Hasil untuk "Microbial ecology"

Benedetta Ciarmoli, Sophie Marbach

Microbes constantly interact with their environment by depleting and transforming food sources. Theoretical studies have mainly focused on Lotka-Volterra models, which do not account for food source dynamics. In contrast, consumer-resource models, which consider food source dynamics, are less explored. In particular, it is still unclear what physical mechanisms control oscillatory dynamics at a single population level, a phenomenon which can only be captured by a consumer-resource model. Here, we present a minimalistic consumer-resource model of a single microbial population with growth and death dynamics, consuming a continuously replenishing substrate. Our model reveals that decaying oscillations can occur around steady state if and only if the timescale of microbial adaptation to food supply changes exceeds the death timescale. This interplay of timescales allows us to rationalize the emergence of oscillatory dynamics when adding various biophysical ingredients to the model. We find that microbial necromass recycling or complementary use of multiple food sources reduces the parameter range for oscillations and increases the decay rate of oscillations. Requiring multiple simultaneous food sources has the opposite effect. Essentially, facilitating growth reduces the likelihood of oscillations around a fixed point. We further demonstrate that such damped oscillatory behavior is correlated with persistent oscillatory behavior in a noisy environment. We hope our work will motivate further investigations of consumer-resource models to improve descriptions of environments where food source distributions vary in space and time.

Huyong Lee, Woori Na, Cheongmin Sohn

Fermented foods are produced through controlled microbial activity and are valued for their extended shelf life, sensory attributes, and potential health benefits. This study examined the effects of production methods on microbial ecology by comparing microbial community structure, Shannon diversity, and pH changes in traditional and commercially produced Korean fermented foods. Cabbage and radish kimchi were fermented for four weeks to assess microbial succession and physicochemical changes, and additional fermented foods, including soy sauce, soybean paste, pepper paste, fruit vinegar, yogurt, and aged kimchi, were compared according to production method. Microbial communities were analyzed using amplicon sequencing targeting the V3–V4 regions of the bacterial 16S rRNA gene and the fungal internal transcribed spacer (ITS) region. Traditionally produced cabbage kimchi exhibited high microbial diversity at the early fermentation stage, initially dominated by <i>Weissella</i> and <i>Leuconostoc</i>, followed by a gradual shift toward lactic acid bacteria dominance at later stages. In contrast, commercially produced cabbage kimchi maintained a simplified microbial community dominated by a limited number of lactic acid bacteria throughout fermentation. Radish kimchi showed production-method-dependent patterns, with the rapid dominance of lactic acid bacteria during traditional fermentation and partial recovery of microbial diversity during commercial fermentation. Shannon diversity was consistently higher in traditionally produced kimchi during fermentation. In contrast, commercially produced kimchi exhibited more rapid acidification. Across other fermented foods, traditionally produced soy-based products exhibited complex microbial communities dominated by <i>Bacillus</i> spp., whereas commercially produced products were characterized by yeast-dominant profiles. Fruit vinegar and yogurt showed low microbial diversity regardless of the production method. These findings demonstrate the importance of production strategies in shaping microbial ecology, fermentation dynamics, and resulting product characteristics across various Korean fermented foods.

Saleheh Ebadirad, Timothy W. Lyons, Gregory P. Fournier

This chapter explores the key carbon compounds that shaped the Archean biogeochemical cycle, delineating their substantial impact on Earth's primordial atmospheric and biospheric evolution. At the heart of the Archean carbon cycle were carbon dioxide and methane, which served as key regulators of Earth's early climate. Particular emphasis is placed on methane cycling, encompassing both abiotic methane production and consumption, as well as their biotic counterparts-methanogenesis and methanotrophy. These ancient microbial pathways not only shaped methane fluxes but were also tightly interwoven with Earth's evolving redox state. We provide a comprehensive exploration of the intertwined evolution of Earth's geochemical environment and microbial life. The interdisciplinary approach of this chapter not only sheds light on the complex dynamics of Earth's early methane cycling but also offers critical insights that could inform the search for life beyond our planet, thereby marking a contribution to Earth sciences, astrobiology, and related fields.

Javier Edo Varg, Jaelle C. Brealey, David Benhaïm et al.

Abstract The impact of microbial composition on stress-related behavior in aquatic organisms is poorly understood. This study explored the link between antipredator behavior, parasitism, and the gut microbiome in wild stickleback from two lakes: clear, spring-fed Galtaból and turbid, glacial-fed Þristikla. Behavioral analysis revealed differences between populations, with each exhibiting unique baseline behaviors. Microbiome analysis showed that a small proportion of its variation was explained by population, likely reflecting differences in lake environments. Only the marine genus Pseudoalteromonas abundance differed between populations. Our findings suggest that behavior and microbiome correlations may primarily reflect environmental adaptations and parasite status rather than direct gut-brain interactions. However, some tentative evidence suggests a potential innate connection between some antipredator behavior and microbiome composition. The study highlights the complexity of the gut-brain axis in wild populations and suggests future research directions, including experimental manipulations to uncover causal relationships between microbiome composition and behavior.

Imed Sbissi, Farah Chouikhi, Faten Ghodhbane-Gtari et al.

Abstract Background The stone-dwelling genus Blastococcus plays a key role in ecosystems facing extreme conditions such as drought, salinity, alkalinity, and heavy metal contamination. Despite its ecological significance, little is known about the genomic factors underpinning its adaptability and resilience in such harsh environments. This study investigates the genomic basis of Blastococcus's adaptability within its specific microniches, offering insights into its potential for biotechnological applications. Results Comprehensive pangenome analysis revealed that Blastococcus possesses a highly dynamic genetic composition, characterized by a small core genome and a large accessory genome, indicating significant genomic plasticity. Ecogenomic assessments highlighted the genus's capabilities in substrate degradation, nutrient transport, and stress tolerance, particularly on stone surfaces and archaeological sites. The strains also exhibited plant growth-promoting traits, enhanced heavy metal resistance, and the ability to degrade environmental pollutants, positioning Blastococcus as a candidate for sustainable agriculture and bioremediation. Interestingly, no correlation was found between the ecological or plant growth-promoting traits (PGPR) of the strains and their isolation source, suggesting that these traits are not linked to their specific environments. Conclusions This research highlights the ecological and biotechnological potential of Blastococcus species in ecosystem health, soil fertility improvement, and stress mitigation strategies. It calls for further studies on the adaptation mechanisms of the genus, emphasizing the need to validate these findings through wet lab experiments. This study enhances our understanding of microbial ecology in extreme environments and supports the use of Blastococcus in environmental management, particularly in soil remediation and sustainable agricultural practices.

Boda Liu, Xiang Li, Jinming Yang et al.

Abstract Background Habitat fragmentation and degradation have led to the critical endangerment of numerous wild plant species. Although significant achievements in the conservation of endangered wild plants in various regions worldwide, the interaction mechanisms between these plants and their associated rhizosphere microorganisms have yet to be fully elucidated. Results Here, we present a communication model between the endangered wild plant Qingdao lily (Lilium tsingtauense) and its associated rhizosphere microorganisms. We isolated a rhizosphere fungus, Trichoderma longibrachiatum QDAU 0920, which effectively colonizes the roots of Qingdao lily and significantly promotes root growth. This growth enhancement is mediated by multiple plant hormones, with auxin playing a particularly prominent role. Further investigation revealed that a non-canonical AUX/IAA protein of the LtIAA16 may augment the transcriptional activation activity of LtARF22 by competitively interacting with LtIAA6, LtIAA17, and LtIAA11, thereby facilitating root growth in Qingdao lily. The growth-promoting effects of this interaction were subsequently validated in several other plant species, including tomato, pepper, corn, pumpkin, and cucumber. Notably, T. longibrachiatum QDAU 0920 forms synthetic microbial consortia (SynComs) in conjunction with other Trichoderma and Penicillium species. These SynComs consistently enhance the growth of Qingdao lily as well as other lily species such as L. lancifolium, Lilium 'Avalon Sunset', and Lilium 'Deliana'. Conclusion Collectively, these findings underscore the considerable potential of native microorganisms in the development of plant growth-promoting agents and the conservation of endangered plant species. Video Abstract

Avaneesh V. Narla, Terence Hwa, Arvind Murugan

Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes often modify their environments so strongly that they are forced out of the exponential state into stressed or non-growing states. Such dynamics are typical of ecological succession in nature and serial-dilution cycles in the laboratory. Here, we introduce a phenomenological model, the Community State model, to gain insight into the dynamic coexistence of microbes due to changes in their physiological states. Our model bypasses specific interactions (e.g., nutrient starvation, stress, aggregation) that lead to different combinations of physiological states, referred to collectively as "community states", and modeled by specifying the growth preference of each species along a global ecological coordinate, taken here to be the total community biomass density. We identify three key features of such dynamical communities that contrast starkly with steady-state communities: increased tolerance of community diversity to fast growth rates of species dominating different community states, enhanced community stability through staggered dominance of different species in different community states, and increased requirement on growth dominance for the inclusion of late-growing species. These features, derived explicitly for simplified models, are proposed here to be principles aiding the understanding of complex dynamical communities. Our model shifts the focus of ecosystem dynamics from bottom-up studies based on idealized inter-species interaction to top-down studies based on accessible macroscopic observables such as growth rates and total biomass density, enabling quantitative examination of community-wide characteristics.

Djuna M. Gulliver, Elliott P. Barnhart, Hannah D. Schweitzer et al.

Can Chen, Xu-Wen Wang, Yang-Yu Liu

The stability of ecological systems is a fundamental concept in ecology, which offers profound insights into species coexistence, biodiversity, and community persistence. In this article, we provide a systematic and comprehensive review on the theoretical frameworks for analyzing the stability of ecological systems. Notably, we survey various stability notions, including linear stability, sign stability, diagonal stability, D-stability, total stability, sector stability, structural stability, and higher-order stability. For each of these stability notions, we examine necessary or sufficient conditions for achieving such stability and demonstrate the intricate interplay of these conditions on the network structures of ecological systems. Finally, we explore the future prospects of these stability notions.

Alba Regueira-Iglesias, Lara Vázquez-González, Carlos Balsa-Castro et al.

Abstract Background Sequencing has been widely used to study the composition of the oral microbiome present in various health conditions. The extent of the coverage of the 16S rRNA gene primers employed for this purpose has not, however, been evaluated in silico using oral-specific databases. This paper analyses these primers using two databases containing 16S rRNA sequences from bacteria and archaea found in the human mouth and describes some of the best primers for each domain. Results A total of 369 distinct individual primers were identified from sequencing studies of the oral microbiome and other ecosystems. These were evaluated against a database reported in the literature of 16S rRNA sequences obtained from oral bacteria, which was modified by our group, and a self-created oral archaea database. Both databases contained the genomic variants detected for each included species. Primers were evaluated at the variant and species levels, and those with a species coverage (SC) ≥75.00% were selected for the pair analyses. All possible combinations of the forward and reverse primers were identified, with the resulting 4638 primer pairs also evaluated using the two databases. The best bacteria-specific pairs targeted the 3-4, 4-7, and 3-7 16S rRNA gene regions, with SC levels of 98.83–97.14%; meanwhile, the optimum archaea-specific primer pairs amplified regions 5-6, 3-6, and 3-6, with SC estimates of 95.88%. Finally, the best pairs for detecting both domains targeted regions 4-5, 3-5, and 5-9, and produced SC values of 95.71–94.54% and 99.48–96.91% for bacteria and archaea, respectively. Conclusions Given the three amplicon length categories (100-300, 301-600, and >600 base pairs), the primer pairs with the best coverage values for detecting oral bacteria were as follows: KP_F048-OP_R043 (region 3-4; primer pair position for Escherichia coli J01859.1: 342-529), KP_F051-OP_R030 (4-7; 514-1079), and KP_F048-OP_R030 (3-7; 342-1079). For detecting oral archaea, these were as follows: OP_F066-KP_R013 (5-6; 784-undefined), KP_F020-KP_R013 (3-6; 518-undefined), and OP_F114-KP_R013 (3-6; 340-undefined). Lastly, for detecting both domains jointly they were KP_F020-KP_R032 (4-5; 518-801), OP_F114-KP_R031 (3-5; 340-801), and OP_F066-OP_R121 (5-9; 784-1405). The primer pairs with the best coverage identified herein are not among those described most widely in the oral microbiome literature. Video Abstract

Yuling Qu, Jianmin Yun, Yanhu Li et al.

IntroductionLongxi bacon is a traditional fermented meat from Gansu province, China. The ripening process of the bacon is crucial for quality and flavor. The aim of this study was to gain deeper knowledges on the bacterial and fungal community diversity and the changes of chemical components including fatty acids and volatile compounds at different time points during the ripening of the bacon and to understand the relationship between microbial profiles and the chemical components related the bacon flavor.MethodsBacon samples were collected from days 0, 15, 30, 60 and 90. The bacterial and fungal compositions were analyzed with next generation sequencing targeting the 16S rDNA loci for bacteria and ITS loci for fungi. The fatty acids and the volatile components were analyzed by headspace solid phase micro extraction followed by gas chromatography/mass spectrometry (HS-SPME-GC/MS).ResultsWe found that the abundance of bacteria in bacon was higher than that of fungi, and Psychrobacter, Brochothrix, Phoma and Trichoderma was the dominant bacon’s population. The largest contributors of volatiles were aldehydes, ketones and esters, and the main fatty acids were palmitic, oleic and linoleic acids. Pearson correlation analysis between microbial succession and key flavor substances showed that the production of Longxi bacon flavor is the result of a combination of bacteria and fungi. Ten bacteria genera and six fungi genera were determined as functional core microbiota for the flavor production based their dominance and functionality in microbial community. In addition, bacteria and fungi are involved in the oxidation and hydrolysis of fatty acids during the ripening of bacon, which also contributes to the formation of bacon flavor.DiscussionThis study provides a comprehensive analysis of the key microbiota involved in shaping bacon’s distinctive flavor. Here, the results presented should provide insight into the influence of the microenvironment on the microbial community in bacon and lay a foundation for further investigations into the food ecology of bacon.

Phil Thomas, Oliver G. G. Knox, Jeff R. Powell et al.

Land plants have an ancient and intimate relationship with microorganisms, which influences the composition of natural ecosystems and the performance of crops. Plants shape the microbiome around their roots by releasing organic nutrients into the soil. Hydroponic horticulture aims to protect crops from damaging soil-borne pathogens by replacing soil with an artificial growing medium, such as rockwool, an inert material made from molten rock spun into fibres. Microorganisms are generally considered a problem to be managed, to keep the glasshouse clean, but the hydroponic root microbiome assembles soon after planting and flourishes with the crop. Hence, microbe–plant interactions play out in an artificial environment that is quite unlike the soil in which they evolved. Plants in a near-ideal environment have little dependency on microbial partners, but our growing appreciation of the role of microbial communities is revealing opportunities to advance practices, especially in agriculture and human health. Hydroponic systems are especially well-suited to active management of the root microbiome because they allow complete control over the root zone environment; however, they receive much less attention than other host–microbiome interactions. Novel techniques for hydroponic horticulture can be identified by extending our understanding of the microbial ecology of this unique environment.

Ada Altieri

In this report, I will review some of the most used models in theoretical ecology along with appealing reformulations and recent results in terms of diversity, stability, and functioning of large well-mixed ecological communities.

Chuan Tian, Duo Jiang, Austin Hammer et al.

Understanding how microbes interact with each other is key to revealing the underlying role that microorganisms play in the host or environment and to identifying microorganisms as an agent that can potentially alter the host or environment. For example, understanding how the microbial interactions associate with parasitic infection can help resolve potential drug or diagnostic test for parasitic infection. To unravel the microbial interactions, existing tools often rely on graphical models to infer the conditional dependence of microbial abundances to represent their interactions. However, current methods do not simultaneously account for the discreteness, compositionality, and heterogeneity inherent to microbiome data. Thus, we build a new approach called "compositional graphical lasso" upon existing tools by incorporating the above characteristics into the graphical model explicitly. We illustrate the advantage of compositional graphical lasso over current methods under a variety of simulation scenarios and on a benchmark study, the Tara Oceans Project. Moreover, we present our results from the analysis of a dataset from the Zebrafish Parasite Infection Study. Our approach identifies changes in interaction degree between infected and uninfected individuals for three taxa, Photobacterium, Gemmobacter, and Paucibacter, which are inversely predicted by other methods. Further investigation of these method-specific taxa interaction changes reveals their biological plausibility. In particular, we speculate on the potential pathobiotic roles of Photobacterium and Gemmobacter in the zebrafish gut, and the potential probiotic role of Paucibacter. Collectively, our analyses demonstrate that compositional graphical lasso provides a powerful means of accurately resolving interactions between microbiota and can thus drive novel biological discovery.

B. Chen, F. J. Zhou, F. Yang et al.

The molybdenum (Mo) non-point source pollution in the mining area has an irreversible impact on the surrounding water and soil ecosystems. Herein, three integrated vertical subsurface flow constructed wetlands (CWs) were constructed to assess the effects of combination substrates and plant on the removal of Mo(VI). Results showed that CW1 with combination substrates and cattail exhibited a favorable removal performance for Mo(VI) at 80.90%. Moreover, most Mo(VI) retained in the CWs was retained in the substrate (58.13–88.04%), and the largest fraction of Mo(VI) retained was the water-soluble fraction on the surface of the combination substrates. Mo(VI) removal was also influenced by the microbial community composition in substrate, especially their co-occurrence networks. The species that showed significant positive correlation with Mo(VI) removal were Planctomycetes, Latescibacteria, Armatimonadetes, and Gemmatimonadetes. Moreover, CWs added plants showed that more co-occurrences interaction between taxa occurs, which means that the wetlands efficiently select recruitment of potential microbial consortia and change the co-occurrences to remove pollution in the substrate. These results could be useful in providing an ecology-based solution for the treatment of Mo(VI) in wastewater, especially in adjusting the microbial communities for Mo(VI) removal at the genetic level. HIGHLIGHTS Complex substrates coupled cattail enhanced Mo(VI) removal in constructed wetlands.; Adsorption was the main Mo(VI) removal mechanism by DWTRs and MCPP.; Mo(VI) removal was also influenced by microbial community composition.; Cattails changed the co-occurrences of microbes to remove pollution in substrates.;

Gianna Dirren-Pitsch, Dominique Bühler, Michaela M. Salcher et al.

Planktonic ciliate species form multiple trophic guilds and are central components of freshwater food webs. Progress in molecular analytical tools has opened new insight into ciliate assemblages. However, high and variable 18S rDNA copy numbers, typical for ciliates, make reliable quantification by amplicon sequencing extremely difficult. For an exact determination of abundances, the classical morphology-based quantitative protargol staining is still the method of choice. Morphotype analyses, however, are time consuming and need specific taxonomic expertise. Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) may represent a promising tool for the analysis of planktonic ciliates by combining molecular identification with microscopic quantification. We tested the applicability of CARD-FISH using nine cultured ciliate species. Eight species- and three genus-specific oligonucleotide probes were designed based on their 18S rRNA genes. The CARD-FISH protocol was adapted and the specificity of probes was established. We subsequently examined the precision of quantitation by CARD-FISH on single cultures and mock assemblages. Successful tests on lake water samples proved that planktonic ciliates could be identified and quantified in field samples by CARD-FISH. Double hybridizations allowed studying interspecific predator prey interactions between two ciliate species. In summary, we demonstrate that CARD-FISH with species-specific probes can facilitate studies on the population dynamics of closely related, small sized or cryptic species at high sampling frequencies.

Corinne Vacher, Claire Francioni, Marion Michel et al.

Helena Junicke

Recent efforts have focused on providing a systematic analysis of syntrophic microbial growth yields. These biokinetic parameters are key to developing an accurate mathematical description of the anaerobic digestion process. The agreement between experimentally determined growth yields and those obtained from bioenergetic estimations is therefore of great interest. Considering five important syntrophic groups, including acetoclastic and hydrogenotrophic methanogens, as well as propionate, butyrate and lactate oxidizers, previous findings suggest that measured and estimated growth yields were consistent only for acetoclastic methanogens. A re-analysis revealed that data are also consistent for lactate oxidizers and hydrogenotrophic methanogens, whereas the limited data available for propionate and butyrate oxidizers are unsupportive of firm conclusions. These results highlight pertinent challenges in the analysis of microbial syntrophy and encourage more accurate measurements of syntrophic microbial growth yields in the future.

Jacob Cook, Samraat Pawar, Robert G. Endres

Non-equilibrium thermodynamics has long been an area of substantial interest to ecologists because most fundamental biological processes, such as protein synthesis and respiration, are inherently energy-consuming. Microbial communities are a natural system to decipher this mechanistic basis because their interactions in the form of substrate consumption, metabolite production, and cross-feeding can be described explicitly in thermodynamic terms. Previous work has considered how thermodynamic constraints impact competition between pairs of species, but restrained from analysing how this manifests in complex dynamical systems. To address this gap, we develop a thermodynamic microbial community model with fully reversible reaction kinetics, which allows direct consideration of free-energy dissipation. This also allows species to interact via products rather than just substrates, increasing the dynamical complexity, and allowing a more nuanced classification of interaction types to emerge. Using this model, we find that community diversity increases with substrate lability, because greater free-energy availability allows for faster generation of niches. Thus, more niches are generated in the time frame of community establishment, leading to higher final species diversity. We also find that allowing species to make use of near-to-equilibrium reactions increases diversity in a low free-energy regime. In such a regime, two new thermodynamic interaction types that we identify here reach comparable strengths to the conventional (competition and facilitation) types, emphasising the key role that thermodynamics plays in community dynamics. Our results suggest that accounting for realistic thermodynamic constraints is vital for understanding the dynamics of real-world microbial communities.

Anahit Penesyan, Ian T. Paulsen, Staffan Kjelleberg et al.

Abstract Biofilms are organised heterogeneous assemblages of microbial cells that are encased within a self-produced matrix. Current estimates suggest that up to 80% of bacterial and archaeal cells reside in biofilms. Since biofilms are the main mode of microbial life, understanding their biology and functions is critical, especially as controlling biofilm growth is essential in industrial, infrastructure and medical contexts. Here we discuss biofilms both as collections of individual cells, and as multicellular biological individuals, and introduce the concept of biofilms as unique incubators of diversity for the microbial world.