Hasil untuk "Microbial ecology"

Shelly A Buffington, G. V. Prisco, T. A. Auchtung et al.

Matthew T. Agler, Jonas Ruhe, Samuel Kroll et al.

Plant-associated microorganisms have been shown to critically affect host physiology and performance, suggesting that evolution and ecology of plants and animals can only be understood in a holobiont (host and its associated organisms) context. Host-associated microbial community structures are affected by abiotic and host factors, and increased attention is given to the role of the microbiome in interactions such as pathogen inhibition. However, little is known about how these factors act on the microbial community, and especially what role microbe–microbe interaction dynamics play. We have begun to address this knowledge gap for phyllosphere microbiomes of plants by simultaneously studying three major groups of Arabidopsis thaliana symbionts (bacteria, fungi and oomycetes) using a systems biology approach. We evaluated multiple potential factors of microbial community control: we sampled various wild A. thaliana populations at different times, performed field plantings with different host genotypes, and implemented successive host colonization experiments under lab conditions where abiotic factors, host genotype, and pathogen colonization was manipulated. Our results indicate that both abiotic factors and host genotype interact to affect plant colonization by all three groups of microbes. Considering microbe–microbe interactions, however, uncovered a network of interkingdom interactions with significant contributions to community structure. As in other scale-free networks, a small number of taxa, which we call microbial “hubs,” are strongly interconnected and have a severe effect on communities. By documenting these microbe–microbe interactions, we uncover an important mechanism explaining how abiotic factors and host genotypic signatures control microbial communities. In short, they act directly on “hub” microbes, which, via microbe–microbe interactions, transmit the effects to the microbial community. We analyzed two “hub” microbes (the obligate biotrophic oomycete pathogen Albugo and the basidiomycete yeast fungus Dioszegia) more closely. Albugo had strong effects on epiphytic and endophytic bacterial colonization. Specifically, alpha diversity decreased and beta diversity stabilized in the presence of Albugo infection, whereas they otherwise varied between plants. Dioszegia, on the other hand, provided evidence for direct hub interaction with phyllosphere bacteria. The identification of microbial “hubs” and their importance in phyllosphere microbiome structuring has crucial implications for plant–pathogen and microbe–microbe research and opens new entry points for ecosystem management and future targeted biocontrol. The revelation that effects can cascade through communities via “hub” microbes is important to understand community structure perturbations in parallel fields including human microbiomes and bioprocesses. In particular, parallels to human microbiome “keystone” pathogens and microbes open new avenues of interdisciplinary research that promise to better our understanding of functions of host-associated microbiomes.

W. Kwong, N. Moran

P. Marsh

G. Turner

A. Barata, M. Malfeito-Ferreira, V. Loureiro

I. Brito

K. Guseva, S. Darcy, Eva Simon et al.

Network analysis has been used for many years in ecological research to analyze organismal associations, for example in food webs, plant-plant or plant-animal interactions. Although network analysis is widely applied in microbial ecology, only recently has it entered the realms of soil microbial ecology, shown by a rapid rise in studies applying co-occurrence analysis to soil microbial communities. While this application offers great potential for deeper insights into the ecological structure of soil microbial ecosystems, it also brings new challenges related to the specific characteristics of soil datasets and the type of ecological questions that can be addressed. In this Perspectives Paper we assess the challenges of applying network analysis to soil microbial ecology due to the small-scale heterogeneity of the soil environment and the nature of soil microbial datasets. We review the different approaches of network construction that are commonly applied to soil microbial datasets and discuss their features and limitations. Using a test dataset of microbial communities from two depths of a forest soil, we demonstrate how different experimental designs and network constructing algorithms affect the structure of the resulting networks, and how this in turn may influence ecological conclusions. We will also reveal how assumptions of the construction method, methods of preparing the dataset, and definitions of thresholds affect the network structure. Finally, we discuss the particular questions in soil microbial ecology that can be approached by analyzing and interpreting specific network properties. Targeting these network properties in a meaningful way will allow applying this technique not in merely descriptive, but in hypothesis-driven research.

J. Wright, K. Konwar, S. Hallam

M. Moran, E. Kujawinski, William F. Schroer et al.

Shuo Jiao, Ziheng Peng, Jiejun Qi et al.

The relationships between soil biodiversity and ecosystem functions are an important yet poorly understood topic in microbial ecology. This study presents an exploratory effort to gain predictive understanding of the factors driving the relationships between microbial diversity and potential soil nutrient cycling in complex terrestrial ecosystems. ABSTRACT Biodiversity is important for supporting ecosystem functioning. To evaluate the factors contributing to the strength of microbial diversity-function relationships in complex terrestrial ecosystems, we conducted a soil survey over different habitats, including an agricultural field, forest, wetland, grassland, and desert. Soil microbial multidiversity was estimated by the combination of bacterial and fungal diversity. Soil ecosystem functions were evaluated using a multinutrient cycling index (MNC) in relation to carbon, nitrate, phosphorus, and potassium cycling. Significant positive relationships between soil multidiversity and multinutrient cycling were observed in all habitats, except the grassland and desert. Specifically, community compositions showed stronger correlations with multinutrient cycling than α-diversity, indicating the crucial role of microbial community composition differences on soil nutrient cycling. Importantly, we revealed that changes in both the neutral processes (Sloan neutral modeling) and the proportion of negative bacterial-fungal associations were linked to the magnitude and direction of the diversity-MNC relationships. The habitats less governed by neutral processes and dominated by negative bacterial-fungal associations exhibited stronger negative microbial α-diversity–MNC relationships. Our findings suggested that the balance between positive and negative bacterial-fungal associations was connected to the link between soil biodiversity and ecosystem function in complex terrestrial ecosystems. This study elucidates the potential factors influencing diversity-function relationships, thereby enabling future studies to forecast the effects of belowground biodiversity on ecosystem function. IMPORTANCE The relationships between soil biodiversity and ecosystem functions are an important yet poorly understood topic in microbial ecology. This study presents an exploratory effort to gain predictive understanding of the factors driving the relationships between microbial diversity and potential soil nutrient cycling in complex terrestrial ecosystems. Our structural equation modeling and random forest analysis revealed that the balance between positive and negative bacterial-fungal associations was clearly linked to the strength of the relationships between soil microbial diversity and multiple nutrients cycling across different habitats. This study revealed the potential factors underpinning diversity-function relationships in terrestrial ecosystems and thus helps us to manage soil microbial communities for better provisioning of key ecosystem services.

Hammed Mogaji, Hammed Mogaji, Hammed Mogaji et al.

IntroductionMore than 15% of Brazil's urban population lives in slums characterized by limited access to essential urban services, heightened vulnerability to infectious pathogens and environmental hazards, and deprivation of citizenship rights. These conditions exacerbate social inequality, perpetuate cycles of poverty, and fuel violence, underscoring the urgent need for sustainable interventions.MethodsFollowing a social justice framework, we developed a community development program rooted in participatory research methods and popular health education to foster collaboration between university researchers and communities. The aim was to identify priorities and co-create locally driven, cost-effective, and sustainable solutions. This article describes our ongoing project in three prominent urban slums of Salvador, Brazil (Alto do Cabrito, Pau da Lima and Marechal Rondon), detailing the methodologies employed, activities initiated, and interventions developed.ResultsWe conducted ethnographic, eco-epidemiological, and collaborative mapping surveys to contextualize diverse health and well-being challenges. Furthermore, we organized consultative and socialization events with dynamic community groups and identified local priorities, leading to the design of thirteen interventions targeting citizenship rights, social cohesion, environmental restoration, waste management, and unemployment.DiscussionHere, we described how our interdisciplinary approach leveraged social capital and fostered inter-sectoral partnerships to empower marginalized urban communities towards addressing their health and environmental challenges through sustainable, locally tailored solutions. While the program has strengthened community trust, facilitated partnerships, and achieved notable environmental improvements, further evaluation is needed to assess the long-term impacts of these interventions on broader social health determinants.

D. Ercolini

U. Tezel, S. Pavlostathis

Álvaro Sánchez, Djordje Bajić, Juan Díaz-Colunga et al.

Quantitatively linking the composition and function of microbial communities is a major aspiration of microbial ecology. Microbial community functions emerge from a complex web of molecular interactions between cells, which give rise to population-level interactions among strains and species. Incorporating this complexity into predictive models is highly challenging. Inspired by a similar problem in genetics of predicting quantitative phenotypes from genotypes, an ecological community-function (or structure-function) landscape could be defined that maps community composition and function. In this piece, we present an overview of our current understanding of these community landscapes, their uses, limitations, and open questions. We argue that exploiting the parallels between both landscapes could bring powerful predictive methodologies from evolution and genetics into ecology, providing a boost to our ability to engineer and optimize microbial consortia.

Matthias Heuberger, Carlotta Marie Wehrkamp, Alina Pfammatter et al.

Abstract Background Lichens are an ancient symbiosis comprising the thalli of lichen-forming fungi, their photoautotrophic partners, and their microbiome. So far, they were poorly studied at the genome sequence level. Here, we present a reference metagenome for the holobiont of Cladonia rangiformis, aiming to illuminate the genomic complexity and evolutionary interactions within lichen symbioses. Results Using long-read sequences from an entire symbiotic complex, plus short-read libraries from 28 additional diverse European lichen samples, we were able to separate genome sequences of 20 individual species. We constructed chromosome-scale assemblies of the C. rangiformis fungus and its trebouxioid green algal photobiont Asterochloris mediterranea. The genome of the fungus comprises ~ 22% transposable elements and is highly compartmentalized into genic regions and large TE-derived segments which show extensive signatures of repeat-induced point mutations (RIP). We found that A. mediterranea centromeres are predominantly derived from two interacting retrotransposon families. We also identified strong candidates for genes that were horizontally transferred from bacteria to both alga and fungus. Furthermore, we isolated 18 near-complete bacterial genomes, of which 13 are enriched in the lichen compared to surrounding soil. Analysis of gene content in fungus, algae, and bacteria identified 22 distinct biosynthetic gene cluster categories for known secondary metabolites. Conclusions Our findings revealed that the thalli of C. rangiformis have a highly complex microbiome, comprising a mix of species that may include opportunists, ecologically obligate symbionts and possibly even lichen-beneficial bacteria. This study provides the first chromosome-scale genomic framework for a lichen holobiont, offering a foundational resource for future research into metagenomics, symbiosis, and microbial ecology in lichens.

Lara Jansen, Eline Loos, Restiana Wisnu Ariyati et al.

ABSTRACT Mangrove ecosystems support a diverse array of animal species and also provide pivotal ecosystem services, such as coastal protection, food provisioning, and carbon capture. However, these vital habitats are in decline, leading to coastal degradation in many parts of the globe. To address this, a mangrove restoration project in Demak, Java, Indonesia, introduced the use of semi‐permeable coastal protective barriers made of bamboo pilings to safeguard the shore zone and hinterlands. The introduction of such hard substrate in the marine environment can attract a range of species, and it is important to be able to monitor changes in biodiversity from a restoration point of view. Here, we assessed whether environmental DNA metabarcoding can be applied to monitor fish biodiversity in an understudied area. Our results show slight but significant differences in species richness and fish community composition within a short timeframe of only 4 months, although we cannot disentangle the effects of seasonal variation from those of the introduction of hard substrate. More importantly, this study demonstrates a useful level of temporal resolution of eDNA metabarcoding and establishes a baseline for fish species richness in an understudied mangrove coastal zone in Demak, Java, Indonesia. Our results are of value for informing future restoration efforts and other (metabarcoding) biodiversity studies in the region.

Katherine J. P. Schwenger, Julia K. Copeland, Yasaman Ghorbani et al.

Abstract Background Metabolic dysfunction-associated steatotic liver disease (MASLD) encompasses a range of histological findings from the generally benign simple steatosis to steatohepatitis (MASH) which can progress to fibrosis and cirrhosis. Several factors, including the microbiome, may contribute to disease progression. Results Here, we demonstrate links between the presence and abundance of specific bacteria in the adipose and liver tissues, inflammatory genes, immune cell responses, and disease severity. Overall, in MASLD patients, we observed a generalized obesity-induced translocation of gut bacteria to hepatic and adipose tissues. We identified microbial patterns unique to more severely diseased tissues. Specifically, Enterococcus, Granulicatella, and Morganellaceae abundance is positively correlated with immune cell counts and inflammatory gene expression levels, and both genera are significantly enriched in MASH patients. Brevibacterium is enriched in adipose tissues of patients with liver fibrosis. Conclusion Together, these results provide further insight into the microbial factors that may be driving disease severity. Video Abstract

Camila Souza Beraldo

ABSTRACT The use of art in science teaching can effectively help students understand complex and abstract concepts, particularly in the fields of Microbiology and Microbial Ecology, where the study objects—the microbes—are invisible to human eyes. To explore how different factors shape host–microbe interactions, I developed the activity MicrobiART, which uses mixed art materials to create analogies that illustrate the dynamic relationships between hosts, microbes, and their environments. MicrobiART was presented as an alternative session at a PhD students’ conference in Espoo, Finland. Participants were invited to combine papers, balls, and paint—representing hosts, microbes, and environmental factors, respectively—to create paintings that depict the outcomes of these interactions. The completed artworks were then displayed in a mini exhibition. Following this session, participants were invited to engage in discussion to identify patterns in the paintings and reflect on the analogies’ meanings and limitations. The activity is adaptable to various age groups and to both non-specialist and specialist audiences. Anecdotal evidence suggests that participants understood how interaction outcomes depend on the specific combination of players (host, microbes, and environment), while also recognizing emergent patterns. For instance, interactions within the same environment often share similar colors, contrasting with those from a different environment. Moreover, participants found the experience enjoyable, particularly due to its interactive and aesthetic appeal. These findings highlight the value of integrating science and art in science communication, especially in conference spaces: such integration fosters connections, inspires new ideas and teaching approaches, and provides a relaxed setting for discussion.

Lucie A. Malard, Antoine Guisan

The environmental niche concept describes the distribution of a taxon in the environment and can be used to understand community dynamics, biological invasions, and the impact of environmental changes. The uses and applications are still restricted in microbial ecology, largely due to the complexity of microbial systems and associated methodological limitations. The development of shotgun metagenomics and metatranscriptomics opens new ways to investigate the microbial niche by focusing on the metabolic niche within the environmental space. Here, we propose the metabolic niche framework, which, by defining the fundamental and realised metabolic niche of microorganisms, has the potential to not only provide novel insights into habitat preferences and the metabolism associated, but also to inform on metabolic plasticity, niche shifts, and microbial invasions.