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Itoh, Hideomi, Seonghan Jang, Kazutaka Takeshita, Tsubasa Ohbayashi, Naomi Ohnishi, Xian-Ying Meng, Yasuo Mitani, and Yoshitomo Kikuchi. "Host–symbiont specificity determined by microbe–microbe competition in an insect gut." Proceedings of the National Academy of Sciences 116, no. 45 (October 21, 2019): 22673–82. http://dx.doi.org/10.1073/pnas.1912397116.
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Despite the omnipresence of specific host–symbiont associations with acquisition of the microbial symbiont from the environment, little is known about how the specificity of the interaction evolved and is maintained. The bean bug Riptortus pedestris acquires a specific bacterial symbiont of the genus Burkholderia from environmental soil and harbors it in midgut crypts. The genus Burkholderia consists of over 100 species, showing ecologically diverse lifestyles, and including serious human pathogens, plant pathogens, and nodule-forming plant mutualists, as well as insect mutualists. Through infection tests of 34 Burkholderia species and 18 taxonomically diverse bacterial species, we demonstrate here that nonsymbiotic Burkholderia and even its outgroup Pandoraea could stably colonize the gut symbiotic organ and provide beneficial effects to the bean bug when inoculated on aposymbiotic hosts. However, coinoculation revealed that the native symbiont always outcompeted the nonnative bacteria inside the gut symbiotic organ, explaining the predominance of the native Burkholderia symbiont in natural bean bug populations. Hence, the abilities for colonization and cooperation, usually thought of as specific traits of mutualists, are not unique to the native Burkholderia symbiont but, to the contrary, competitiveness inside the gut is a derived trait of the native symbiont lineage only and was thus critical in the evolution of the insect gut symbiont.
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Fang, Ferric C., and Arturo Casadevall. "Competitive Science: Is Competition Ruining Science?" Microbe Magazine 10, no. 6 (June 1, 2015): 224–25. http://dx.doi.org/10.1128/microbe.10.224.1.
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Heinken, Almut, and Ines Thiele. "Anoxic Conditions Promote Species-Specific Mutualism between Gut MicrobesIn Silico." Applied and Environmental Microbiology 81, no. 12 (April 3, 2015): 4049–61. http://dx.doi.org/10.1128/aem.00101-15.
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ABSTRACTThe human gut is inhabited by thousands of microbial species, most of which are still uncharacterized. Gut microbes have adapted to each other's presence as well as to the host and engage in complex cross feeding. Constraint-based modeling has been successfully applied to predicting microbe-microbe interactions, such as commensalism, mutualism, and competition. Here, we apply a constraint-based approach to model pairwise interactions between 11 representative gut microbes. Microbe-microbe interactions were computationally modeled in conjunction with human small intestinal enterocytes, and the microbe pairs were subjected to three diets with various levels of carbohydrate, fat, and protein in normoxic or anoxic environments. Each microbe engaged in species-specific commensal, parasitic, mutualistic, or competitive interactions. For instance,Streptococcus thermophilusefficiently outcompeted microbes with which it was paired, in agreement with the domination of streptococci in the small intestinal microbiota. Under anoxic conditions, the probiotic organismLactobacillus plantarumdisplayed mutualistic behavior toward six other species, which, surprisingly, were almost entirely abolished under normoxic conditions. This finding suggests that the anoxic conditions in the large intestine drive mutualistic cross feeding, leading to the evolvement of an ecosystem more complex than that of the small intestinal microbiota. Moreover, we predict that the presence of the small intestinal enterocyte induces competition over host-derived nutrients. The presented framework can readily be expanded to a larger gut microbial community. This modeling approach will be of great value for subsequent studies aiming to predict conditions favoring desirable microbes or suppressing pathogens.
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Wardle, D. A., and Marie-Charlotte Nilsson. "Microbe-plant competition, allelopathy and arctic plants." Oecologia 109, no. 2 (January 10, 1997): 291–93. http://dx.doi.org/10.1007/s004420050086.
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Xiong, Xiyan, Sara L. Loo, Li Zhang, and Mark M. Tanaka. "Modelling the effect of birth and feeding modes on the development of human gut microbiota." Proceedings of the Royal Society B: Biological Sciences 288, no. 1942 (January 13, 2021): 20201810. http://dx.doi.org/10.1098/rspb.2020.1810.
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The human gut microbiota is transmitted from mother to infant through vaginal birth and breastfeeding. Bifidobacterium , a genus that dominates the infants’ gut, is adapted to breast milk in its ability to metabolize human milk oligosaccharides; it is regarded as a mutualist owing to its involvement in the development of the immune system. The composition of microbiota, including the abundance of Bifidobacteria, is highly variable between individuals and some microbial profiles are associated with diseases. However, whether and how birth and feeding practices contribute to such variation remains unclear. To understand how early events affect the establishment of microbiota, we develop a mathematical model of two types of Bifidobacteria and a generic compartment of commensal competitors. We show how early events affect competition between mutualists and commensals and microbe-host-immune interactions to cause long-term alterations in gut microbial profiles. Bifidobacteria associated with breast milk can trigger immune responses with lasting effects on the microbial community structure. Our model shows that, in response to a change in birth environment, competition alone can produce two distinct microbial profiles post-weaning. Adding immune regulation to our competition model allows for variations in microbial profiles in response to different feeding practices. This analysis highlights the importance of microbe–microbe and microbe–host interactions in shaping the gut populations following different birth and feeding modes.
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Glatthardt, Thaís, Rayssa Durães Lima, Raquel Monteiro de Mattos, and Rosana Barreto Rocha Ferreira. "Microbe Interactions within the Skin Microbiome." Antibiotics 13, no. 1 (January 4, 2024): 49. http://dx.doi.org/10.3390/antibiotics13010049.
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The skin is the largest human organ and is responsible for many important functions, such as temperature regulation, water transport, and protection from external insults. It is colonized by several microorganisms that interact with each other and with the host, shaping the microbial structure and community dynamics. Through these interactions, the skin microbiota can inhibit pathogens through several mechanisms such as the production of bacteriocins, proteases, phenol soluble modulins (PSMs), and fermentation. Furthermore, these commensals can produce molecules with antivirulence activity, reducing the potential of these pathogens to adhere to and invade human tissues. Microorganisms of the skin microbiota are also able to sense molecules from the environment and shape their behavior in response to these signals through the modulation of gene expression. Additionally, microbiota-derived compounds can affect pathogen gene expression, including the expression of virulence determinants. Although most studies related to microbial interactions in the skin have been directed towards elucidating competition mechanisms, microorganisms can also use the products of other species to their benefit. In this review, we will discuss several mechanisms through which microorganisms interact in the skin and the biotechnological applications of products originating from the skin microbiota that have already been reported in the literature.
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Moreau, Delphine, Barbara Pivato, David Bru, Hugues Busset, Florence Deau, Céline Faivre, Annick Matejicek, Florence Strbik, Laurent Philippot, and Christophe Mougel. "Plant traits related to nitrogen uptake influence plant-microbe competition." Ecology 96, no. 8 (August 2015): 2300–2310. http://dx.doi.org/10.1890/14-1761.1.
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Burgos, Hector L., Emanuel F. Burgos, Andrew J. Steinberger, Garret Suen, and Mark J. Mandel. "Multiplexed Competition in a Synthetic Squid Light Organ Microbiome Using Barcode-Tagged Gene Deletions." mSystems 5, no. 6 (December 15, 2020): e00846-20. http://dx.doi.org/10.1128/msystems.00846-20.
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ABSTRACTBeneficial symbioses between microbes and their eukaryotic hosts are ubiquitous and have widespread impacts on host health and development. The binary symbiosis between the bioluminescent bacterium Vibrio fischeri and its squid host Euprymna scolopes serves as a model system to study molecular mechanisms at the microbe-animal interface. To identify colonization factors in this system, our lab previously conducted a global transposon insertion sequencing (INSeq) screen and identified over 300 putative novel squid colonization factors in V. fischeri. To pursue mechanistic studies on these candidate genes, we present an approach to quickly generate barcode-tagged gene deletions and perform high-throughput squid competition experiments with detection of the proportion of each strain in the mixture by barcode sequencing (BarSeq). Our deletion approach improves on previous techniques based on splicing by overlap extension PCR (SOE-PCR) and tfoX-based natural transformation by incorporating a randomized barcode that results in unique DNA sequences within each deletion scar. Amplicon sequencing of the pool of barcoded strains before and after colonization faithfully reports on known colonization factors and provides increased sensitivity over colony counting methods. BarSeq enables rapid and sensitive characterization of the molecular factors involved in establishing the Vibrio-squid symbiosis and provides a valuable tool to interrogate the molecular dialogue at microbe-animal host interfaces.IMPORTANCE Beneficial microbes play essential roles in the health and development of their hosts. However, the complexity of animal microbiomes and general genetic intractability of their symbionts have made it difficult to study the coevolved mechanisms for establishing and maintaining specificity at the microbe-animal host interface. Model symbioses are therefore invaluable for studying the mechanisms of beneficial microbe-host interactions. Here, we present a combined barcode-tagged deletion and BarSeq approach to interrogate the molecular dialogue that ensures specific and reproducible colonization of the Hawaiian bobtail squid by Vibrio fischeri. The ability to precisely manipulate the bacterial genome, combined with multiplex colonization assays, will accelerate the use of this valuable model system for mechanistic studies of how environmental microbes—both beneficial and pathogenic—colonize specific animal hosts.
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Dong, Yue, and Xinzhu Meng. "Stochastic dynamic analysis of a chemostat model of intestinal microbes with migratory effect." AIMS Mathematics 8, no. 3 (2023): 6356–74. http://dx.doi.org/10.3934/math.2023321.
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<abstract><p>This paper proposes a stochastic intestinal chemostat model considering microbial migration, intraspecific competition and stochastic perturbation. First, the extinction and persistence in mean of the intestinal microbe of the chemostat model are investigated by constructing the appropriate Lyapunov functions. Second, we explore and obtain sufficient conditions for the existence and uniqueness of an ergodic stationary distribution of the model by using ergodic theory. The results show stochastic interference has a critical impact on the extinction and sustainable survival of the intestinal microbe. Eventually, numerical simulations are carried out to verify the theoretical results.</p></abstract>
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LINDÉN, Sara, Jafar MAHDAVI, Jan HEDENBRO, Thomas BORÉN, and Ingemar CARLSTEDT. "Effects of pH on Helicobacter pylori binding to human gastric mucins: identification of binding to non-MUC5AC mucins." Biochemical Journal 384, no. 2 (November 23, 2004): 263–70. http://dx.doi.org/10.1042/bj20040402.
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Helicobacter pylori causes gastritis, peptic ulcer disease and gastric cancer. The microbe is found in the gastric mucus layer where a pH gradient ranging from acidic in the lumen to neutral at the cell surface is maintained. The aim of the present study was to investigate the effects of pH on H. pylori binding to gastric mucins from healthy individuals. At pH 3, all strains bound to the most charged MUC5AC glycoform and to a putative mucin of higher charge and larger size than subunits of MUC5AC and MUC6, irrespective of host blood-group. In contrast, at pH 7.4 only Leb-binding BabA-positive strains bound to Leb-positive MUC5AC and to smaller mucin-like molecules, including MUC1. H. pylori binding to the latter component(s) seems to occur via the H-type-1 structure. All strains bound to a proteoglycan containing chondroitin sulphate/dermatan sulphate side chains at acidic pH, whereas binding to secreted MUC5AC and putative membrane-bound strains occurred both at neutral and acidic pH. The binding properties at acidic pH are thus common to all H. pylori strains, whereas mucin binding at neutral pH occurs via the bacterial BabA adhesin and the Leb antigen/related structures on the glycoprotein. Our work shows that microbe binding to membrane-bound mucins must be considered in H. pylori colonization, and the potential of these glycoproteins to participate in signalling events implies that microbe binding to such structures may initiate signal transduction over the epithelial layer. Competition between microbe binding to membrane-bound and secreted mucins is therefore an important aspect of host–microbe interaction.
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YANDIGERI, Mahesh S., Manoj Kumar SOLANKI, Sudheer KUMAR, Rajesh Kumar SINGH, and Alok K. SRIVASTAVA. "Nutrient Competition Mediated Antagonism of Microbes Against Rhizoctonia solani." Notulae Scientia Biologicae 10, no. 3 (September 27, 2018): 392–99. http://dx.doi.org/10.15835/nsb10310312.
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Plant growth-promoting (PGP) microorganisms are beneficial soil micro creatures which may facilitate plant growth by direct or indirect ways. Bacillus amyloliquefaciens MB101 (BA), Streptomyces atrovirens N23 (SA) and Hypocrea lixii NAIMCC-F-01760 (HL) were earlier reported to have the ability to manage the tomato root rot disease caused by Rhizoctonia solani (RS) at some extent. In the present study, effect of nutrient supplementation like potato dextrose broth (PDB) and tomato root extract (TRE) on antagonism of these three microbes was characterized under the soil microcosm in order to understand the role of nutrient in microbe-microbe interaction. A moderate influence on the population of all three antagonists was resulted by PDB and TRE with RS. However, TRE and PDB were causing a significant impact on cell wall degrading enzymes and antifungal activity in the presence of RS. Moreover, hyphal degradation of RS was proved by scanning electron micrographs in the absence of substrates. Nutrient competition enhanced the call wall degrading enzyme production. Therefore, the present study concluded the role of substrate in the mycoparasitism and also sustain the potential of the hereby methodology (soil microcosm) for screening of other soil-inhibiting organism in the future.
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Zak, Donald R., Peter M. Groffman, Kurt S. Pregitzer, Soren Christensen, and James M. Tiedje. "The Vernal Dam: Plant-Microbe Competition for Nitrogen in Northern Hardwood Forests." Ecology 71, no. 2 (April 1990): 651–56. http://dx.doi.org/10.2307/1940319.
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Ruxton, Graeme D., David M. Wilkinson, H. Martin Schaefer, and Thomas N. Sherratt. "Why fruit rots: theoretical support for Janzen's theory of microbe–macrobe competition." Proceedings of the Royal Society B: Biological Sciences 281, no. 1782 (May 7, 2014): 20133320. http://dx.doi.org/10.1098/rspb.2013.3320.
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We present a formal model of Janzen's influential theory that competition for resources between microbes and vertebrates causes microbes to be selected to make these resources unpalatable to vertebrates. That is, fruit rots, seeds mould and meat spoils, in part, because microbes gain a selective advantage if they can alter the properties of these resources to avoid losing the resources to vertebrate consumers. A previous model had failed to find circumstances in which such a costly spoilage trait could flourish; here, we present a simple analytic model of a general situation where costly microbial spoilage is selected and persists. We argue that the key difference between the two models lies in their treatments of microbial dispersal. If microbial dispersal is sufficiently spatially constrained that different resource items can have differing microbial communities, then spoilage will be selected; however, if microbial dispersal has a strong homogenizing effect on the microbial community then spoilage will not be selected. We suspect that both regimes will exist in the natural world, and suggest how future empirical studies could explore the influence of microbial dispersal on spoilage.
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Pei, Yu, Hans Hagdorn, Thomas Voigt, Jan-Peter Duda, and Joachim Reitner. "Palaeoecological Implications of Lower-Middle Triassic Stromatolites and Microbe-Metazoan Build-Ups in the Germanic Basin: Insights into the Aftermath of the Permian–Triassic Crisis." Geosciences 12, no. 3 (March 14, 2022): 133. http://dx.doi.org/10.3390/geosciences12030133.
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Following the end-Permian crisis, microbialites were ubiquitous worldwide. For instance, Triassic deposits in the Germanic Basin provide a rich record of stromatolites as well as of microbe-metazoan build-ups with nonspicular demosponges. Despite their palaeoecological significance, however, all of these microbialites have only rarely been studied. This study aims to fill this gap by examining and comparing microbialites from the Upper Buntsandstein (Olenekian, Lower Triassic) and the lower Middle Muschelkalk (Anisian, Middle Triassic) in Germany. By combining analytical petrography (optical microscopy, micro X-ray fluorescence, and Raman spectroscopy) and geochemistry (δ13Ccarb, δ18Ocarb), we show that all the studied microbialites formed in slightly evaporitic environments. Olenekian deposits in the Jena area and Anisian strata at Werbach contain stromatolites. Anisian successions at Hardheim, in contrast, host microbe-metazoan build-ups. Thus, the key difference is the absence or presence of nonspicular demosponges in microbialites. It is plausible that microbes and nonspicular demosponges had a mutualistic relationship, and it is tempting to speculate that the investigated microbial-metazoan build-ups reflect an ancient evolutionary and ecological association. The widespread occurrence of microbialites (e.g., stromatolites/microbe-metazoan build-ups) after the catastrophe may have resulted from suppressed ecological competition and the presence of vacant ecological niches. The distribution of stromatolites and/or microbe-metazoan build-ups might have been controlled by subtle differences in salinity and water depth, the latter influencing hydrodynamic processes and nutrient supply down to the microscale. To obtain a more complete picture of the distribution of such build-ups in the earth’s history, more fossil records need to be (re)investigated. For the time being, environmental and taphonomic studies of modern nonspicular demosponges are urgently required.
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Chung, Y. Anny, and Jennifer A. Rudgers. "Plant–soil feedbacks promote negative frequency dependence in the coexistence of two aridland grasses." Proceedings of the Royal Society B: Biological Sciences 283, no. 1835 (July 27, 2016): 20160608. http://dx.doi.org/10.1098/rspb.2016.0608.
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Understanding the mechanisms of species coexistence is key to predicting patterns of species diversity. Historically, the ecological paradigm has been that species coexist by partitioning resources: as a species increases in abundance, self-limitation kicks in, because species-specific resources decline. However, determining coexistence mechanisms has been a particular puzzle for sedentary organisms with high overlap in their resource requirements, such as plants. Recent evidence suggests that plant-associated microbes could generate the stabilizing self-limitation (negative frequency dependence) that is required for species coexistence. Here, we test the key assumption that plant–microbe feedbacks cause such self-limitation. We used competition experiments and modelling to evaluate how two common groups of soil microbes (rhizospheric microbes and biological soil crusts) influenced the self-limitation of two competing desert grass species. Negative feedbacks between the dominant plant competitor and its rhizospheric microbes magnified self-limitation, whereas beneficial interactions between both plant species and biological soil crusts partly counteracted this stabilizing effect. Plant–microbe interactions have received relatively little attention as drivers of vegetation dynamics in dry land ecosystems. Our results suggest that microbial mechanisms can contribute to patterns of plant coexistence in arid grasslands.
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Jamieson, Nicola, and Kenneth Killham. "Biocide manipulation of N flow to investigate root/microbe competition in forest soil." Plant and Soil 159, no. 2 (February 1994): 283–90. http://dx.doi.org/10.1007/bf00009291.
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Liu, Hui, Jing Chen, Tianzi Qin, Xinjian Shi, Yubao Gao, and Anzhi Ren. "Removal of Soil Microbes Alters Interspecific Competitiveness of Epichloë Endophyte-Infected over Endophyte-Free Leymus chinensis." Microorganisms 8, no. 2 (February 6, 2020): 219. http://dx.doi.org/10.3390/microorganisms8020219.
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Epichloë endophytes may not only affect the growth and resistances of host grasses, but may also affect soil environment including soil microbes. Can Epichloë endophyte-mediated modification of soil microbes affect the competitive ability of host grasses? In this study, we tested whether Epichloë endophytes and soil microbes alter intraspecific competition between Epichloë endophyte-colonized (EI) and endophyte-free (EF) Leymus chinensis and interspecific competition between L. chinensis and Stipa krylovii. The results demonstrated that Epichloë endophyte colonization significantly enhanced the intraspecific competitive ability of L. chinensis and that this beneficial effect was not affected by soil microbes. Under interspecific competition, however, significant interactions between Epichloë endophytes and soil microbes were observed. The effect of Epichloë endophytes on interspecific competitiveness of the host changed from positive to neutral with soil microbe removal. Here higher mycorrhizal colonization rates probably contributed to interspecific competitive advantages of EI over EF L. chinensis. Our result suggests that Epichloë endophytes can influence the competitive ability of the host through plant soil feedbacks from the currently competing plant species.
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Neumann, Wilma, Rose C. Hadley, and Elizabeth M. Nolan. "Transition metals at the host–pathogen interface: how Neisseria exploit human metalloproteins for acquiring iron and zinc." Essays in Biochemistry 61, no. 2 (May 9, 2017): 211–23. http://dx.doi.org/10.1042/ebc20160084.
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Transition metals are essential nutrients for all organisms and important players in the host–microbe interaction. During bacterial infection, a tug-of-war between the host and microbe for nutrient metals occurs: the host innate immune system responds to the pathogen by reducing metal availability and the pathogen tries to outmaneuver this response. The outcome of this competition, which involves metal-sequestering host-defense proteins and microbial metal acquisition machinery, is an important determinant for whether infection occurs. One strategy bacterial pathogens employ to overcome metal restriction involves hijacking abundant host metalloproteins. The obligate human pathogens Neisseria meningitidis and N. gonorrhoeae express TonB-dependent transport systems that capture human metalloproteins, extract the bound metal ions, and deliver these nutrients into the bacterial cell. This review highlights structural and mechanistic investigations that provide insights into how Neisseria acquire iron from the Fe(III)-transport protein transferrin (TF), the Fe(III)-chelating host-defense protein lactoferrin (LF), and the oxygen-transport protein hemoglobin (Hb), and obtain zinc from the metal-sequestering antimicrobial protein calprotectin (CP).
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Aivelo, Tuomas, Anna Norberg, and Barbara Tschirren. "Bacterial microbiota composition of Ixodes ricinus ticks: the role of environmental variation, tick characteristics and microbial interactions." PeerJ 7 (December 19, 2019): e8217. http://dx.doi.org/10.7717/peerj.8217.
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Ecological factors, host characteristics and/or interactions among microbes may all shape the occurrence of microbes and the structure of microbial communities within organisms. In the past, disentangling these factors and determining their relative importance in shaping within-host microbiota communities has been hampered by analytical limitations to account for (dis)similar environmental preferences (‘environmental filtering’). Here we used a joint species distribution modelling (JSDM) approach to characterize the bacterial microbiota of one of the most important disease vectors in Europe, the sheep tick Ixodes ricinus, along ecological gradients in the Swiss Alps. Although our study captured extensive environmental variation along elevational clines, the explanatory power of such large-scale ecological factors was comparably weak, suggesting that tick-specific traits and behaviours, microhabitat and -climate experienced by ticks, and interactions among microbes play an important role in shaping tick microbial communities. Indeed, when accounting for shared environmental preferences, evidence for significant patterns of positive or negative co-occurrence among microbes was found, which is indicative of competition or facilitation processes. Signals of facilitation were observed primarily among human pathogens, leading to co-infection within ticks, whereas signals of competition were observed between the tick endosymbiont Spiroplasma and human pathogens. These findings highlight the important role of small-scale ecological variation and microbe-microbe interactions in shaping tick microbial communities and the dynamics of tick-borne disease.
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Hood-Pishchany, M. Indriati, and Seth Rakoff-Nahoum. "#85: Nutrient Availability Drives Community Dynamics in the Vaginal Microbiota." Journal of the Pediatric Infectious Diseases Society 10, Supplement_1 (March 1, 2021): S9. http://dx.doi.org/10.1093/jpids/piaa170.027.
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Abstract Background Nutrient utilization is both critical for niche occupation and is the driver of competitive and cooperative interactions in microbial communities. The FRT is replete with host-associated glycans in the form of glycoproteins, epithelial glycogen stores, and the breakdown products of these glycans. I hypothesized that host-associated glycans drive environment, microbe–microbe and host–microbe interactions in the FRT. Methods We have developed robust, scalable, high-throughput culturing systems to empirically define the substrate utilization traits from more than 60 unique bacterial species capable of colonizing the vagina. In addition, we are using batch and continuous culture in vitro cultivation of multispecies communities to study vaginal bacteria within the complex community, that closely recapitulate key dynamics observed in vivo. Results Demonstrating the power of these in vitro models, I have defined the carbohydrate utilization profiles of hundreds of unique FRT isolates, identifying species and strain-level variation in utilization of host-derived carbohydrates. Given the known abundance of glycogen in the vaginal epithelium, I hypothesized that the utilization of host-associated glycogen represents an adaptation to the vaginal environment. Indeed, we identify glycogen degradation enzymes in diverse species resident in the reproductive tract, and find enrichment in genes encoding glycogen-degrading enzymes in L. crispatus strains derived from vaginal as opposed to intestinal sites. Metatranscriptomic analyses from human samples demonstrate that bacterial glycogen and maltose (a breakdown product of glycogen) utilization genes are highly expressed in the vagina and elucidate patterns of gene expression suggestive of context-dependent competition and cooperation for glycogen utilization in vivo. To empirically investigate the impact of glycogen availability and glycogen utilization in FRT microbiota communities, I assembled type strains or co-resident consortia into model, polymicrobial communities in vitro. These studies demonstrate that among health-associated L. crispatus strains, those that use glycogen have a competitive advantage during growth in a complex community. However, preliminary results suggest that some strains may benefit from cross-fed nutrients liberated by other members of the consortium. Conclusions Taken together, these data establish that strain-level variability in glycan utilization contributes to competitive fitness during growth in community, and suggest that these traits may influence community stability or persistence in vivo. Moreover, the methods we have developed provide a scalable system in which to empirically study ecological dynamics within complex community ex vivo.
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Usyskin-Tonne, Alla, Yitzhak Hadar, and Dror Minz. "Spike Formation Is a Turning Point Determining Wheat Root Microbiome Abundance, Structures and Functions." International Journal of Molecular Sciences 22, no. 21 (November 4, 2021): 11948. http://dx.doi.org/10.3390/ijms222111948.
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Root selection of their associated microbiome composition and activities is determined by the plant’s developmental stage and distance from the root. Total gene abundance, structure and functions of root-associated and rhizospheric microbiomes were studied throughout wheat growth season under field conditions. On the root surface, abundance of the well-known wheat colonizers Proteobacteria and Actinobacteria decreased and increased, respectively, during spike formation, whereas abundance of Bacteroidetes was independent of spike formation. Metagenomic analysis combined with functional co-occurrence networks revealed a significant impact of plant developmental stage on its microbiome during the transition from vegetative growth to spike formation. For example, gene functions related to biofilm and sensorial movement, antibiotic production and resistance and carbons and amino acids and their transporters. Genes associated with these functions were also in higher abundance in root vs. the rhizosphere microbiome. We propose that abundance of transporter-encoding genes related to carbon and amino acid, may mirror the availability and utilization of root exudates. Genes related to antibiotic resistance mechanisms were abundant during vegetative growth, while after spike formation, genes related to the biosynthesis of various antibiotics were enriched. This observation suggests that during root colonization and biofilm formation, bacteria cope with competitor’s antibiotics, whereas in the mature biofilm stage, they invest in inhibiting new colonizers. Additionally, there is higher abundance of genes related to denitrification in rhizosphere compared to root-associated microbiome during wheat growth, possibly due to competition with the plant over nitrogen in the root vicinity. We demonstrated functional and phylogenetic division in wheat root zone microbiome in both time and space: pre- and post-spike formation, and root-associated vs. rhizospheric niches. These findings shed light on the dynamics of plant–microbe and microbe–microbe interactions in the developing root zone.
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Zhu, Qing, William J. Riley, and Jinyun Tang. "A new theory of plant-microbe nutrient competition resolves inconsistencies between observations and model predictions." Ecological Applications 27, no. 3 (March 13, 2017): 875–86. http://dx.doi.org/10.1002/eap.1490.
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Li, Xiang-Yi, Tim Lachnit, Sebastian Fraune, Thomas C. G. Bosch, Arne Traulsen, and Michael Sieber. "Temperate phages as self-replicating weapons in bacterial competition." Journal of The Royal Society Interface 14, no. 137 (December 2017): 20170563. http://dx.doi.org/10.1098/rsif.2017.0563.
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Microbial communities are accompanied by a diverse array of viruses. Through infections of abundant microbes, these viruses have the potential to mediate competition within the community, effectively weakening competitive interactions and promoting coexistence. This is of particular relevance for host-associated microbial communities, because the diversity of the microbiota has been linked to host health and functioning. Here, we study the interaction between two key members of the microbiota of the freshwater metazoan Hydra vulgaris . The two commensal bacteria Curvibacter sp. and Duganella sp. protect their host from fungal infections, but only if both of them are present. Coexistence of the two bacteria is thus beneficial for Hydra . Intriguingly, Duganella sp. appears to be the superior competitor in vitro due to its higher growth rate when both bacteria are grown separately, but in co-culture the outcome of competition depends on the relative initial abundances of the two species. The presence of an inducible prophage in the Curvibacter sp. genome, which is able to lytically infect Duganella sp., led us to hypothesize that the phage modulates the interaction between these two key members of the Hydra microbiota. Using a mathematical model, we show that the interplay of the lysogenic life cycle of the Curvibacter phage and the lytic life cycle on Duganella sp. can explain the observed complex competitive interaction between the two bacteria. Our results highlight the importance of taking lysogeny into account for understanding microbe–virus interactions and show the complex role phages can play in promoting coexistence of their bacterial hosts.
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Blanchette, Melanie L., and Mark A. Lund. "Aquatic Ecosystems of the Anthropocene: Limnology and Microbial Ecology of Mine Pit Lakes." Microorganisms 9, no. 6 (June 3, 2021): 1207. http://dx.doi.org/10.3390/microorganisms9061207.
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Mine pit lakes (‘pit lakes’) are new aquatic ecosystems of the Anthropocene. Potentially hundreds of meters deep, these lakes are prominent in the landscape and in the public consciousness. However, the ecology of pit lakes is underrepresented in the literature. The broad goal of this research was to determine the environmental drivers of pelagic microbe assemblages in Australian coal pit lakes. The overall experimental design was four lakes sampled three times, top and bottom, in 2019. Instrument chains were installed in lakes and measurements of in situ water quality and water samples for metals, metalloids, nutrients and microbe assemblage were collected. Lakes were monomictic and the timing of mixing was influenced by high rainfall events. Water quality and microbial assemblages varied significantly across space and time, and most taxa were rare. Lakes were moderately saline and circumneutral; Archeans were not prevalent. Richness also varied by catchment. Microbial assemblages correlated to environmental variables, and no one variable was consistently significant, spatially or temporally. Study lakes were dominated by ‘core’ taxa exhibiting temporal turnover likely driven by geography, water quality and interspecific competition, and the presence of water chemistry associated with an artificial aquifer likely influenced microbial community composition. Pit lakes are deceptively complex aquatic ecosystems that host equally complex pelagic microbial communities. This research established links between microbial assemblages and environmental variables in pit lakes and determined core communities; the first steps towards developing a monitoring program using microbes.
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Zilelidou, Evangelia A., and Aspasia Nisiotou. "Understanding Wine through Yeast Interactions." Microorganisms 9, no. 8 (July 29, 2021): 1620. http://dx.doi.org/10.3390/microorganisms9081620.
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Wine is a product of microbial activities and microbe–microbe interactions. Yeasts are the principal microorganisms responsible for the evolution and fulfillment of alcoholic fermentation. Several species and strains coexist and interact with their environment and with each other during the fermentation course. Yeast–yeast interactions occur even from the early stages of fermentation, determining yeast community structure and dynamics during the process. Different types of microbial interactions (e.g., mutualism and commensalism or competition and amensalism) may exert positive or negative effects, respectively, on yeast populations. Interactions are intimately linked to yeast metabolic activities that influence the wine analytical profile and shape the wine character. In this context, much attention has been given during the last years to the interactions between Saccharomyces cerevisiae (SC) and non-Saccharomyces (NS) yeast species with respect to their metabolic contribution to wine quality. Yet, there is still a significant lack of knowledge on the interaction mechanisms modulating yeast behavior during mixed culture fermentation, while much less is known about the interactions between the various NS species or between SC and Saccharomyces non-cerevisiae (SNC) yeasts. There is still much to learn about their metabolic footprints and the genetic mechanisms that alter yeast community equilibrium in favor of one species or another. Gaining deeper insights on yeast interactions in the grape–wine ecosystem sets the grounds for understanding the rules underlying the function of the wine microbial system and provides means to better control and improve oenological practices.
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Than, Anh The, Fleur Ponton, and Juliano Morimoto. "Integrative developmental ecology: a review of density-dependent effects on life-history traits and host-microbe interactions in non-social holometabolous insects." Evolutionary Ecology 34, no. 5 (September 2, 2020): 659–80. http://dx.doi.org/10.1007/s10682-020-10073-x.
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Abstract Population density modulates a wide range of eco-evolutionary processes including inter- and intra-specific competition, fitness and population dynamics. In holometabolous insects, the larval stage is particularly susceptible to density-dependent effects because the larva is the resource-acquiring stage. Larval density-dependent effects can modulate the expression of life-history traits not only in the larval and adult stages but also downstream for population dynamics and evolution. Better understanding the scope and generality of density-dependent effects on life-history traits of current and future generations can provide useful knowledge for both theory and experiments in developmental ecology. Here, we review the literature on larval density-dependent effects on fitness of non-social holometabolous insects. First, we provide a functional definition of density to navigate the terminology in the literature. We then classify the biological levels upon which larval density-dependent effects can be observed followed by a review of the literature produced over the past decades across major non-social holometabolous groups. Next, we argue that host-microbe interactions are yet an overlooked biological level susceptible to density-dependent effects and propose a conceptual model to explain how density-dependent effects on host-microbe interactions can modulate density-dependent fitness curves. In summary, this review provides an integrative framework of density-dependent effects across biological levels which can be used to guide future research in the field of ecology and evolution.
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Zhang, Xiaoyan, Ruifang Ye, Fengxian Hu, Yitao Zheng, Shuhong Gao, Yingping Zhuang, Qiyao Wang, and Yunpeng Bai. "Learning from Competition: An Outcome-Based Introductory Activity for First-Year Biotechnology Undergraduates." American Biology Teacher 81, no. 7 (September 1, 2019): 467–73. http://dx.doi.org/10.1525/abt.2019.81.7.467.
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In recent years, accreditation standards for international engineering education have led to a dramatic rise in the use of outcome-based education at universities. In this system, enticing new undergraduate students to science and engineering, although challenging, is the first important step toward building students' career competencies. An ongoing effort to attract students to biotechnology was initiated 13 years ago in the School of Biotechnology at the East China University of Science and Technology in Shanghai. We describe the design and organization of the Microbe Competition, a program attracting a total of nearly 6,500 students as of 2018. In the competition, students need to pass the microbiology knowledge test, provide a practical experiment proposal related to the topic of competition, and finish the experiment under the supervision of teachers before getting final prizes. The competition develops students' competencies in acquiring and applying knowledge, problem solving, teamwork, communication, and experimental skills. By investigating students' feedback, we have been continuously improving the quality of competition to attract more students from the biotechnology major. We hope that by sharing our experience, we can help educators at other universities organize similar introductory activities on their own campuses.
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Zhang, Chi, Jiangman He, Huiling Dai, Gang Wang, Xiaowei Zhang, Chao Wang, Jincai Shi, Xi Chen, Dapeng Wang, and Ertao Wang. "Discriminating symbiosis and immunity signals by receptor competition in rice." Proceedings of the National Academy of Sciences 118, no. 16 (April 14, 2021): e2023738118. http://dx.doi.org/10.1073/pnas.2023738118.
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Plants encounter various microbes in nature and must respond appropriately to symbiotic or pathogenic ones. In rice, the receptor-like kinase OsCERK1 is involved in recognizing both symbiotic and immune signals. However, how these opposing signals are discerned via OsCERK1 remains unknown. Here, we found that receptor competition enables the discrimination of symbiosis and immunity signals in rice. On the one hand, the symbiotic receptor OsMYR1 and its short-length chitooligosaccharide ligand inhibit complex formation between OsCERK1 and OsCEBiP and suppress OsCERK1 phosphorylating the downstream substrate OsGEF1, which reduces the sensitivity of rice to microbe-associated molecular patterns. Indeed, OsMYR1 overexpression lines are more susceptible to the fungal pathogen Magnaporthe oryzae, whereas Osmyr1 mutants show higher resistance. On the other hand, OsCEBiP can bind OsCERK1 and thus block OsMYR1–OsCERK1 heteromer formation. Consistently, the Oscebip mutant displayed a higher rate of mycorrhizal colonization at early stages of infection. Our results indicate that OsMYR1 and OsCEBiP receptors compete for OsCERK1 to determine the outcome of symbiosis and immunity signals.
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Butterbach-Bahl, Klaus, Elizabeth M. Baggs, Michael Dannenmann, Ralf Kiese, and Sophie Zechmeister-Boltenstern. "Nitrous oxide emissions from soils: how well do we understand the processes and their controls?" Philosophical Transactions of the Royal Society B: Biological Sciences 368, no. 1621 (July 5, 2013): 20130122. http://dx.doi.org/10.1098/rstb.2013.0122.
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Although it is well established that soils are the dominating source for atmospheric nitrous oxide (N 2 O), we are still struggling to fully understand the complexity of the underlying microbial production and consumption processes and the links to biotic (e.g. inter- and intraspecies competition, food webs, plant–microbe interaction) and abiotic (e.g. soil climate, physics and chemistry) factors. Recent work shows that a better understanding of the composition and diversity of the microbial community across a variety of soils in different climates and under different land use, as well as plant–microbe interactions in the rhizosphere, may provide a key to better understand the variability of N 2 O fluxes at the soil–atmosphere interface. Moreover, recent insights into the regulation of the reduction of N 2 O to dinitrogen (N 2 ) have increased our understanding of N 2 O exchange. This improved process understanding, building on the increased use of isotope tracing techniques and metagenomics, needs to go along with improvements in measurement techniques for N 2 O (and N 2 ) emission in order to obtain robust field and laboratory datasets for different ecosystem types. Advances in both fields are currently used to improve process descriptions in biogeochemical models, which may eventually be used not only to test our current process understanding from the microsite to the field level, but also used as tools for up-scaling emissions to landscapes and regions and to explore feedbacks of soil N 2 O emissions to changes in environmental conditions, land management and land use.
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Maynard, Daniel S., Kenneth E. Leonard, John M. Drake, David W. Hall, Thomas W. Crowther, and Mark A. Bradford. "Modelling the multidimensional niche by linking functional traits to competitive performance." Proceedings of the Royal Society B: Biological Sciences 282, no. 1811 (July 22, 2015): 20150516. http://dx.doi.org/10.1098/rspb.2015.0516.
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Linking competitive outcomes to environmental conditions is necessary for understanding species' distributions and responses to environmental change. Despite this importance, generalizable approaches for predicting competitive outcomes across abiotic gradients are lacking, driven largely by the highly complex and context-dependent nature of biotic interactions. Here, we present and empirically test a novel niche model that uses functional traits to model the niche space of organisms and predict competitive outcomes of co-occurring populations across multiple resource gradients. The model makes no assumptions about the underlying mode of competition and instead applies to those settings where relative competitive ability across environments correlates with a quantifiable performance metric. To test the model, a series of controlled microcosm experiments were conducted using genetically related strains of a widespread microbe. The model identified trait microevolution and performance differences among strains, with the predicted competitive ability of each organism mapped across a two-dimensional carbon and nitrogen resource space. Areas of coexistence and competitive dominance between strains were identified, and the predicted competitive outcomes were validated in approximately 95% of the pairings. By linking trait variation to competitive ability, our work demonstrates a generalizable approach for predicting and modelling competitive outcomes across changing environmental contexts.
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Liu-Xu, Luisa, Ana Isabel González-Hernández, Gemma Camañes, Begonya Vicedo, Loredana Scalschi, and Eugenio Llorens. "Harnessing Green Helpers: Nitrogen-Fixing Bacteria and Other Beneficial Microorganisms in Plant–Microbe Interactions for Sustainable Agriculture." Horticulturae 10, no. 6 (June 11, 2024): 621. http://dx.doi.org/10.3390/horticulturae10060621.
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The health of soil is paramount for sustaining life, as it hosts diverse communities of microorganisms that interact with plants, influencing their growth, health, and resilience. Beneficial microorganisms, including fungi and bacteria, form symbiotic relationships with plants, providing essential nutrients, promoting growth, and enhancing stress tolerance. These microorganisms, such as mycorrhizal fungi and plant growth-promoting bacteria, play crucial roles in nutrient cycling, soil health, and plant productivity. Additionally, they help lessen reliance on chemical fertilizers, thereby mitigating the environmental risks associated with their use. Advances in agricultural practices harness the potential of these beneficial microorganisms to improve crop yields while minimizing the environmental impact. However, challenges such as competition with indigenous microbial strains and environmental factors limit the universal utilization of microbial inoculants. Despite these challenges, understanding and leveraging the interactions between plants and beneficial microorganisms hold promise for sustainable agriculture and enhanced food security.
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Cao, Juan, Ruirui Yan, Xiaoyong Chen, Xu Wang, Qiang Yu, Yunlong Zhang, Chen Ning, Lulu Hou, Yongjuan Zhang, and Xiaoping Xin. "Grazing Affects the Ecological Stoichiometry of the Plant–Soil–Microbe System on the Hulunber Steppe, China." Sustainability 11, no. 19 (September 24, 2019): 5226. http://dx.doi.org/10.3390/su11195226.
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Grazing affects nutrient cycling processes in grasslands, but little is known by researchers about effects on the nutrient stoichiometry of plant–soil–microbe systems. In this study, the influence of grazing intensity (0, 0.23, 0.34, 0.46, 0.69, and 0.92 AU ha−1) on carbon (C), nitrogen (N) and phosphorus (P) and their stoichiometric ratios in plants, soil, and microbes was investigated in a Hulunber meadow steppe, Northeastern China. The C:N and C:P ratios of shoots decreased with grazing increased. Leaf N:P ratios <10 suggested that the plant communities under grazing were N-limited. Heavy grazing intensities increased the C:N and C:P ratios of microbial biomass, but grazing intensity had no significant effects on the stoichiometry of soil nutrients. The coupling relationship of C:N ratio in plant–soil–microbial systems was tightly significant compared to C:P ratio and N:P ratio according to the correlation results. The finding suggested grazing exacerbated the competition between plants and microorganisms for N and P nutrition by the stoichiometric changes (%) in each grazing level relative to the no grazing treatment. Therefore, for the sustainability of grasslands in Inner Mongolia, N inputs need to be increased and high grazing intensities reduced in meadow steppe ecosystems, and the grazing load should be controlled within G0.46.
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Lipson, David A., and Russell K. Monson. "Plant-microbe competition for soil amino acids in the alpine tundra: effects of freeze-thaw and dry-rewet events." Oecologia 113, no. 3 (January 28, 1998): 406–14. http://dx.doi.org/10.1007/s004420050393.
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Ushio, Masayuki, Takeshi Miki, and Kanehiro Kitayama. "Phenolic Control of Plant Nitrogen Acquisition through the Inhibition of Soil Microbial Decomposition Processes: A Plant-Microbe Competition Model." Microbes and Environments 24, no. 2 (2009): 180–87. http://dx.doi.org/10.1264/jsme2.me09107.
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Agathokleous, Evgenios, Zhaozhong Feng, Elina Oksanen, Pierre Sicard, Qi Wang, Costas J. Saitanis, Valda Araminiene, et al. "Ozone affects plant, insect, and soil microbial communities: A threat to terrestrial ecosystems and biodiversity." Science Advances 6, no. 33 (August 2020): eabc1176. http://dx.doi.org/10.1126/sciadv.abc1176.
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Elevated tropospheric ozone concentrations induce adverse effects in plants. We reviewed how ozone affects (i) the composition and diversity of plant communities by affecting key physiological traits; (ii) foliar chemistry and the emission of volatiles, thereby affecting plant-plant competition, plant-insect interactions, and the composition of insect communities; and (iii) plant-soil-microbe interactions and the composition of soil communities by disrupting plant litterfall and altering root exudation, soil enzymatic activities, decomposition, and nutrient cycling. The community composition of soil microbes is consequently changed, and alpha diversity is often reduced. The effects depend on the environment and vary across space and time. We suggest that Atlantic islands in the Northern Hemisphere, the Mediterranean Basin, equatorial Africa, Ethiopia, the Indian coastline, the Himalayan region, southern Asia, and Japan have high endemic richness at high ozone risk by 2100.
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Rozen, D. E., D. J. P. Engelmoer, and P. T. Smiseth. "Antimicrobial strategies in burying beetles breeding on carrion." Proceedings of the National Academy of Sciences 105, no. 46 (November 10, 2008): 17890–95. http://dx.doi.org/10.1073/pnas.0805403105.
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Rich and ephemeral resources, such as carrion, are a source of intense interspecific competition among animal scavengers and microbial decomposers. Janzen [Janzen DH (1977) Am Nat 111:691–713] hypothesized that microbes should be selected to defend such resources by rendering them unpalatable or toxic to animals, and that animals should evolve counterstrategies of avoidance or detoxification. Despite the ubiquity of animal-microbe competition, there are few tests of Janzen's hypothesis, in particular with respect to antimicrobial strategies in animals. Here, we use the burying beetle Nicrophorus vespilloides, a species that obligately breeds on carcasses of small vertebrates, to investigate the role of parental care and avoidance as antimicrobial strategies. We manipulated competition between beetle larvae and microbes by providing beetles with either fresh carcasses or old ones that had reached advanced putrefaction. We found evidence for a strong detrimental effect of microbial competition on beetle reproductive success and larval growth. We also found that parental care can largely compensate for these negative effects, and that when given a choice between old and fresh carcasses, parents tended to choose to rear their broods on the latter. We conclude that parental care and carcass avoidance can function as antimicrobial strategies in this species. Our findings extend the range of behavioral counterstrategies used by animals during competition with microbes, and generalize the work of Janzen to include competition between microbes and insects that rely on carrion as an obligate resource for breeding and not just as an opportunistic meal.
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Si, Meiru, Chao Zhao, Brianne Burkinshaw, Bing Zhang, Dawei Wei, Yao Wang, Tao G. Dong, and Xihui Shen. "Manganese scavenging and oxidative stress response mediated by type VI secretion system in Burkholderia thailandensis." Proceedings of the National Academy of Sciences 114, no. 11 (February 27, 2017): E2233—E2242. http://dx.doi.org/10.1073/pnas.1614902114.
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Type VI secretion system (T6SS) is a versatile protein export machinery widely distributed in Gram-negative bacteria. Known to translocate protein substrates to eukaryotic and prokaryotic target cells to cause cellular damage, the T6SS has been primarily recognized as a contact-dependent bacterial weapon for microbe–host and microbial interspecies competition. Here we report contact-independent functions of the T6SS for metal acquisition, bacteria competition, and resistance to oxidative stress. We demonstrate that the T6SS-4 in Burkholderia thailandensis is critical for survival under oxidative stress and is regulated by OxyR, a conserved oxidative stress regulator. The T6SS-4 is important for intracellular accumulation of manganese (Mn2+) under oxidative stress. Next, we identified a T6SS-4–dependent Mn2+-binding effector TseM, and its interacting partner MnoT, a Mn2+-specific TonB-dependent outer membrane transporter. Similar to the T6SS-4 genes, expression of mnoT is regulated by OxyR and is induced under oxidative stress and low Mn2+ conditions. Both TseM and MnoT are required for efficient uptake of Mn2+ across the outer membrane under Mn2+-limited and -oxidative stress conditions. The TseM–MnoT-mediated active Mn2+ transport system is also involved in contact-independent bacteria–bacteria competition and bacterial virulence. This finding provides a perspective for understanding the mechanisms of metal ion uptake and the roles of T6SS in bacteria–bacteria competition.
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Frank, Steven A. "Microbial secretor–cheater dynamics." Philosophical Transactions of the Royal Society B: Biological Sciences 365, no. 1552 (August 27, 2010): 2515–22. http://dx.doi.org/10.1098/rstb.2010.0003.
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Microbial secretions manipulate the environment and communicate information to neighbours. The secretions of an individual microbe typically act externally and benefit all members of the local group. Secreting imposes a cost in terms of growth, so that cheaters that do not secrete gain by sharing the benefits without paying the costs. Cheaters have been observed in several experimental and natural settings. Given that cheaters grow faster than secretors when in direct competition, what maintains the widely observed patterns of secretion? Recent theory has emphasized the genetic structure of populations, in which secretors tend to associate spatially with other secretors, reducing direct competition and allowing highly secreting groups to share mutual benefits. Such kin selection can be a powerful force favouring cooperative traits. Here, I argue that, although kin selection is a factor, the combination of mutation and demographic processes dominate in determining the relative fitness of secretors versus cheaters when measured over the full cycle of microbial life history. Key demographic factors include the local density of microbes at which secretion significantly alters the environment, the extent to which secretion enhances microbial growth and maximum local density, and the ways in which secretion alters colony survival and dispersal.
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Ferrando, Maria Laura, Alex Gussak, Saskia Mentink, Marcela Fernandez Gutierrez, Peter van Baarlen, and Jerry Mark Wells. "Active Human and Porcine Serum Induce Competence for Genetic Transformation in the Emerging Zoonotic Pathogen Streptococcus suis." Pathogens 10, no. 2 (February 3, 2021): 156. http://dx.doi.org/10.3390/pathogens10020156.
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The acquisition of novel genetic traits through natural competence is a strategy used by bacteria in microbe-rich environments where microbial competition, antibiotics, and host immune defenses threaten their survival. Here, we show that virulent strains of Streptococcus suis, an important zoonotic agent and porcine pathogen, become competent for genetic transformation with plasmid or linear DNA when cultured in active porcine and human serum. Competence was not induced in active fetal bovine serum, which contains less complement factors and immunoglobulins than adult serum and was strongly reduced in heat-treated or low-molecular weight fractions of active porcine serum. Late competence genes, encoding the uptake machinery for environmental DNA, were upregulated in the active serum. Competence development was independent of the early competence regulatory switch involving XIP and ComR, as well as sigma factor ComX, suggesting the presence of an alternative stress-induced pathway for regulation of the late competence genes required for DNA uptake.
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Rennison, Diana J., Seth M. Rudman, and Dolph Schluter. "Parallel changes in gut microbiome composition and function during colonization, local adaptation and ecological speciation." Proceedings of the Royal Society B: Biological Sciences 286, no. 1916 (December 4, 2019): 20191911. http://dx.doi.org/10.1098/rspb.2019.1911.
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The processes of local adaptation and ecological speciation are often strongly shaped by biotic interactions such as competition and predation. One of the strongest lines of evidence that biotic interactions drive evolution comes from the repeated divergence of lineages in association with repeated changes in the community of interacting species. Yet relatively little is known about the repeatability of changes in gut microbial communities and their role in adaptation and divergence of host populations in nature. Here we use three cases of rapid, parallel adaptation and speciation in freshwater threespine stickleback to test for parallel changes in associated gut microbiomes. We find that features of the gut microbial communities have shifted repeatedly in the same direction in association with parallel divergence and speciation of stickleback hosts. These results suggest that changes to gut microbiomes can occur rapidly and predictably in conjunction with host evolution, and that host–microbe interactions might play an important role in host adaptation and diversification.
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Trienens, Monika, Nancy P. Keller, and Marko Rohlfs. "Fruit, flies and filamentous fungi - experimental analysis of animal-microbe competition using Drosophila melanogaster and Aspergillus mould as a model system." Oikos 119, no. 11 (May 13, 2010): 1765–75. http://dx.doi.org/10.1111/j.1600-0706.2010.18088.x.
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Hill, Paul W., and Davey L. Jones. "Plant–microbe competition: does injection of isotopes of C and N into the rhizosphere effectively characterise plant use of soil N?" New Phytologist 221, no. 2 (September 9, 2018): 796–806. http://dx.doi.org/10.1111/nph.15433.
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Hoptroff, Michael J., Simon V. Avery, and Simon Thomas. "Influence of altered plasma membrane fatty acid composition on cesium transport characteristics and toxicity inSaccharomyces cerevisiae." Canadian Journal of Microbiology 43, no. 10 (October 1, 1997): 954–62. http://dx.doi.org/10.1139/m97-137.
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The influence of altered plasma membrane fatty acid composition on cesium uptake and toxicity was investigated in Saccharomyces cerevisiae. Detailed kinetic studies revealed that both the Vmaxand Kmvalues for Cs+transport increased (by approximately twofold in the latter case) when S. cerevisiae was grown in medium supplemented with the polyunsaturated fatty acid linoleate. In addition, Cs+uptake by linoleate-enriched cells was considerably less sensitive to the competitive effects of other monovalent cations (K+, Rb+, and NH4+) than that by unsupplemented cells. Stimulation of Cs+uptake in the presence of certain K+and Rb+concentrations was only evident in linoleate-enriched S. cerevisiae. At 100 mM CsCl, the initial rate of Cs+uptake was greater in linoleate-supplemented cells than in unsupplemented cells and this was reflected in a more rapid displacement of cellular K+. However, little difference in net Cs+accumulation between linoleate-supplemented and unsupplemented cells was evident during prolonged incubation in buffer or during growth. Thus, Cs+toxicity was similar in linoleate-supplemented and unsupplemented cells. The results were consistent with the Cs+(K+) transport mechanism adopting an altered conformational state in linoleate-enriched S. cerevisiae.Key words: monovalent cation transport, plasma membrane fatty acid composition, lipid–protein interactions, metal–microbe interactions, cation competition.
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Menalled, Uriel D., K. Ann Bybee-Finley, Richard G. Smith, Antonio DiTommaso, Sarah J. Pethybridge, and Matthew R. Ryan. "Soil-Mediated Effects on Weed-Crop Competition: Elucidating the Role of Annual and Perennial Intercrop Diversity Legacies." Agronomy 10, no. 9 (September 12, 2020): 1373. http://dx.doi.org/10.3390/agronomy10091373.
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Crop diversity may mediate the intensity of weed-crop competition by altering soil nutrient availability and plant-soil microbe interactions. A greenhouse experiment was conducted to analyze weed-crop competition in soils with varying crop diversity legacies. Soil greenhouse treatments included field soils (i.e., soil nutrient and microbial legacies), a sterile greenhouse potting mix inoculated with microorganisms of the field soils (i.e., microbial legacies), and a sterile greenhouse potting mix. Soils for the greenhouse experiment were sampled and assessed after two-years of conditioning with annual and perennial cropping systems under four levels of intercrop diversity. The greenhouse experiment involved growing one sorghum sudangrass (Sorghum bicolor (L.) Moench × S. sudanese Piper) crop plant and zero to six common lambsquarters (Chenopodium album L.) weed plants in soil from each diversity and cropping system treatment. The weed density treatments created a weed-crop competition gradient, which was used to quantify legacy effects of crop diversity. Weed-crop competition increased with crop diversity in both the field soil and inoculated soil treatments in the annual system. In the perennial system, differences in weed-crop competition intensity were driven by crop yield potential. In the perennial field soil treatment, crop yield potential was greatest in the highest diversity treatment, whereas in the perennial inoculated soil treatment, crop yield potential was greatest in the lowest diversity treatment. Results show potential for negative effects from previous crop diversity on weed-crop competition, and the divergent impact of microbial and nutrient legacies on crop yield potential. Future research should aim to evaluate the consistency of legacy effects and identify principles that can guide soil and crop management, especially in conservation agriculture where soil tillage and its microbial legacy reducing effects are minimized.
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Mantovani, Hilario. "90 Microbiome-Derived Bioactive Molecules to Reduce Enteric Methane Emissions." Journal of Animal Science 101, Supplement_2 (October 28, 2023): 234–35. http://dx.doi.org/10.1093/jas/skad341.264.
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Abstract Microorganisms are pivotal for the development, health, and productivity of livestock. In adult ruminants, the microbiota colonizing the rumen is essential for efficient depolymerization of indigestible carbohydrates from plant biomass and their conversion into microbial protein and fermentation end-products that are used by the host for growth. In the last decades, next-generation sequencing and omics technologies provided unparalleled insights into the composition, structure, and function of the gastrointestinal (GI) tract microbiome of ruminants and helped improve our understanding of relationships between the rumen microbiota with cattle performance (efficiency) traits, as well as health and disease and greenhouse gas emissions. The ecological interactions between microbes within the rumen ecosystem are complex and involve, among others, cross-feeding, predation, parasitism, antagonism, and competition for novel (empty) niches and available resources. These diverse associations of ecological traits across distinct microbial populations that coexist in the same ecosystem represent a goldmine for the discovery of novel bioactive molecules, including compounds with potential to modulate rumen fermentation and inhibit methane emissions from enteric fermentation. These effects often result from metabolic shifts in the rumen fermentation that lead to increased production of propionate, but can also be caused by direct inhibition of methanogenic archaea or through a reduction in the production of substrates for methanogenesis. Culture-independent approaches based on genome mining and functional metagenomics demonstrated that the rumen is an underexplored resource for bioactive molecules, such as antimicrobial peptides, non-ribosomal peptides, polyketides, and secondary metabolites involved in intercellular (microbe-microbe) communication. Rumen metatranscriptomic data indicate that the expression of genes potentially encoding some of these molecules is increased during the colonization of plant biomass that enters the rumen. Nonetheless, some representatives of key taxa from the core rumen microbiome cannot be found in culture collections, which is critical to validate phenotypic predictions from genomic and metagenomic data and obtain ecological insights about the interplay between individual microbial populations in the microbiome. Culturomic technologies and high-throughput identification and characterization of microbial species that colonize the rumen could contribute to building a unique biotechnological resource that can be explored for sourcing novel bioactive compounds with anti-methanogenic activity and developing fermentation products that could reduce rumen methanogenesis while improving the health status and productivity of cattle.
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Wang, Lu, Zhangtao Li, Yan Wang, Philip C. Brookes, Fan Wang, Qichun Zhang, Jianming Xu, and Xingmei Liu. "Performance and mechanisms for remediation of Cd(II) and As(III) co-contamination by magnetic biochar-microbe biochemical composite: Competition and synergy effects." Science of The Total Environment 750 (January 2021): 141672. http://dx.doi.org/10.1016/j.scitotenv.2020.141672.
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Brugger, Silvio D., Sara M. Eslami, Melinda M. Pettigrew, Isabel F. Escapa, Matthew T. Henke, Yong Kong, and Katherine P. Lemon. "Dolosigranulum pigrum Cooperation and Competition in Human Nasal Microbiota." mSphere 5, no. 5 (September 9, 2020). http://dx.doi.org/10.1128/msphere.00852-20.
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ABSTRACT Multiple epidemiological studies identify Dolosigranulum pigrum as a candidate beneficial bacterium based on its positive association with health, including negative associations with nasal/nasopharyngeal colonization by the pathogenic species Staphylococcus aureus and Streptococcus pneumoniae. Using a multipronged approach to gain new insights into D. pigrum function, we observed phenotypic interactions and predictions of genomic capacity that support the idea of a role for microbe-microbe interactions involving D. pigrum in shaping the composition of human nasal microbiota. We identified in vivo community-level and in vitro phenotypic cooperation by specific nasal Corynebacterium species. Also, D. pigrum inhibited S. aureus growth in vitro, whereas robust inhibition of S. pneumoniae required both D. pigrum and a nasal Corynebacterium together. D. pigrum l-lactic acid production was insufficient to account for these inhibitions. Genomic analysis of 11 strains revealed that D. pigrum has a small genome (average 1.86 Mb) and multiple predicted auxotrophies consistent with D. pigrum relying on its human host and on cocolonizing bacteria for key nutrients. Further, the accessory genome of D. pigrum harbored a diverse repertoire of biosynthetic gene clusters, some of which may have a role in microbe-microbe interactions. These new insights into D. pigrum’s functions advance the field from compositional analysis to genomic and phenotypic experimentation on a potentially beneficial bacterial resident of the human upper respiratory tract and lay the foundation for future animal and clinical experiments. IMPORTANCE Staphylococcus aureus and Streptococcus pneumoniae infections cause significant morbidity and mortality in humans. For both, nasal colonization is a risk factor for infection. Studies of nasal microbiota identify Dolosigranulum pigrum as a benign bacterium present when adults are free of S. aureus or when children are free of S. pneumoniae. Here, we validated these in vivo associations with functional assays. We found that D. pigrum inhibited S. aureus in vitro and, together with a specific nasal Corynebacterium species, also inhibited S. pneumoniae. Furthermore, genomic analysis of D. pigrum indicated that it must obtain key nutrients from other nasal bacteria or from humans. These phenotypic interactions support the idea of a role for microbe-microbe interactions in shaping the composition of human nasal microbiota and implicate D. pigrum as a mutualist of humans. These findings support the feasibility of future development of microbe-targeted interventions to reshape nasal microbiota composition to exclude S. aureus and/or S. pneumoniae.
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Ford, Suzanne A., Georgia C. Drew, and Kayla C. King. "Immune-mediated competition benefits protective microbes over pathogens in a novel host species." Heredity, November 9, 2022. http://dx.doi.org/10.1038/s41437-022-00569-3.
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AbstractMicrobes that protect against infection inhabit hosts across the tree of life. It is unclear whether and how the host immune system may affect the formation of new protective symbioses. We investigated the transcriptomic response of Caenorhabditis elegans following novel interactions with a protective microbe (Enterococcus faecalis) able to defend against infection by pathogenic Staphylococcus aureus. We have previously shown that E. faecalis can directly limit pathogen growth within hosts. In this study, we show that colonisation by protective E. faecalis caused the differential expression of 1,557 genes in pathogen infected hosts, including the upregulation of immune genes such as lysozymes and C-type lectins. The most significantly upregulated host lysozyme gene, lys-7, impacted the competitive abilities of E. faecalis and S. aureus when knocked out. E. faecalis has an increased ability to resist lysozyme activity compared to S. aureus, suggesting that the protective microbe could gain a competitive advantage from this host response. Our finding that protective microbes can benefit from immune-mediated competition after introduction opens up new possibilities for biocontrol design and our understanding of symbiosis evolution. Crosstalk between the host immune response and microbe-mediated protection should favour the continued investment in host immunity and avoid the potentially risky evolution of host dependence.
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Chung, Y. Anny, Po‐Ju Ke, and Peter B. Adler. "Mechanistic approaches to investigate soil microbe‐mediated plant competition." Journal of Ecology, July 3, 2023. http://dx.doi.org/10.1111/1365-2745.14156.
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Qu, Yaobing, Tianzi Qin, Xinjian Shi, Jing Chen, Hui Liu, Nianxi Zhao, Yubao Gao, and Anzhi Ren. "The effects of Epichloë endophytes on the growth and competitiveness of Achnatherum sibiricum are mediated by soil microbe diversity." Journal of Plant Ecology, March 4, 2022. http://dx.doi.org/10.1093/jpe/rtac028.
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Abstract Aims Many grasses are infected by systemic fungal endophytes that occur in aboveground plant tissues. Both aboveground endophytic fungi and belowground soil microbes can influence plant growth, but studies on their simultaneous effects on plant growth and competitiveness are limited. This study aims to investigate whether the role of aboveground endophytic fungi in the growth and competitive ability of the host grasses was influenced by soil microbes. Methods In this study, we used Epichloë endophyte-infected (EI) and endophyte-free (EF) Achnatherum sibiricum as plant materials. A wet sieving method was adopted to obtain microbial inocula with different diversities (com, combined microbe fraction, high diversity; sm, small microbe fraction, low diversity). A three-factor randomized block design was used. The first factor was the endophyte infection status of A. sibiricum. The second factor was the microbial composition of the soil inocula. The third factor was the planting type. Growth and competitive characters were measured after 16 weeks. Important Findings The results showed that a soil microbe inoculation was detrimental to the growth of A. sibiricum. Epichloë endophytes significantly mitigated the inhibitory effect of soil microbes on A. sibiricum planted alone. When A. sibiricum was planted with Stipa grandis, there was a significant interaction between Epichloë endophytes and soil microbes on the interspecific competition of A. sibiricum. When inoculated with small microbial community fraction, Epichloë endophytes significantly improved the interspecific competitive ability of host plants. When inoculated with combined microbial community fraction, however, Epichloë endophytes had no significant effect on host competition. The results showed that the interaction between Epichloë endophytes and soil microbes contributed more to the interspecific competitive ability than either Epichloë endophytes or soil microbes alone.