Introducing carbon assimilation in yeasts using photosynthetic directed endosymbiosis.

Conversion of heterotrophic organisms into partially or completely autotrophic organisms is primarily accomplished by extensive metabolic engineering and laboratory evolution efforts that channel CO2 into central carbon metabolism. Here, we develop a directed endosymbiosis approach to introduce carbon assimilation in budding yeasts. Particularly, we engineer carbon assimilating and sugar-secreting photosynthetic cyanobacterial endosymbionts within the yeast cells, which results in the generation of yeast/cyanobacteria chimeras that propagate under photosynthetic conditions in the presence of CO2 and in the absence of feedstock carbon sources like glucose or glycerol. We demonstrate that the yeast/cyanobacteria chimera can be engineered to biosynthesize natural products under the photosynthetic conditions. Additionally, we expand our directed endosymbiosis approach to standard laboratory strains of yeasts, which transforms them into photosynthetic yeast/cyanobacteria chimeras. We anticipate that our studies will have significant implications for sustainable biotechnology, synthetic biology, and experimentally studying the evolutionary adaptation of an additional organelle in yeast.

The complex world of kefir: Structural insights and symbiotic relationships.

Kefir milk, known for its high nutritional value and health benefits, is traditionally produced by fermenting milk with kefir grains. These grains are a complex symbiotic community of lactic acid bacteria, acetic acid bacteria, yeasts, and other microorganisms. However, the intricate coexistence mechanisms within these microbial colonies remain a mystery, posing challenges in predicting their biological and functional traits. This uncertainty often leads to variability in kefir milk's quality and safety. This review delves into the unique structural characteristics of kefir grains, particularly their distinctive hollow structure. We propose hypotheses on their formation, which appears to be influenced by the aggregation behaviors of the community members and their alliances. In kefir milk, a systematic colonization process is driven by metabolite release, orchestrating the spatiotemporal rearrangement of ecological niches. We place special emphasis on the dynamic spatiotemporal changes within the kefir microbial community. Spatially, we observe variations in species morphology and distribution across different locations within the grain structure. Temporally, the review highlights the succession patterns of the microbial community, shedding light on their evolving interactions.Furthermore, we explore the ecological mechanisms underpinning the formation of a stable community composition. The interplay of cooperative and competitive species within these microorganisms ensures a dynamic balance, contributing to the community's richness and stability. In kefir community, competitive species foster diversity and stability, whereas cooperative species bolster mutualistic symbiosis. By deepening our understanding of the behaviors of these complex microbial communities, we can pave the way for future advancements in the development and diversification of starter cultures for food fermentation processes.

A mechanistic modelling approach of the host-microbiota interactions to investigate beneficial symbiotic resilience in the human gut.

The health and well-being of a host are deeply influenced by the interactions with its gut microbiota. Contrasted environmental conditions, such as diseases or dietary habits, play a pivotal role in modulating these interactions, impacting microbiota composition and functionality. Such conditions can also lead to transitions from beneficial to detrimental symbiosis, viewed as alternative stable states of the host-microbiota dialogue. This article introduces a novel mathematical model exploring host-microbiota interactions, integrating dynamics of the colonic epithelial crypt, microbial metabolic functions, inflammation sensitivity and colon flows in a transverse section. The model considers metabolic shifts in epithelial cells based on butyrate and hydrogen sulfide concentrations, innate immune pattern recognition receptor activation, microbial oxygen tolerance and the impact of antimicrobial peptides on the microbiota. Using the model, we demonstrated that a high-protein, low-fibre diet exacerbates detrimental interactions and compromises beneficial symbiotic resilience, underscoring a destabilizing effect towards an unhealthy state. Moreover, the proposed model provides essential insights into oxygen levels, fibre and protein breakdown, and basic mechanisms of innate immunity in the colon and offers a crucial understanding of factors influencing the colon environment.

Characterizing algal-bacterial symbiotic biofilms: Insights into coexistence of algae and anaerobic microorganisms.

This study constructed an integrated algae/partial nitrification/anammox biofilm system and operated it for 240 days. The total nitrogen removal efficiency exceeded 90 %. The structure, compositions, and function of this symbiotic biofilm, which played a pivotal role in the system, were analyzed in detail. Microscope photos and fluorescence in situ hybridization both showed that bacteria and algae were well integrated. The dissolved oxygen gradient further confirmed that different functional microorganisms grew at varying depths within biofilm. Algae formed an oxygen-producing zone (0-0.48 mm), followed by ammonia oxidizing bacteria (AOB) consuming oxygen to form an oxygen-consuming zone (0.48-0.86 mm), and anaerobic ammonia oxidizing bacteria (AnAOB) removed nitrogen in anaerobic zone (>0.86 mm). Chlorella, Nitrosomonas and Candidatus_Kuenenia were identified as the dominant algae, AOB and AnAOB, with relative abundances of 11.80 %, 19.77 % and 3.07 %, respectively. This layered biofilm benefitted providing a suitable environment for various microorganisms to survive within a complex biofilm.

Dynamic modulation of nodulation factor receptor levels by phosphorylation-mediated functional switch of a RING-type E3 ligase during legume nodulation.

The precise control of receptor levels is crucial for initiating cellular signaling transduction in response to specific ligands; however, such mechanisms regulating nodulation factor (NF) receptor (NFR)-mediated perception of NFs to establish symbiosis remain unclear. In this study, we unveil the pivotal role of the NFR-interacting RING-type E3 ligase 1 (NIRE1) in regulating NFR1/NFR5 homeostasis to optimize rhizobial infection and nodule development in Lotus japonicus. We demonstrated that NIRE1 has a dual function in this regulatory process. It associates with both NFR1 and NFR5, facilitating their degradation through K48-linked polyubiquitination before rhizobial inoculation. However, following rhizobial inoculation, NFR1 phosphorylates NIRE1 at a conserved residue, Tyr-109, inducing a functional switch in NIRE1, which enables NIRE1 to mediate K63-linked polyubiquitination, thereby stabilizing NFR1/NFR5 in infected root cells. The introduction of phospho-dead NIRE1Y109F leads to delayed nodule development, underscoring the significance of phosphorylation at Tyr-109 in orchestrating symbiotic processes. Conversely, expression of the phospho-mimic NIRE1Y109E results in the formation of spontaneous nodules in L. japonicus, further emphasizing the critical role of the phosphorylation-dependent functional switch in NIRE1. In summary, these findings uncover a fine-tuned symbiotic mechanism that a single E3 ligase could undergo a phosphorylation-dependent functional switch to dynamically and precisely regulate NF receptor protein levels.

Biohydrogen utilization in legume-rhizobium symbiosis reveals a novel mechanism of accelerated tetrachlorobiphenyl transformation.

Symbiosis between Glycine max and Bradyrhizobium diazoefficiens were used as a model system to investigate whether biohydrogen utilization promotes the transformation of the tetrachlorobiphenyl PCB77. Both a H2 uptake-positive (Hup+) strain (wild type) and a Hup- strain (a hupL deletion mutant) were inoculated into soybean nodules. Compared with Hup- nodules, Hup+ nodules increased dechlorination significantly by 61.1 % and reduced the accumulation of PCB77 in nodules by 37.7 % (p < 0.05). After exposure to nickel, an enhancer of uptake hydrogenase, dechlorination increased significantly by 2.2-fold, and the accumulation of PCB77 in nodules decreased by 54.4 % (p < 0.05). Furthermore, the tetrachlorobiphenyl transformation in the soybean root nodules was mainly testified to be mediated by nitrate reductase (encoded by the gene NR) for tetrachlorobiphenyl dechlorination and biphenyl-2,3-diol 1,2-dioxygenase (bphC) for biphenyl degradation. This study demonstrates for the first time that biohydrogen utilization has a beneficial effect on tetrachlorobiphenyl biotransformation in a legume-rhizobium symbiosis.

The long proboscis of the aphid Stomaphis yanonis (Aphididae Lachninae) is advantageous for avoiding predation by tending ants.

Whether in ant-aphid mutualism the ants exert evolutionary selection pressure on aphid morphology has not yet been fully tested. Here, we tested whether the long proboscises of Stomaphis yanonis (Aphididae Lachninae) aphids confer an advantage in preventing predation by the tending ants. Specifically, we tested the hypothesis that aphids with a shorter proboscis would excrete less honeydew, making them more likely to be preyed upon by ants. Our results showed that aphid individuals with a shorter proboscis took up less phloem sap and excreted less honeydew than individuals with a longer proboscis. In addition, among aphids with a similar body size, those with a shorter proboscis were more susceptible to predation by ants than those with a longer proboscis. These results suggest that predation by tending ants, by exerting selection pressure on aphid proboscis morphology, has caused the aphids to evolve longer proboscises.

Joint evolution of mutualistic interactions, pollination, seed dispersal mutualism, and mycorrhizal symbiosis in trees.

Mycorrhizal symbiosis, seed dispersal, and pollination are recognized as the most prominent mutualistic interactions in terrestrial ecosystems. However, it remains unclear how these symbiotic relationships have interacted to contribute to current plant diversity. We analyzed evolutionary relationships among mycorrhizal type, seed dispersal mode, and pollination mode in two global databases of 699 (database I) and 10 475 (database II) tree species. Although database II had been estimated from phylogenetic patterns and therefore had lower certainty of the mycorrhizal type than database I, whose mycorrhizal type was determined by direct observation, database II allowed analysis of many more taxa from more regions than database I. We found evidence of joint evolution of all three features in both databases. This result is robust to the effects of both sampling bias and missing taxa. Most arbuscular mycorrhizal-associated trees had endozoochorous (biotic) seed dispersal and biotic pollination, with long dispersal distances, whereas most ectomycorrhizal-associated trees had anemochorous (abiotic) seed dispersal and wind (abiotic) pollination mode, with shorter dispersal distances. These results provide a novel scenario in mutualistic interactions, seed dispersal, pollination, and mycorrhizal symbiosis types, which have jointly evolved and shaped current tree diversity and forest ecosystem world-wide.

Plant-fungus symbiosis: One receptor to switch on the green light.

Arbuscular mycorrhiza, an ancient symbiosis with soil fungi, support mineral nutrition in most plants. How roots recognize such symbiotic fungi has long been debated. Recent research identifies a Medicago truncatula receptor as a key player in triggering symbiont accommodation responses.

The global significance of Scleractinian corals without photoendosymbiosis.

Globally tropical Scleractinian corals have been a focal point for discussions on the impact of a changing climate on marine ecosystems and biodiversity. Research into tropical Scleractinian corals, particularly the role and breakdown of photoendosymbiosis in response to warming, has been prolific in recent decades. However, research into their subtropical, temperate, cold- and deep-water counterparts, whose number is dominated by corals without photoendosymbiosis, has not been as prolific. Approximately 50% of Scleractinian corals (> 700 species) do not maintain photoendosymbiosis and as such, do not rely upon the products of photosynthesis for homeostasis. Some species also have variable partnerships with photendosymbionts depending on life history and ecological niche. Here we undertake a systematic map of literature on Scleractinian corals without, or with variable, photoendosymbiosis. In doing so we identify 482 publications spanning 5 decades. In mapping research effort, we find publications have been sporadic over time, predominately focusing on a limited number of species, with greater research effort directed towards deep-water species. We find only 141 species have been studied, with approximately 30% of the total identified research effort directed toward a single species, Desmophyllum pertusum, highlighting significant knowledge gaps into Scleractinian diversity. We find similar limitations to studied locations, with 78 identified from the global data, of which only few represent most research outputs. We also identified inconsistencies with terminology used to describe Scleractinia without photoendosymbiosis, likely contributing to difficulties in accounting for their role and contribution to marine ecosystems. We propose that the terminology requires re-evaluation to allow further systematic assessment of literature, and to ensure it's consistent with changes implemented for photoendosymbiotic corals. Finally, we find that knowledge gaps identified over 20 years ago are still present for most aphotoendosymbiotic Scleractinian species, and we show data deficiencies remain regarding their function, biodiversity and the impacts of anthropogenic stressors.

Production of sounds by squirrelfish during symbiotic relationships with cleaner wrasses.

Examples of symbiotic relationships often include cleaning mutualisms, typically involving interactions between cleaner fish and other fish, called the clients. While these cleaners can cooperate by removing ectoparasites from their clients, they can also deceive by feeding on client mucus, a behavior usually referred to as "cheating behavior" that often leads to a discernible jolt from the client fish. Despite extensive studies of these interactions, most research has focused on the visual aspects of the communication. In this study, we aimed to explore the role of acoustic communication in the mutualistic relationship between cleaner fishes and nine holocentrid client species across four regions of the Indo-Pacific Ocean: French Polynesia, Guam, Seychelles, and the Philippines. Video cameras coupled with hydrophones were positioned at various locations on reefs housing Holocentridae fish to observe their acoustic behaviors during interactions. Our results indicate that all nine species of holocentrids can use acoustic signals to communicate to cleaner fish their refusal of the symbiotic interaction or their desire to terminate the cooperation. These sounds were predominantly observed during agonistic behavior and seem to support visual cues from the client. This study provides a novel example of acoustic communication during a symbiotic relationship in teleosts. Interestingly, these vocalizations often lacked a distinct pattern or structure. This contrasts with numerous other interspecific communication systems where clear and distinguishable signals are essential. This absence of a clear acoustic pattern may be because they are used in interspecific interactions to support visual behavior with no selective pressure for developing specific calls required in conspecific recognition. The different sound types produced could also be correlated with the severity of the client response. There is a need for further research into the effects of acoustic behaviors on the quality and dynamics of these mutualistic interactions.

Bacterial growth dynamics in a rhythmic symbiosis.

The symbiotic relationship between the bioluminescent bacterium Vibrio fischeri and the bobtail squid Euprymna scolopes serves as a valuable system to investigate bacterial growth and peptidoglycan (PG) synthesis within animal tissues. To better understand the growth dynamics of V. fischeri in the crypts of the light-emitting organ of its juvenile host, we showed that, after the daily dawn-triggered expulsion of most of the population, the remaining symbionts rapidly proliferate for ∼6 h. At that point the population enters a period of extremely slow growth that continues throughout the night until the next dawn. Further, we found that PG synthesis by the symbionts decreases as they enter the slow-growing stage. Surprisingly, in contrast to the most mature crypts (i.e., Crypt 1) of juvenile animals, most of the symbiont cells in the least mature crypts (i.e., Crypt 3) were not expelled and, instead, remained in the slow-growing state throughout the day, with almost no cell division. Consistent with this observation, the expression of the gene encoding the PG-remodeling enzyme, L,D-transpeptidase (LdtA), was greatest during the slowly growing stage of Crypt 1 but, in contrast, remained continuously high in Crypt 3. Finally, deletion of the ldtA gene resulted in a symbiont that grew and survived normally in culture, but was increasingly defective in competing against its parent strain in the crypts. This result suggests that remodeling of the PG to generate additional 3-3 linkages contributes to the bacterium's fitness in the symbiosis, possibly in response to stresses encountered during the very slow-growing stage.

Arbuscular mycorrhizal symbiosis modulates nitrogen uptake and assimilation to enhance drought tolerance of Populus cathayana.

This study aims to investigate effects of arbuscular mycorrhizal fungi (AMF) inoculation on nitrogen (N) uptake and assimilation in Populus cathayana under drought stress (DS). Herein, we measured photosynthetic performance, antioxidant enzyme system, N level and N assimilation enzymes, proteins content and distribution, transcripts of genes associated with N uptake or transport in P. cathayana with AMF (AM) or without AMF (NM) under soil water limitation and adequate irrigation. Compared with NM-DS P. cathayana, the growth, gas exchange properties, antioxidant enzyme activities, total N content and the proportion of water-soluble and membrane-bound proteins in AM-DS P. cathayana were increased. Meanwhile, nitrate reductase (NR) activity, NO3- and NO2- concentrations in AM-DS P. cathayana were reduced, while NH4+ concentration, glutamine synthetase (GS) and glutamate synthetase (GOGAT) activities were elevated, indicating that AM symbiosis reduces NO3- assimilation while promoting NH4+ assimilation. Furthermore, the transcriptional levels of NH4+ transporter genes (PcAMT1-4 and PcAMT2-1) and NO3- transporter genes (PcNRT2-1 and PcNRT3-1) in AM-DS P. cathayana roots were significantly down-regulated, as well as NH4+ transporter genes (PcAMT1-6 and PcAMT4-3) in leaves. In AM P. cathayana roots, DS significantly up-regulated the transcriptional levels of RiCPSI and RiURE, the key N transport regulatory genes in AMF compared with adequate irrigation. These results indicated that AM N transport pathway play an essential role on N uptake and utilization in AM P. cathayana to cope with DS. Therefore, this research offers a novel perspective on how AM symbiosis enhances plant resilience to drought at aspect of N acquisition and assimilation.

Influence of sipunculan (peanut worm) activity on orifice formation in scleractinian Heterocyathus for adaptation to soft substrates.

Mutualism profoundly affects the morphology and ecological evolution of both hosts and symbionts involved. Heterocyathus is a solitary scleractinian coral that lives on soft substrata, and sipunculan worms live symbiotically in the tube-like cavities (orifice) inside the coral skeletons. This habitat provides protection to the sipunculan worms against predators and-owing to the mobility of the worms-prevents the coral from being buried with sediments. The orifice growth is closely related to the symbiont sipunculan worms; however, this has not been previously elucidated. Here, we clarified the growth process of scleractinian coral orifices and the influence of sipunculan activity on this. The orifices were originally formed by rapid accretion deposits. The coral soft tissue enveloping the growth edge of the orifice repeatedly retreated to the outer side due to direct damage to the soft part and/or excessive stress caused by the rubbing of the sipunculan through locomotion, excretion, and feeding behaviour. This resulted in a toppled-domino microskeletal structure appearance and maintenance of the orifice growth. These outcomes demonstrate the first example of the direct influence of symbionts on the skeletal morphogenesis of scleractinian corals. The mutualism between the two organisms is maintained by the beneficial confrontation in forming orifices.

Localization and symbiotic status of probiotics in the coral holobiont.

Corals establish symbiotic relationships with microorganisms, especially endosymbiotic photosynthetic algae. Although other microbes have been commonly detected in coral tissues, their identity and beneficial functions for their host are unclear. Here, we confirm the beneficial outcomes of the inoculation of bacteria selected as probiotics and use fluorescence in situ hybridization (FISH) to define their localization in the coral Pocillopora damicornis. Our results show the first evidence of the inherent presence of Halomonas sp. and Cobetia sp. in native coral tissues, even before their inoculation. Furthermore, the relative enrichment of these coral tissue-associated bacteria through their inoculation in corals correlates with health improvements, such as increases in photosynthetic potential, and productivity. Our study suggests the symbiotic status of Halomonas sp. and Cobetia sp. in corals by indicating their localization within coral gastrodermis and epidermis and correlating their increased relative abundance through active inoculation with beneficial outcomes for the holobiont. This knowledge is crucial to facilitate the screening and application of probiotics that may not be transient members of the coral microbiome. IMPORTANCE: Despite the promising results indicating the beneficial outcomes associated with the application of probiotics in corals and some scarce knowledge regarding the identity of bacterial cells found within the coral tissue, the correlation between these two aspects is still missing. This gap limits our understanding of the actual diversity of coral-associated bacteria and whether these symbionts are beneficial. Some researchers, for example, have been suggesting that probiotic screening should only focus on the very few known tissue-associated bacteria, such as Endozoicomonas sp., assuming that the currently tested probiotics are not tissue-associated. Here, we provide specific FISH probes for Halomonas sp. and Cobetia sp., expand our knowledge of the identity of coral-associated bacteria and confirm the probiotic status of the tested probiotics. The presence of these beneficial microorganisms for corals (BMCs) inside host tissues and gastric cavities also supports the notion that direct interactions with the host may underpin their probiotic role. This is a new breakthrough; these results argue against the possibility that the positive effects of BMCs are due to factors that are not related to a direct symbiotic interaction, for example, that the host simply feeds on inoculated bacteria or that the bacteria change the water quality.

Morphological and physiological properties of lupine nodule bacteria (Bradyrhizobium lupini) when grown on a typical urban soil.

In the conducted studies, the moorphological and physiological properties of nodule bacteria of lupine were studied. Lupine plants were grown under the conditions of a microfield experiment on a typical medium loamy urban soil. In the study, a pure culture of Bradyrhizobium lupini was isolated. Then, the morphological properties of nodule bacteria cells and the chemical composition of cell membranes of nodule bacteria were determined. The acid resistance and physiological properties of lupine nodule bacteria were also determined, as well as the ratio of Bradyrhizobium lupini to antibiotics. All studies were carried out according to generally accepted methods. The results of the research showed that during the cultivation of lupine on a typical urban soil, nodule bacteria Bradyrhizobium lupini were isolated, which can be characterized as gram-negative, non-spore-forming rods that do not exhibit amylolytic activity. It was revealed that the rhizobia of nodule bacteria are not acid-resistant. Nodule bacteria turned out to be the least resistant to polymyxin, then to levomycetin, and Bradyrhizobium lupini showed the greatest resistance to tetracycline.