Causes and consequences of biotic interactions within microbiomes

Pediococcus spp.-mediated competition interaction within Daqu microbiota determines the temperature formation and metabolic profiles

Fermented microbiota is critical to the formation of microenvironment and metabolic profiles in spontaneous fermentation. Microorganisms generate a diverse array of metabolites concurrent with the release of heat energy. In the case of Daqu fermentation, the peak temperature exceeded 60°C, forming a typical high-temperature fermentation system known as high-temperature Daqu. However, microorganisms that cause the quality variation in Daqu and how they affect the functional microbiota and microenvironment in the fermentation process are not yet clear. This study adopted high-throughput sequencing and monitored the dynamic fluctuations of metabolites and environmental factors to identify the pivotal microorganism responsible for the alterations in interaction patterns of functional keystone taxa and quality decline in the fermentation system of different operational areas during the in situ fermentation process that had been mainly attributed to operational taxonomic unit (OTU)_22 (Pediococcus acidilactici). Additionally, we used isothermal microcalorimetry, plate inhibition experiments, and in vitro simulation fermentation experiments to explore the impact of Pediococcus spp. on heat generation, microorganisms, and metabolite profiles. Results showed the heat peak generated by Pediococcus spp. was significantly lower than that of Bacillus spp., filamentous fungi, and yeast. In addition, the preferential growth of P. acidilactici strain AA3 would obviously affect other strains to colonize through competition, and its metabolites made a significant impact on filamentous fungi. The addition of P. acidilactici strain AA3 in simulated fermentation would cause the loss of pyrazines and acids in metabolites. These evidences showed that the overgrowth of Pediococcus spp. greatly influenced the formation of high temperatures and compounds in solid-state fermentation systems. Our work illustrated the vital impact of interaction variability mediated by Pediococcus spp. for microbial assembly and metabolites, as well as in forming temperature. These results emphasized the functional role of Daqu microbiota in metabolites and heat production and the importance of cooperation in improving the fermentation quality.IMPORTANCEThe stable and high-quality saccharifying and fermenting starter in traditional solid-state fermentation was the prerequisite for liquor brewing. An imbalance of microbial homeostasis in fermentation can adversely impact production quality. Identification of such critical microorganisms and verifying their associations with other fermentation parameters pose a challenge in a traditional fermentation environment. To enhance the quality of spontaneous fermented products, strategies such as bioaugmentation or the control of harmful microorganisms would be employed. This work started with the differences in high-temperature Daqu metabolites to explore a series of functional microorganisms that could potentially contribute to product disparities, and found that the differences in interactions facilitated directly or indirectly by Pediococcus spp. seriously affected the development of microbial communities and metabolites, as well as the formation of the microenvironment. This study not only identified functional microbiota in Daqu that affected fermentation quality, but also demonstrated how microorganisms interact to affect the fermentation system, which would provide guidance for microbial supervision in the actual production process. Besides, the application of isothermal microcalorimetry in this study was helpful for us to understand the heat production capacity of microorganisms and their adaptability to the environment. This study presented a commendable framework for improving and controlling the quality of traditional fermentation and inspired further investigations in similar systems.

Bioaerosols in the coastal region of Qingdao: Community diversity, impact factors and synergistic effect

Atmospheric bioaerosols are influenced by multiple factors, including physical, chemical, and biotic interactions, and pose a significant threat to the public health and the environment. The nonnegligible truth however is that the primary driver of the changes in bioaerosol community diversity remains unknown. In this study, putative biological association (PBA) was obtained by constructing an ecological network. The relationship between meteorological conditions, atmospheric pollutants, water-soluble inorganic ions, PBA and bioaerosol community diversity was analyzed using random forest regression (RFR)-An ensemble learning algorithm based on a decision tree that performs regression tasks by constructing multiple decision trees and integrating the predicted results, and the contribution of different rich species to PBA was predicted. The species richness, evenness and diversity varied significantly in different seasons, with the highest in summer, followed by autumn and spring, and was lowest in winter. The RFR suggested that the explanation rate of alpha diversity increased significantly from 73.74 % to 85.21 % after accounting for the response of the PBA to diversity. The PBA, temperature, air pollution, and marine source air masses were the most crucial factors driving community diversity. PBA, particularly putative positive association (PPA), had the highest significance in diversity. We found that under changing external conditions, abundant taxa tend to cooperate to resist external pressure, thereby promoting PPA. In contrast, rare taxa were more responsive to the putative negative association because of their sensitivity to environmental changes. The results of this research provided scientific advance in the understanding of the dynamic and temporal changes in bioaerosols, as well as support for the prevention and control of microbial contamination of the atmosphere.

Insights into the mechanisms driving microbial community succession during pepper fermentation: Roles of microbial interactions and endogenous environmental changes

Elucidating the driving mechanism of microbial community succession during pepper fermentation contributes to establishing efficient fermentation regulation strategies. This study utilized three-generation high-throughput sequencing technology, microbial co-occurrence network analysis, and random forest analysis to reveal microbial community succession processes and driving mechanisms during pepper fermentation. The results showed that more positive correlations than negative correlations were observed among microorganisms, with positive correlation proportions of 60 %, 51.03 %, and 71.43 % between bacteria and bacteria, fungi and fungi, and bacteria and fungi in sipingtou peppers, and 69.23 %, 54.93 %, and 79.44 % in zhudachang peppers, respectively. Microbial interactions, mainly among Weissella hellenica, Lactobacillus plantarum, Hanseniaspora opuntiae, and Kazachstania humillis, could drive bacterial and fungal community succession. Notably, the bacterial community successions during the fermentation of two peppers were similar, showing the transition from Leuconostoc pseudomesenteroides, Lactococcus lactis, Weissella ghanensis to Weissella hellenica and Lactobacillus plantarum. However, the fungal community successions in the two fermented peppers differed significantly, and the differential biomarkers were Dipodascus geotrichum and Kazachstania humillis. Differences in autochthonous microbial composition and inherent constituents brought by pepper varieties resulted in different endogenous environmental changes, mainly in fructose, malic acid, and citric acid. Furthermore, endogenous environmental factors could also drive microbial community succession, with succinic acid, lactic acid, and malic acid being the main potential drivers of bacterial community succession, whereas fructose, glucose, and succinic acid were the main drivers of fungal community succession. These results will provide insights into controlling fermentation processes by raw material combinations, optimization of environmental parameters, and microbial interactions.

Microbiome-Mediated Protection against Pathogens in Woody Plants

Pathogens, especially invasive species, have caused significant global ecological, economic, and social losses in forests. Plant disease research has traditionally focused on direct interactions between plants and pathogens in an appropriate environment. However, recent research indicates that the microbiome can interact with the plant host and pathogens to modulate plant resistance or pathogen pathogenicity, thereby altering the outcome of plant-pathogen interactions. Thus, this presents new opportunities for studying the microbial management of forest diseases. Compared to parallel studies on human and crop microbiomes, research into the forest tree microbiome and its critical role in forest disease progression has lagged. The rapid development of microbiome sequencing and analysis technologies has resulted in the rapid accumulation of a large body of evidence regarding the association between forest microbiomes and diseases. These data will aid the development of innovative, effective, and environmentally sustainable methods for the microbial management of forest diseases. Herein, we summarize the most recent findings on the dynamic structure and composition of forest tree microbiomes in belowground and aboveground plant tissues (i.e., rhizosphere, endosphere, and phyllosphere), as well as their pleiotropic impact on plant immunity and pathogen pathogenicity, highlighting representative examples of biological control agents used to modulate relevant tree microbiomes. Lastly, we discuss the potential application of forest tree microbiomes in disease control as well as their future prospects and challenges.

Microbiome Assembly in Fermented Foods

For thousands of years, humans have enjoyed the novel flavors, increased shelf-life, and nutritional benefits that microbes provide in fermented foods and beverages. Recent sequencing surveys of ferments have mapped patterns of microbial diversity across space, time, and production practices. But a mechanistic understanding of how fermented food microbiomes assemble has only recently begun to emerge. Using three foods as case studies (surface-ripened cheese, sourdough starters, and fermented vegetables), we use an ecological and evolutionary framework to identify how microbial communities assemble in ferments. By combining in situ sequencing surveys with in vitro models, we are beginning to understand how dispersal, selection, diversification, and drift generate the diversity of fermented food communities. Most food producers are unaware of the ecological processes occurring in their production environments, but the theory and models of ecology and evolution can provide new approaches for managing fermented food microbiomes, from farm to ferment.

Antarctic snow algae: unraveling the processes underlying microbial community assembly during blooms formation

BACKGROUND AND AIMS

At the West Antarctic Peninsula, snow algae blooms are composed of complex microbial communities dominated by green microalgae and bacteria. During their progression, the assembly of these microbial communities occurs under harsh environmental conditions and variable nutrient content due to fast snow melting. To date, it is still unclear what are the ecological mechanisms governing the composition and abundance of microorganisms during the formation of snow algae blooms. In this study, we aim to examine the main ecological mechanisms governing the assembly of snow algae blooms from early stages to colorful stages blooms.

METHODS

The composition of the microbial communities within snow algae blooms was recorded in the West Antarctic Peninsula (Isabel Riquelme Islet) during a 35-day period using 16S rRNA and 18S rRNA metabarcoding. In addition, the contribution of different ecological processes to the assembly of the microbial community was quantified using phylogenetic bin-based null model analysis.

RESULTS

Our results showed that alpha diversity indices of the eukaryotic communities displayed a higher variation during the formation of the algae bloom compared with the bacterial community. Additionally, in a macronutrients rich environment, the content of nitrate, ammonium, phosphate, and organic carbon did not play a major role in structuring the community. The quantification of ecological processes showed that the bacterial community assembly was governed by selective processes such as homogenous selection. In contrast, stochastic processes such as dispersal limitation and drift, and to a lesser extent, homogenous selection, regulate the eukaryotic community.

CONCLUSIONS

Overall, our study highlights the differences in the microbial assembly between bacteria and eukaryotes in snow algae blooms and proposes a model to integrate both assembly processes. Video Abstract.

Bacterial-fungal interactions promote parallel evolution of global transcriptional regulators in a widespread Staphylococcus species

Experimental studies of microbial evolution have largely focused on monocultures of model organisms, but most microbes live in communities where interactions with other species may impact rates and modes of evolution. Using the cheese rind model microbial community, we determined how species interactions shape the evolution of the widespread food- and animal-associated bacterium Staphylococcus xylosus. We evolved S. xylosus for 450 generations alone or in co-culture with one of three microbes: the yeast Debaryomyces hansenii, the bacterium Brevibacterium aurantiacum, and the mold Penicillium solitum. We used the frequency of colony morphology mutants (pigment and colony texture phenotypes) and whole-genome sequencing of isolates to quantify phenotypic and genomic evolution. The yeast D. hansenii strongly promoted diversification of S. xylosus. By the end of the experiment, all populations co-cultured with the yeast were dominated by pigment and colony morphology mutant phenotypes. Populations of S. xylosus grown alone, with B. aurantiacum, or with P. solitum did not evolve novel phenotypic diversity. Whole-genome sequencing of individual mutant isolates across all four treatments identified numerous unique mutations in the operons for the SigB, Agr, and WalRK global regulators, but only in the D. hansenii treatment. Phenotyping and RNA-seq experiments highlighted altered pigment and biofilm production, spreading, stress tolerance, and metabolism of S. xylosus mutants. Fitness experiments revealed antagonistic pleiotropy, where beneficial mutations that evolved in the presence of the yeast had strong negative fitness effects in other biotic environments. This work demonstrates that bacterial-fungal interactions can have long-term evolutionary consequences within multispecies microbiomes by facilitating the evolution of strain diversity.

QCMI: A method for quantifying putative biotic associations of microbes at the community level

A workflow has been compiled as "qcmi" R package-the quantifying community-level microbial interactions-to identify and quantify the putative biotic associations of microbes at the community level from ecological networks.

Opportunities and Challenges of Understanding Community Assembly in Spontaneous Food Fermentation

Spontaneous fermentations that do not rely on backslopping or industrial starter cultures were especially important to the early development of society and are still practiced around the world today. While current literature on spontaneous fermentations is observational and descriptive, it is important to understand the underlying mechanism of microbial community assembly and how this correlates with changes observed in microbial succession, composition, interaction, and metabolite production. Spontaneous food and beverage fermentations are home to autochthonous bacteria and fungi that are naturally inoculated from raw materials, environment, and equipment. This review discusses the factors that play an important role in microbial community assembly, particularly focusing on commonly reported yeasts and bacteria isolated from spontaneously fermenting food and beverages, and how this affects the fermentation dynamics. A wide range of studies have been conducted in spontaneously fermented foods that highlight some of the mechanisms that are involved in microbial interactions, niche adaptation, and lifestyle of these microorganisms. Moreover, we will also highlight how controlled culture experiments provide greater insight into understanding microbial interactions, a modest attempt in decoding the complexity of spontaneous fermentations. Further research using specific in vitro microbial models to understand the role of core microbiota are needed to fill the knowledge gap that currently exists in understanding how the phenotypic and genotypic expression of these microorganisms aid in their successful adaptation and shape fermentation outcomes. Furthermore, there is still a vast opportunity to understand strain level implications on community assembly. Translating these findings will also help in improving other fermentation systems to help gain more control over the fermentation process and maintain consistent and superior product quality.

Knowns and unknowns of the soil fungal necrobiome

Dead microbial cells, commonly referred to as necromass, are increasingly recognized as an important source of both persistent carbon as well as nutrient availability in soils. Studies of the microbial communities associated with decomposing fungal necromass have accumulated rapidly in recent years across a range of different terrestrial ecosystems. Here we identify the primary ecological patterns regarding the structure and dynamics of the fungal necrobiome as well as highlight new research frontiers that will likely be key to gaining a full understanding of fungal necrobiome composition and its associated role in soil biogeochemical cycling. Because many members of the fungal necrobiome are culturable, combining laboratory functional assays with field-based surveys and experiments will allow ongoing studies of the fungal necrobiome to move from largely descriptive to increasingly predictive.

Research progress of rhizosphere microorganisms in Fritillaria L. medicinal plants

The soil's rhizosphere is a highly active place where the exchange of substances and information occurs among plants, soils, and microorganisms. The microorganisms involved are crucial to the activities of plant growth and development, metabolism, and reproduction. Fritillaria L. medicinal plants are unique Chinese medicinal ingredients, but the continuous cropping obstacles formed in the artificial planting process is severely harmful to the growth and development of these medicinal plants. In this review, we summarized the current species and distribution of Fritillaria L. in China, and analyzed the changes in microbial diversity (mainly among bacteria and fungi) in the rhizosphere of these plants under long-term continuous cropping. The fungi showed an increasing trend in the soil rhizosphere, resulting in the transition of the soil from the high-fertility "bacterial type" to the low-fertility "fungal type" as planting years increased. Furthermore, the interaction between Fritillaria L. medicinal plants and the rhizosphere microorganisms was reviewed, and promising applications for the rhizosphere microbiome in the cultivation of Fritillaria L. medicinal plants were suggested. It is expected that this review will facilitate the in-depth understanding of rhizosphere microorganisms in the growth, accumulation of active ingredients, and disease control of Fritillaria L.

Cross-kingdom co-occurrence networks in the plant microbiome: Importance and ecological interpretations

Microbial co-occurrence network analysis is being widely used for data exploration in plant microbiome research. Still, challenges lie in how well these microbial networks represent natural microbial communities and how well we can interpret and extract eco-evolutionary insights from the networks. Although many technical solutions have been proposed, in this perspective, we touch on the grave problem of kingdom-level bias in network representation and interpretation. We underscore the eco-evolutionary significance of using cross-kingdom (bacterial-fungal) co-occurrence networks to increase the network’s representability of natural communities. To do so, we demonstrate how ecosystem-level interpretation of plant microbiome evolution changes with and without multi-kingdom analysis. Then, to overcome oversimplified interpretation of the networks stemming from the stereotypical dichotomy between bacteria and fungi, we recommend three avenues for ecological interpretation: (1) understanding dynamics and mechanisms of co-occurrence networks through generalized Lotka-Volterra and consumer-resource models, (2) finding alternative ecological explanations for individual negative and positive fungal-bacterial edges, and (3) connecting cross-kingdom networks to abiotic and biotic (host) environments.

Quorum Sensing Regulates the Hydrolytic Enzyme Production and Community Composition of Heterotrophic Bacteria in Coastal Waters

Heterotrophic microbial communities play a central role in biogeochemical cycles in the ocean by degrading organic matter through the synthesis of extracellular hydrolytic enzymes. Their hydrolysis rates result from the community’s genomic potential and the differential expression of this genomic potential. Cell-cell communication pathways such as quorum sensing (QS) could impact both aspects and, consequently, structure marine ecosystem functioning. However, the role of QS communications in complex natural assemblages remains largely unknown. In this study, we investigated whether N-acylhomoserine lactones (AHLs), a type of QS signal, could regulate both hydrolytic activities and the bacterial community composition (BCC) of marine planktonic assemblages. To this extent, we carried out two microcosm experiments, adding five different AHLs to bacterial communities sampled in coastal waters (during early and peak bloom) and monitoring their impact on enzymatic activities and diversity over 48 h. Several specific enzymatic activities were impacted during both experiments, as early as 6 h after the AHL amendments. The BCC was also significantly impacted by the treatments after 48 h, and correlated with the expression of the hydrolytic activities, suggesting that changes in hydrolytic intensities may drive changes in BCC. Overall, our results suggest that QS communication could participate in structuring both the function and diversity of marine bacterial communities.

Symbiosis and the Anthropocene

Recent human activity has profoundly transformed Earth biomes on a scale and at rates that are unprecedented. Given the central role of symbioses in ecosystem processes, functions, and services throughout the Earth biosphere, the impacts of human-driven change on symbioses are critical to understand. Symbioses are not merely collections of organisms, but co-evolved partners that arise from the synergistic combination and action of different genetic programs. They function with varying degrees of permanence and selection as emergent units with substantial potential for combinatorial and evolutionary innovation in both structure and function. Following an articulation of operational definitions of symbiosis and related concepts and characteristics of the Anthropocene, we outline a basic typology of anthropogenic change (AC) and a conceptual framework for how AC might mechanistically impact symbioses with select case examples to highlight our perspective. We discuss surprising connections between symbiosis and the Anthropocene, suggesting ways in which new symbioses could arise due to AC, how symbioses could be agents of ecosystem change, and how symbioses, broadly defined, of humans and “farmed” organisms may have launched the Anthropocene. We conclude with reflections on the robustness of symbioses to AC and our perspective on the importance of symbioses as ecosystem keystones and the need to tackle anthropogenic challenges as wise and humble stewards embedded within the system.

Microbial Interactions within the Cheese Ecosystem and Their Application to Improve Quality and Safety

The cheese microbiota comprises a consortium of prokaryotic, eukaryotic and viral populations, among which lactic acid bacteria (LAB) are majority components with a prominent role during manufacturing and ripening. The assortment, numbers and proportions of LAB and other microbial biotypes making up the microbiota of cheese are affected by a range of biotic and abiotic factors. Cooperative and competitive interactions between distinct members of the microbiota may occur, with rheological, organoleptic and safety implications for ripened cheese. However, the mechanistic details of these interactions, and their functional consequences, are largely unknown. Acquiring such knowledge is important if we are to predict when fermentations will be successful and understand the causes of technological failures. The experimental use of "synthetic" microbial communities might help throw light on the dynamics of different cheese microbiota components and the interplay between them. Although synthetic communities cannot reproduce entirely the natural microbial diversity in cheese, they could help reveal basic principles governing the interactions between microbial types and perhaps allow multi-species microbial communities to be developed as functional starters. By occupying the whole ecosystem taxonomically and functionally, microbiota-based cultures might be expected to be more resilient and efficient than conventional starters in the development of unique sensorial properties.

Impact of Facultative Bacteria on the Metabolic Function of an Obligate Insect-Bacterial Symbiosis

Beneficial microorganisms associated with animals derive their nutritional requirements entirely from the animal host, but the impact of these microorganisms on host metabolism is largely unknown. The focus of this study was the experimentally tractable tripartite symbiosis between the pea aphid Acyrthosiphon pisum, its obligate intracellular bacterial symbiont Buchnera, and the facultative bacterium Hamiltonella which is localized primarily to the aphid hemolymph (blood). Metabolome experiments on, first, multiple aphid genotypes that naturally bear or lack Hamiltonella and, second, one aphid genotype from which Hamiltonella was experimentally eliminated revealed no significant effects of Hamiltonella on aphid metabolite profiles, indicating that Hamiltonella does not cause major reconfiguration of host metabolism. However, the titer of just one metabolite, 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR), displayed near-significant enrichment in Hamiltonella-positive aphids in both metabolome experiments. AICAR is a by-product of biosynthesis of the essential amino acid histidine in Buchnera and, hence, an index of histidine biosynthetic rates, suggesting that Buchnera-mediated histidine production is elevated in Hamiltonella-bearing aphids. Consistent with this prediction, aphids fed on [¹³C]histidine yielded a significantly elevated ¹²C/¹³C ratio of histidine in Hamiltonella-bearing aphids, indicative of increased (∼25%) histidine synthesized de novo by Buchnera However, in silico analysis predicted an increase of only 0.8% in Buchnera histidine synthesis in Hamiltonella-bearing aphids. We hypothesize that Hamiltonella imposes increased host demand for histidine, possibly for heightened immune-related functions. These results demonstrate that facultative bacteria can alter the dynamics of host metabolic interactions with co-occurring microorganisms, even when the overall metabolic homeostasis of the host is not substantially perturbed.IMPORTANCE Although microbial colonization of the internal tissues of animals generally causes septicemia and death, various animals are persistently associated with benign or beneficial microorganisms in their blood or internal organs. The metabolic consequences of these persistent associations for the animal host are largely unknown. Our research on the facultative bacterium Hamiltonella, localized primarily to the hemolymph of pea aphids, demonstrated that although Hamiltonella imposed no major reconfiguration of the aphid metabolome, it did alter the metabolic relations between the aphid and its obligate intracellular symbiont, Buchnera Specifically, Buchnera produced more histidine in Hamiltonella-positive aphids to support both Hamiltonella demand for histidine and Hamiltonella-induced increase in host demand. This study demonstrates how microorganisms associated with internal tissues of animals can influence specific aspects of metabolic interactions between the animal host and co-occurring microorganisms.

Incorporating functional trade-offs into studies of the gut microbiota

Trade-offs constrain evolution through genetic linkages and environmental limitations, impacting organismal physiology, morphology, and behavior. They are likely to also play a role in modulating functions of the microbiota, but previous research has not included tests of trade-off theory. Here, we review broadly how gut microbial functions are typically studied and outline evolutionarily-informed mechanisms to improve such research. These include measuring a diverse set of functions, with a focus on changes in host phenotype; more explicitly articulating the selective forces relevant to the microbiota; and using functionally relevant models. We present dietary intervention as a case study where trade-offs are likely to be relevant and discuss how the health effects of the modern human diet could be better understood in light of trade-offs. Appreciating microbial functional trade-offs as well as host trade-offs will be necessary to design effective interventions targeting the microbiota and, more generally, to understand the evolution of host-microbe interactions.