C]glucose, [1,6–13C]glucose, and [4,5,6–13C]glucose. • Within E. coli colonies two subpopulations emerge that engage in acetate cross-feeding. • The dominant cell population converts 40% of consumed glucose into secreted acetate. • The second smaller E. coli population utilizes acetate as the only carbon source. [ABSTRACT FROM AUTHOR]

The quest to understand and subsequently improve the role played by bacteria and archaea in the degradation of organic matter both in natural and engineered anaerobic ecosystems has intensified the utilization of nanoparticles. Microbial communities are known to syntrophically cooperate during the anaerobic conversion of substrates into methane gas via the direct exchange of electrons. In this study, the role of hematite (Fe2O3—750 mg/L) and multi-walled carbon nanotubes (MWCNTs—1500 mg/L) during the degradation of beet sugar industrial wastewater (BSIW) in a batch experiment was investigated. Hematite and MWCNTs enhanced methane gas generation by 35 and 20%, respectively. Furthermore, microbial syntrophic communities might have exchanged metabolic electrons more directly, with hematite and MWCNTs serving as electron conduits between the homoacetogens and methanogens, thereby establishing a direct interspecies electron transfer (DIET) pathway. Additionally, hematite and MWCNTs enriched the bacteria Firmicutes while Chloroflexi reduced in abundance. Scanning electron microscopy and confocal laser scanning microscopy demonstrated that extracellular polymeric substances had noticeable interactions with both hematite and MWCNTs. Our findings provide vital information for more understanding of the response of microbes to hematite and MWCNTs in a complex natural environment. [ABSTRACT FROM AUTHOR]

Nitrate is considered as a contamination since it’s over discharging to water incurs environmental problems. However, nitrate is an ideal electron sink for anaerobic pollutant degraders desiring electron acceptors due to the high redox potential. Unfortunately, not all degraders can directly reduce nitrate, and the anaerobic direct interspecies electron transfer (DIET) between degraders and denitrifiers has not been confirmed yet. Here we demonstrated that syntrophic growth of Geobacter sulfurreducens PCA with denitrifying microbial community at anaerobic condition eliminated the lag phase of 15 h and improved the denitrification rate by 13∼51% over a broad C/N ratio of 0.5 to 9. Quantitative PCR revealed that G. sulfurreducens selectively enhanced the expression of nirS coding for a cytochrome cd1-nitrite reductase, resulting in a fast and more complete denitrification. Geobacter also selectively enriched its potential denitrifying partners – Diaphorobacter, Delftia, and Shinella – to form spherical aggregates. More studies of the binary culture system need to be carried out to confirm the syntrophic mechanism of Geobacter and denitrifiers in the future. These findings extend our knowledge on understanding the anaerobic bacterial interspecies electron transfer in the denitrification process, which has broader implications in fast selection and stabilization of denitrifiers in wastewater treatment plant, and general understanding of ecology for nitrogen and metal cycling. [ABSTRACT FROM AUTHOR]

Microbial syntrophy is a thermodynamically-based cooperation between microbial partners that share the small amounts of free energy for anaerobic growth. To gain insights into the mechanism by which syntrophic microorganisms coordinate their metabolism, we constructed cocultures of propionate-oxidizing Pelotomaculum thermopropionicum and hydrogenotrophic Methanocella conradii and compared them to monocultures. Transcriptome analysis was performed on these cultures using strand-specific mRNA sequencing (RNA-Seq). The results showed that in coculture both P. thermopropionicum and M. conradii significantly upregulated the expression of genes involved in catabolism but downregulated those for anabolic biosynthesis. Specifically, genes coding for the methylmalonyl-CoA pathway in P. thermopropionicum and key genes for methanogenesis in M. conradii were substantially upregulated in coculture compared to monoculture. The putative flavin-based electron bifurcation/confurcation systems in both organisms were also upregulated in coculture. Formate dehydrogenase encoding genes in both organisms were markedly upregulated, indicating that formate was produced and utilized by P. thermopropionicum and M. conradii, respectively. The inhibition of syntrophic activity by formate and 2-bromoethanesulphonate (2-BES) but not H2/CO2 also suggested that formate production was used by P. thermopropionicum for the recycling of intracellular redox mediators. Finally, flagellum-induced signal transduction and amino acids exchange was upregulated for syntrophic interactions. Together, our study suggests that syntrophic organisms employ multiple strategies including global metabolic shift, utilization of electron bifurcation/confurcation and employing formate as an alternate electron carrier to optimize their metabolisms for syntrophic growth. [ABSTRACT FROM AUTHOR]

Literature covered: early 2000s to late 2017 Bacteria frequently exchange metabolites with other micro- and macro-organisms. In these often obligate cross-feeding interactions, primary metabolites such as vitamins, amino acids, nucleotides, or growth factors are exchanged. The widespread distribution of this type of metabolic interactions, however, is at odds with evolutionary theory: why should an organism invest costly resources to benefit other individuals rather than using these metabolites to maximize its own fitness? Recent empirical work has shown that bacterial genotypes can significantly benefit from trading metabolites with other bacteria relative to cells not engaging in such interactions. Here, we will provide a comprehensive overview over the ecological factors and evolutionary mechanisms that have been identified to explain the evolution and maintenance of metabolic mutualisms among microorganisms. Furthermore, we will highlight general principles that underlie the adaptive evolution of interconnected microbial metabolic networks as well as the evolutionary consequences that result for cells living in such communities. [ABSTRACT FROM AUTHOR]

Resource scarcity is a common stress in nature and has a major impact on microbial physiology. This review highlights microbial acclimations to resource scarcity, focusing on resource investment strategies for chemoheterotrophs from the molecular level to the pathway level. Competitive resource allocation strategies often lead to a phenotype known as overflow metabolism; the resulting overflow byproducts can stabilize cooperative interactions in microbial communities and can lead to cross-feeding consortia. These consortia can exhibit emergent properties such as enhanced resource usage and biomass productivity. The literature distilled here draws parallels between in silico and laboratory studies and ties them together with ecological theories to better understand microbial stress responses and mutualistic consortia functioning. [ABSTRACT FROM AUTHOR]

Common mycorrhizal networks (CMNs) formed by arbuscular mycorrhizal fungi (AMF) interconnect plants of the same and/or different species, redistributing nutrients and draining carbon (C) from the different plant partners at different rates. Here, we conducted a plant co-existence (intercropping) experiment testing the role of AMF in resource sharing and exploitation by simplified plant communities composed of two congeneric grass species (Panicum spp.) with different photosynthetic metabolism types (C3 or C4). The grasses had spatially separated rooting zones, conjoined through a root-free (but AMF-accessible) zone added with 15N-labeled plant (clover) residues. The plants were grown under two different temperature regimes: high temperature (36/32 °C day/night) or ambient temperature (25/21 °C day/night) applied over 49 days after an initial period of 26 days at ambient temperature. We made use of the distinct C-isotopic composition of the two plant species sharing the same CMN (composed of a synthetic AMF community of five fungal genera) to estimate if the CMN was or was not fed preferentially under the specific environmental conditions by one or the other plant species. Using the C-isotopic composition of AMF-specific fatty acid (C16:1ω5) in roots and in the potting substrate harboring the extraradical AMF hyphae, we found that the C3-Panicum continued feeding the CMN at both temperatures with a significant and invariable share of C resources. This was surprising because the growth of the C3 plants was more susceptible to high temperature than that of the C4 plants and the C3-Panicum alone suppressed abundance of the AMF (particularly Funneliformis sp.) in its roots due to the elevated temperature. Moreover, elevated temperature induced a shift in competition for nitrogen between the two plant species in favor of the C4-Panicum, as demonstrated by significantly lower 15N yields of the C3-Panicum but higher 15N yields of the C4-Panicum at elevated as compared to ambient temperature. Although the development of CMN (particularly of the dominant Rhizophagus and Funneliformis spp.) was somewhat reduced under high temperature, plant P uptake benefits due to AMF inoculation remained well visible under both temperature regimes, though without imminent impact on plant biomass production that actually decreased due to inoculation with AMF. [ABSTRACT FROM AUTHOR]

Bifidobacteria represent one of the first colonizers of the mammalian gut, where such colonization is facilitated by their saccharolytic capabilities. Genomic analyses of bifidobacteria have revealed intriguing genetic strategies employed by these bacteria to access a variety of dietary and host-produced glycans. Bifidobacterial genome evolution therefore represents a fascinating example of how their chromosomes were molded to contain a large number of genes involved in carbohydrate metabolism. One of the reasons as to why bifidobacteria are such dominant and prevalent members of the (early) microbiota is that they may access glycans in the gut through mutualistic cross-feeding or resource-sharing activities, which is indicative of ‘social behavior’ among bifidobacterial strains. [ABSTRACT FROM AUTHOR]

The origin of mitochondria was a major evolutionary transition leading to eukaryotes and is a hotly debated issue. It is unknown whether mitochondria were acquired early or late and whether it was captured via phagocytosis or syntrophic integration. We present dynamical models to directly simulate the emergence of mitochondria in an ecoevolutionary context. Our results show that regulated farming of prey bacteria and delayed digestion can facilitate the establishment of stable endosymbiosis if prey-rich and prey-poor periods alternate. Stable endosymbiosis emerges without assuming any initial metabolic benefit provided by the engulfed partner, in a wide range of parameters, despite that during good periods farming is costly. Our approach lends support to the appearance of mitochondria before any metabolic coupling has emerged, but after the evolution of primitive phagocytosis by the urkaryote. [ABSTRACT FROM AUTHOR]

Granule-based partial denitrification and anammox (PDA) process is affected by microbial community. To reveal how the nitrogen conversion rate varies with microbial composition caused by the granule size, PDA granules were divided into five sizes (<0.2, 0.2–0.5, 0.5–0.9, 0.9–1.6, and 1.6–2.0 mm). The abundance of anammox bacteria (dominated by Candidatus Brocadia) increased with particle size and peaked at 14.6% for 0.9–1.6 mm. In contrast, the abundance of denitrifiers (dominated by Thauera) decreased from 83.3% to 23.5% when granule size increased from <0.2 mm to 0.5–0.9 mm, but increased to 48.1% with further increases in particle size to 1.6–2.0 mm. The nitrogen conversion rate was affected by the microbial composition in granules. Nitrogen was autonomously removed in the granules of 0.9–2.0 mm. However, nitrite was accumulated in granules of <0.9 mm. Nitrite cross-feeding occurred inside and between granules. The findings provide a reference for the regulation of granule-based PDA systems. [Display omitted] • Enhanced nitrogen removal and forming PDA granular sludge were achieved. • Microbial community of PDA granular sludge is affected by particle size. • Nitrogen conversion rate of granular sludge is affected by microbial community. • Nitrite cross-feeding occurred inside and between PDA granules. • A regulation strategy was proposed for optimizing the efficiency of PDA system. [ABSTRACT FROM AUTHOR]

[Display omitted] • Xylan consumption was led by Bacteroides species. • Xylan degradation by Bacteroides ovatus allowed Bifidobacterium longum growth. • Proteomics studies showed sugars cross-feeding between B. ovatus and B. longum. The intestinal microbiome is a community of anaerobic microorganisms whose activities significantly impact human health. Its composition can be modulated by consuming foods rich in dietary fiber, such as xylan, a complex polysaccharide that can be considered an emerging prebiotic. In this work, we evaluated how certain gut bacteria acted as primary degraders, fermenting dietary fibers, and releasing metabolites that other bacteria can further use. Different bacterial strains of Lactobacillus , Bifidobacterium , and Bacteroides were evaluated for their ability to consume xylan and interact with one another. Results from unidirectional assays gave indications of possible cross-feeding between bacteria using xylan as a carbon source. Bidirectional assays showed that Bifidobacterium longum PT4 increased its growth in the presence of Bacteroides ovatus HM222. Proteomic analyses indicated that B. ovatus HM222 synthesizes enzymes facilitating xylan degradation, such as β-xylanase, arabinosidase, L-arabinose isomerase, and xylosidase. Interestingly, the relative abundance of these proteins remains largely unaffected in the presence of Bifidobacterium longum PT4. In the presence of B. ovatus , B. longum PT4 increased the production of enzymes such as α-L-arabinosidase, L-arabinose isomerase, xylulose kinase, xylose isomerase, and sugar transporters. These results show an example of positive interaction between bacteria mediated by xylan consumption. Bacteroides degraded this substrate to release xylooligosaccharides, or monosaccharides (xylose, arabinose), which might support the growth of secondary degraders such as B. longum. [ABSTRACT FROM AUTHOR]

Mucus production is initiated before birth and provides mucin glycans to the infant gut microbiota. Bifidobacteria are the major bacterial group in the feces of vaginally delivered and breast milk-fed infants. Among the bifidobacteria, only Bifidobacterium bifidum is able to degrade mucin and to release monosaccharides which can be used by other gut microbes colonizing the infant gut. Eubacterium hallii is an early occurring commensal that produces butyrate and propionate from fermentation metabolites but that cannot degrade complex oligo- and polysaccharides. We aimed to demonstrate that mucin cross-feeding initiated by B. bifidum enables growth and metabolite formation of E. hallii leading to short-chain fatty acid (SCFA) formation. Growth and metabolite formation of co-cultures of B. bifidum, of Bifidobacterium breve or Bifidobacterium infantis, which use mucin-derived hexoses and fucose, and of E. hallii were determined. Growth of E. hallii in the presence of lactose and mucin monosaccharides was tested. In co-culture fermentations, the presence of B. bifidum enabled growth of the other strains. B. bifidum/ B. infantis co-cultures yielded acetate, formate, and lactate while co-cultures of B. bifidum and E. hallii formed acetate, formate, and butyrate. In three-strain co-cultures, B. bifidum, E. hallii, and B. breve or B. infantis produced up to 16 mM acetate, 5 mM formate, and 4 mM butyrate. The formation of propionate (approximately 1 mM) indicated cross-feeding on fucose. Lactose, galactose, and GlcNAc were identified as substrates of E. hallii. This study shows that trophic interactions of bifidobacteria and E. hallii lead to the formation of acetate, butyrate, propionate, and formate, potentially contributing to intestinal SCFA formation with potential benefits for the host and for microbial colonization of the infant gut. The ratios of SCFA formed differed depending on the microbial species involved in mucin cross-feeding. [ABSTRACT FROM AUTHOR]

Recent findings have shaken our picture of the biology of the archaea and revealed novel traits beyond archaeal extremophily and supposed ‘primitiveness’. The archaea constitute a considerable fraction of the Earth’s ecosystems, and their potential to shape their surroundings by a profound interaction with their biotic and abiotic environment has been recognized. Moreover, archaea have been identified as a substantial component, or even as keystone species, in complex microbiomes – in the environment or accompanying a holobiont. Species of the Euryarchaeota (methanogens, halophiles) and Thaumarchaeota, in particular, have the capacity to coexist in plant, animal, and human microbiomes, where syntrophy allows them to thrive under energy-deficiency stress. Due to methodological limitations, the archaeome remains mysterious, and many questions with respect to potential pathogenicity, function, and structural interactions with their host and other microorganisms remain. [ABSTRACT FROM AUTHOR]

Fifty years ago, Lynn Margulis, inspiring in early twentieth-century ideas that put forward a symbiotic origin for some eukaryotic organelles, proposed a unified theory for the origin of the eukaryotic cell based on symbiosis as evolutionary mechanism. Margulis was profoundly aware of the importance of symbiosis in the natural microbial world and anticipated the evolutionary significance that integrated cooperative interactions might have as mechanism to increase cellular complexity. Today, we have started fully appreciating the vast extent of microbial diversity and the importance of syntrophic metabolic cooperation in natural ecosystems, especially in sediments and microbial mats. Also, not only the symbiogenetic origin of mitochondria and chloroplasts has been clearly demonstrated, but improvement in phylogenomic methods combined with recent discoveries of archaeal lineages more closely related to eukaryotes further support the symbiogenetic origin of the eukaryotic cell. Margulis left us in legacy the idea of ‘eukaryogenesis by symbiogenesis’. Although this has been largely verified, when, where, and specifically how eukaryotic cells evolved are yet unclear. Here, we shortly review current knowledge about symbiotic interactions in the microbial world and their evolutionary impact, the status of eukaryogenetic models and the current challenges and perspectives ahead to reconstruct the evolutionary path to eukaryotes. [ABSTRACT FROM AUTHOR]

The aggregation of syntrophic Geobacter metallireducens and Geobacter sulfurreducens is beneficial for enhancing direct interspecies electron transfer (DIET). Although DIET was suspected to occur on the microbial community surface, the surface chemical speciation of such cocultured communities remains unclear. In order to better understand surface interactions related to DIET, the authors characterized a series of samples associated with syntrophic G. metallireducens and G. sulfurreducens using surface sensitive time-of-flight secondary ion mass spectrometry (ToF-SIMS). Principal component analysis was used in spectral analysis. Our results show that the syntrophic Geobacter aggregates are significantly different from their planktonic cells, indicating a distinct chemical composition (i.e., amino acids, fatty acids, and lipids) and structure formed on their surface. Among these characteristic components, amino acid fragments dominated in the variance, suggesting the importance of proteins in the coculture. Additionally, the quorum sensing signal molecule N-butyryl-Lhomoserine lactone was observed in cocultured Geobacter aggregates, implying its role in syntrophic growth and aggregate formation. Furthermore, the electron acceptor organism G. sulfurreducens was shown to be the dominant species in syntrophic communities that drove the syntrophic growth. These results demonstrate that unique chemical compositions distinguish syntrophic Geobacter aggregates from planktonic cells and suggest that ToF-SIMS may be a promising tool to understand the syntrophic mechanism and investigate interspecies electron transfer pathways in complex biofilms. [ABSTRACT FROM AUTHOR]

Direct interspecies electron transfer (DIET) is a recently discovered microbial syntrophy where cell-to-cell electron transfer occurs between syntrophic microbial species. DIET between bacteria and methanogenic archaea in anaerobic digestion can accelerate the syntrophic conversion of various reduced organic compounds to methane. DIET-based syntrophy can naturally occur in some anaerobic digester via conductive pili, however, can be engineered via the addition of various non-biological conductive materials. In recent years, research into understanding and engineering DIET-based syntrophy has emerged with the aim of improving methanogenesis kinetics in anaerobic digestion. This article presents a state-of-art review focusing on the fundamental mechanisms, key microbial players, the role of electrical conductivity, the effectiveness of various conductive additives, the significance of substrate characteristics and organic loading rates in promoting DIET in anaerobic digestion. [ABSTRACT FROM AUTHOR]

Syntrophomonas wolfei syntrophically oxidizes short-chain fatty acids (four to eight carbons in length) when grown in coculture with a hydrogen- and/or formateusing methanogen. The oxidation of 3-hydroxybutyryl-coenzyme A (CoA), formed during butyrate metabolism, results in the production of NADH. The enzyme systems involved in NADH reoxidation in S. wolfei are not well understood. The genome of S. wolfei contains a multimeric [FeFe]-hydrogenase that may be a mechanism for NADH reoxidation. The S. wolfei genes for the multimeric [FeFe]-hydrogenase (hyd1ABC; SWOL_RS05165, SWOL_RS05170, SWOL_RS05175) and [FeFe]-hydrogenase maturation proteins (SWOL_ RS05180, SWOL_RS05190, SWOL_RS01625) were coexpressed in Escherichia coli, and the recombinant Hyd1ABC was purified and characterized. The purified recombinant Hyd1ABC was a heterotrimer with an αβγ configuration and a molecular mass of 115 kDa. Hyd1ABC contained 29.2 ± 1.49 mol of Fe and 0.7 mol of flavin mononucleotide (FMN) per mole enzyme. The purified, recombinant Hyd1ABC reduced NAD+ and oxidized NADH without the presence of ferredoxin. The HydB subunit of the S. wolfei multimeric [FeFe]-hydrogenase lacks two ironsulfur centers that are present in known confurcating NADH- and ferredoxindependent [FeFe]-hydrogenases. Hyd1ABC is a NADH-dependent hydrogenase that produces hydrogen from NADH without the need of reduced ferredoxin, which differs from confurcating [FeFe]-hydrogenases. Hyd1ABC provides a mechanism by which S. wolfei can reoxidize NADH produced during syntrophic butyrate oxidation when low hydrogen partial pressures are maintained by a hydrogen-consuming microorganism. IMPORTANCE Our work provides mechanistic understanding of the obligate metabolic coupling that occurs between hydrogen-producing fatty and aromatic aciddegrading microorganisms and their hydrogen-consuming partners in the process called syntrophy (feeding together). The multimeric [FeFe]-hydrogenase used NADH without the involvement of reduced ferredoxin. The multimeric [FeFe]-hydrogenase would produce hydrogen from NADH only when hydrogen concentrations were low. Hydrogen production from NADH by Syntrophomonas wolfei would likely cease before any detectable amount of cell growth occurred. Thus, continual hydrogen production requires the presence of a hydrogen-consuming partner to keep hydrogen concentrations low and explains, in part, the obligate requirement that S. wolfei has for a hydrogen-consuming partner organism during growth on butyrate. We have successfully expressed genes encoding a multimeric [FeFe]-hydrogenase in E. coli, demonstrating that such an approach can be advantageous to characterize complex redox proteins from difficult-to-culture microorganisms. [ABSTRACT FROM AUTHOR]

The Earth surface contains various oxic and anoxic environments. The later include natural wetlands, river and lake sediments, paddy field soils and landfills. In the last few decades, the biogeochemical cycle of carbon in anoxic environments, which leads to the production and emission of methane, a potent greenhouse gas in the atmosphere, has drawn great attentions from both scientific and public sectors. New organisms and mechanisms involved in methanogenesis and carbon cycling have been uncovered. Interspecies electron transfer is considered as a crucial step in methanogenesis in anoxic environments. Electron-carrying mediators, like H and formate, are known to play the key role in electron transfer. Recently, it has been found that in addition to the conventional electron transfer via chemical mediators, direct interspecies electron transfer (DIET) can occur. In this Review, we describe the ecology and biogeochemistry of methanogenesis and highlight the effect of microbe-mineral interaction on microbial syntrophy. Recent advances in the study of DIET may pave the way towards a mechanistic understanding of methanogenesis and the influence of microbe-mineral interaction on this process. [ABSTRACT FROM AUTHOR]

Nutrient cross-feeding can stabilize microbial mutualisms, including those important for carbon cycling in nutrient-limited anaerobic environments. It remains poorly understood how nutrient limitation within natural environments impacts mutualist growth, cross-feeding levels and ultimately mutualism dynamics. We examined the effects of nutrient limitation within a mutualism using theoretical and experimental approaches with a synthetic anaerobic coculture pairing fermentative Escherichia coli and phototrophic Rhodopseudomonas palustris. In this coculture, E. coli and R. palustris resemble an anaerobic food web by cross-feeding essential carbon (organic acids) and nitrogen (ammonium) respectively. Organic acid cross-feeding stemming from E. coli fermentation can continue in a growth-independent manner during nitrogen limitation, while ammonium cross-feeding by R. palustris is growth-dependent. When ammonium cross-feeding was limited, coculture trends changed yet coexistence persisted under both homogenous and heterogenous conditions. Theoretical modelling indicated that growth-independent fermentation was crucial to sustain cooperative growth under conditions of low nutrient exchange. In contrast to stabilization at most cell densities, growth-independent fermentation inhibited mutualistic growth when the E. coli cell density was adequately high relative to that of R. palustris. Thus, growth-independent fermentation can conditionally stabilize or destabilize a mutualism, indicating the potential importance of growth-independent metabolism for nutrient-limited mutualistic communities. [ABSTRACT FROM AUTHOR]

Anaerobic hydrocarbon biodegradation not only diminishes fuel quality, but also exacerbates the biocorrosion of the metallic infrastructure. While successional events in marine microbial ecosystems impacted by petroleum are well documented, far less is known about the response of communities chronically exposed to hydrocarbons. Shipboard oily wastewater was used to assess the biotransformation of different diesel fuels and their propensity to impact carbon steel corrosion. When amended with sulfate and an F76 military diesel fuel, the sulfate removal rate in the assay mixtures was elevated (26.8 μM/d) relative to incubations receiving a hydroprocessed biofuel (16.1 μM/d) or a fuel-unamended control (17.8 μM/d). Microbial community analysis revealed the predominance of Anaerolineae and Deltaproteobacteria in F76-amended incubations, in contrast to the Beta- and Gammaproteobacteria in the original wastewater. The dominant Smithella- like sequences suggested the potential for syntrophic hydrocarbon metabolism. The general corrosion rate was relatively low (0.83 − 1.29 ± 0.12 mpy) and independent of the particular fuel, but pitting corrosion was more pronounced in F76-amended incubations. Desulfovibrionaceae constituted 50–77% of the sessile organisms on carbon steel coupons. Thus, chronically exposed microflora in oily wastewater were differentially acclimated to the syntrophic metabolism of traditional hydrocarbons but tended to resist isoalkane-laden biofuels. [ABSTRACT FROM AUTHOR]

The operation performance of a novel micro-granule based syntrophic system of nitritation and anammox was studied by controlling the oxygen concentration and maintaining a constant temperature of 25 °C. With the oxygen concentration of around 0.11 (<0.15) mg/L, the single-stage nitritation-anammox system was startup successfully at a nitrogen loading rate (NLR) of 1.5 kgN/m 3 /d. The reactor was successfully operated at volumetric N loadings ranging from 0.5 to 2.5 kgN/m 3 /d with a high nitrogen removal of 82%. The microbial community was composed by ammonia oxidizing bacteria (AOB) and anammox bacteria forming micro-granules with an average diameter of 0.8 mm and good settleability. Results from pyrosequencing analysis revealed that Ca. Kuenenia and Nitrosomonas were selected and enriched in the community over the startup period, and these were identified as the dominant anammox bacteria and AOB species, respectively. [ABSTRACT FROM AUTHOR]

Coumarins are widely found in plants as natural constituents having antimicrobial activity. When considering plants that are rich in coumarins for biogas production, adverse effects on microorganisms driving the anaerobic digestion process are expected. Furthermore, coumarin derivatives, like warfarin, which are used as anticoagulating medicines, are found in wastewater, affecting its treatment. Coumarin, the structure common to all coumarins, inhibits the anaerobic digestion process. However, the details of this inhibition are still elusive. Here, we studied the impact of coumarin on acetogenesis and methanogenesis. First, coumarin was applied at four concentrations between 0.25 and 1 g · liter-1 to pure cultures of the methanogens Methanosarcina barkeri and Methanospirillum hungatei, which resulted in up to 25% less methane production. Acetate production of syntrophic propionate- and butyrate-degrading cultures of Syntrophobacter fumaroxidans and Syntrophomonas wolfei was inhibited by 72% at a coumarin concentration of 1 g · liter-1. Coumarin also inhibited acetogenesis and acetoclastic methanogenesis in a complex biogas reactor microbiome. When a coumarin-adapted microbiome was used, acetogenesis and methanogenesis were not inhibited. According to amplicon sequencing of bacterial 16S rRNA genes and mcrA genes, the communities of the two microbiomes were similar, although Methanoculleus was more abundant and Methanobacterium less abundant in the coumarin-adapted than in the nonadapted microbiome. Our results suggest that well-dosed feeding with coumarin-rich feedstocks to full-scale biogas reactors while keeping the coumarin concentrations below 0.5 g · liter-1 will allow adaptation to coumarins by structural and functional community reorganization and coumarin degradation. IMPORTANCE Coumarins from natural and anthropogenic sources have an inhibitory impact on the anaerobic digestion process. Here, we studied in detail the adverse effects of the model compound coumarin on acetogenesis and methanogenesis, which are two important steps of the anaerobic digestion process. Coumarin concentrations lower than 0.5 g · liter-1 had only a minor impact. Even though similar inhibitory effects can be assumed for coumarin derivatives, little effects on the anaerobic treatment of wastewater are expected where concentrations of coumarin derivatives are lower than 0.5 g · liter-1. However, when full-scale reactors are fed with coumarin-rich feedstocks, the biogas processes might be inhibited. Hence, these feedstocks should be utilized in a well-dosed manner or after adaptation of the microbial community. [ABSTRACT FROM AUTHOR]