Physiological and Biochemical Changes and Microbial Community Succession During the Postharvest Rot Process of Stropharia rugosoannulata.

Identifying the mechanisms underlying microbial community succession is necessary for predicting how microbial communities, and their functioning, will respond to future environmental change. Dispersal is one mechanism expected to affect microbial succession, yet the difficult nature of manipulating microorganisms in the environment has limited our understanding of its contribution. Using a dispersal exclusion experiment, this study isolates the specific effect of environmental dispersal on bacterial and fungal community assembly over time following a wildfire. The work demonstrates the potential to quantify dispersal impacts on soil microbial communities over time and test how dispersal might further interact with other assembly processes in response to environmental change.

Microbial community succession in tailings materials is poorly understood at present, and likely to be substantially different from similar processes in natural primary successional environments due to the unusual geochemical properties of tailings and the isolated design of tailings storage facilities. This is the first study to evaluate processes of primary succession in microbial communities colonizing unamended tailings, and compare the relative importance of stochastic (predominantly dust-borne dispersal) and deterministic (strong selection pressures from extreme geochemical properties) processes in governing community assembly rates and trajectories to those observed in natural environments. Dispersal-based recruitment required > 6 months to shift microbial community composition in unamended, field-weathered gold tailings; and in the absence of targeted inoculants, recruitment was dominated by salt- and alkali-tolerant species. In addition, cell numbers were less than 106 cells/g tailings until > 6 months after deposition. Laboratory experiments simulating microbial cell addition via dust revealed that high (>6 months’ equivalent) dust addition rates were required to effect stabilization of microbial cell counts in tailings. In field-weathered tailings, topsoil addition during rehabilitation works exerted a double effect, acting as a microbial inoculant and correcting geochemical properties of tailings. However, microbial communities in rehabilitated tailings remained compositionally distinct from those of reference soils in surrounding environments. pH, water extractable Mg, and water extractable Fe emerged as major controls on microbial community composition in the field-weathered gold tailings. Overall, this study highlights the need for application of targeted microbial inoculants to accelerate rates of microbial community succession in tailings, which are limited primarily by slow dispersal due to physical and spatial isolation of tailings facilities from inoculant sources; and for geochemical properties of tailings to be amended to moderate values to encourage microbial community diversification and succession.

In order to investigate the effect of antibiotics on composting behavior, enzymatic activity, and microbial community succession during the aerobic composting of human feces using sawdust as the bulk carrier, tetracycline (TC) was added to the composting system at four different concentrations (0, 100, 250, and 500 mg·kg-1). Microbial community succession was examined by high-throughput 16S rRNA gene sequencing. The results showed that the influence of TC on the physical and chemical properties of compost was related to its concentration. With the increase in TC concentration, the temperature increase during aerobic composting was inhibited, the water-soluble carbon (WSC) residue was increased, the germination index (GI) was decreased, and the dehydrogenase activity (DHA) was also hindered. Parameters, such as temperature, WSC, GI, and DHA, are widely accepted and representative indicators to evaluate compost maturity. Overall, when the concentration of TC was higher than 500 mg·kg-1, the aerobic composting process and the maturity of the final compost were inhibited. Furthermore, elevated TC caused significant changes in microbial community succession and reductions in community diversity and abundance. Therefore, interference in microbial community structures and a hindrance to biological activity are believed to be the main adverse effects of TC on the composting process and maturity of the composting products.

Microbial community succession during decomposition has been proven to be a useful tool for postmortem interval (PMI) estimation. Numerous studies have shown that the intestinal microbial community presented chronological changes after death and was stable in terrestrial corpses with different causes of death. However, the postmortem pattern of intestinal microbial community succession in cadavers retrieved from water remains unclear. For immersed corpses, the postmortem submersion interval (PMSI) is a useful indicator of PMI. To provide reliable estimates of PMSI in forensic investigations, we investigated the gut microbial community succession of corpses submersed in freshwater and explored its potential application in forensic investigation. In this study, the intestinal microbial community of mouse submersed in freshwater that died of drowning or CO2 asphyxia (i.e., postmortem submersion) were characterized by 16S rDNA amplification and high-throughput sequencing, followed by bioinformatic analyses. The results demonstrated that the chronological changes in intestinal bacterial communities were not different between the drowning and postmortem submersion groups. α-diversity decreased significantly within 14 days of decomposition in both groups, and the β-diversity bacterial community structure ordinated chronologically, inferring the functional pathway and phenotype. To estimate PMSI, a regression model was established by random forest (RF) algorithm based on the succession of postmortem microbiota. Furthermore, 15 genera, including Proteus, Enterococcus, and others, were selected as candidate biomarkers to set up a concise predicted model, which provided a prediction of PMSI [MAE (± SE) = 0.818 (± 0.165) d]. Overall, our present study provides evidence that intestinal microbial community succession would be a valuable marker to estimate the PMSI of corpses submerged in an aquatic habitat.

Effects of initial temperature on microbial community succession rate and volatile flavors during Baijiu fermentation process

Microbial community succession patterns and metabolite profiles in cigar tobacco during different mildew stages

IntroductionFlue-cured tobacco (FCT) requires fermentation to increase quality, with microorganisms playing a key role. However, microbial succession and functions during long-term fermentation remain unclear. Artificial microbial fermentation, which is more controllable and efficient, focuses on mining functional strains to optimize the process.MethodsIn this study, the microbial community structure and function of FCT fermentated for 0–4 years were analyzed, and the changes of metabolites in tobacco leaves in different years were analyzed. Functional microorganisms were screened, and their potential for application in FCT fermentation was evaluated.ResultsThe results revealed that the FCT aging process was typified by the metabolic, transformative, and synthetic processes of alkaloids, their derivatives, and benzene ring compounds. Microbial succession leads to changes in metabolites, with Escherichia, Bacillus, Enterococcus, Alternaria, Vibrio, and Halomonas playing crucial roles in the breakdown of fundamental substances during the initial year of FCT fermentation. Bacillus, one of the dominant and highly active genus of the microbial community on the surface of tobacco leaves, exhibits significantly increased abundance during FCT fermentation and improves the aroma and flavor of tobacco leaves by participating in aromatic amino acid metabolism. After 15 days of treatment with a combination of four Bacillus strains (Bacillus altitudinis YS193, Bacillus pumilus YH186, Bacillus tequilensis YS154, and Bacillus velezensis YS157), the sugar‒nicotine ratio of FCT was effectively optimized, the sensory flavor was enhanced, and the levels of volatile compounds associated with the aromatic amino acid metabolic pathway were significantly increased.DiscussionThis study reveals the critical role of microbial succession in FCT fermentation and demonstrates that targeted inoculation of functional Bacillus strains can significantly improve tobacco quality by modulating key metabolic pathways, providing a scientific basis for artificial microbial fermentation in tobacco processing.

Construction of a succession model for the microbiome in water from submerged corpses based on single-molecule real-time sequencing.

Aerobic composting of anaerobic digested residue (DR) is an effective post-treatment method to develop a zero emission process; however, there are knowledge gaps in the understanding of this process. Microbial succession is a critical parameter for examining the principle of material transformation and maturity throughout the composting process. This study compared the total (DNA level) and active (RNA level) microbial community succession during the DR composting process by using 16S rRNA gene high-throughput sequencing. A significantly higher richness and diversity for the microbial community on the RNA level compared with the DNA level was observed. Beta-diversity analysis revealed significant differences in community composition and dynamics between the DNA and RNA of microbes. Moreover, DNA analysis exhibited large parts of anaerobic microbes in composting samples, indicating its bias to assess the metabolically active microbial community succession. The RNA dataset showed that Proteobacteria, Firmicutes, and Bacteroidetes predominated in the phylum level, while Crenarchaeota was distinctive. This indicated that the members in these phyla are crucial to material transformation and product maturity during the aerobic composting of DR.

Impact of bamboo sphere amendment on composting performance and microbial community succession in food waste composting

The gut microbiota plays a critical role in human health and disease. Microbial community assembly and succession early in life are influenced by numerous factors. In turn, assembly of this microbial community is known to influence the host, including immune system development, and has been linked to outcomes later in life. To date, the role of host-mediated nutritional immunity and metal availability in shaping microbial community assembly and succession early in life has not been explored in depth. Using a human infant cohort, we show that the metal-chelating protein calprotectin is highly abundant in infants. Taxa previously shown to be successful early colonizers of the infant gut, such as Enterococcus, Enterobacteriaceae, and Bacteroides, are highly resistant to experimental metal starvation in culture. Lactobacillus, meanwhile, is highly susceptible to metal restriction, pointing to a possible mechanism by which host-mediated metal limitation shapes the fitness of early colonizing taxa in the infant gut. We further demonstrate that formula-fed infants harbor markedly higher levels of metals in their gastrointestinal tract compared to breastfed infants. Formula-fed infants with high levels of metals harbor distinct microbial communities compared to breastfed infants, with higher levels of Enterococcus, Enterobacter, and Klebsiella, taxa which show increased resistance to the toxic effects of high metal concentrations. These data highlight a new paradigm in microbial community assembly and suggest an unappreciated role for nutritional immunity and dietary metals in shaping the earliest colonization events of the microbiota.IMPORTANCEEarly life represents a critical window for microbial colonization of the human gastrointestinal tract. Surprisingly, we still know little about the rules that govern the successful colonization of infants and the factors that shape the success of early life microbial colonizers. In this study, we report that metal availability is an important factor in the assembly and succession of the early life microbiota. We show that the host-derived metal-chelating protein, calprotectin, is highly abundant in infants and successful early life colonizers can overcome metal restriction. We further demonstrate that feeding modality (breastmilk vs formula) markedly impacts metal levels in the gut, potentially influencing microbial community succession. Our work suggests that metals, a previously unexplored aspect of early life ecology, may play a critical role in shaping the early events of microbiota assembly in infants.

The microbial diversity and community succession of a circulation flush toilet were investigated by terminal restriction fragment length polymorphism and cloning analyses. Clonal libraries of 16S rRNA gene on day 3 and day 127 were constructed. On day 3, 102 clones were sequenced; Proteobacteria and Bacteroidetes accounted for 27% and 45%, respectively. On day 127, Proteobacteria had increased to 43% and Bacteroidetes had decreased to 26% of a total of 100 clones. Terminal restriction fragment length polymorphism peaks were identified by in silico analysis of clone libraries. The relative abundances of Nitrosomonas increased from 1% to 6% with commencement of nitrification and denitrification. Similarly, the relative abundance of terminal restriction fragments generated from Xanthomonas increased from 3% to 10%. Therefore, these bacteria could play a prominent role in this process. To reveal the relationship between stability of the microbial community and performance of the system, microbial community succession was visualized by multidimensional scaling analysis. The microbial community structure changed markedly, particularly during the start-up period of the system. The plots then became stable after the start of nitrification and denitrification. This result suggests that the succession of microbial community structure had a correlation with the performance of the system.

Environmental factors drive the succession of microbial community structure during wheat Qu fermentation

For perennial plants, newly emerged organs are fresh hot spots for environmental microbes to occupy and assemble to form mature microbial communities. In the microbial community, some commensal fungi can play important roles in microbial succession, thus significantly improving host plant growth and disease resistance. However, their participating patterns in microbial assembly and succession remain largely unknown. In this study, we profiled the fungal community and found a similar fungal succession pattern of spring-emerged leaves from March to October in two pomelo orchards. Specifically, the fungal species, tracked on the old leaves, dominated the spring leaves after emergence and then decreased in relative abundance. This reduction in priority effects on the spring leaves was then followed by an increase in the number of observed species, Shannon and phylogenetic diversity indices, and the pathogen-associated fungal groups. In addition, we found that the temporal fungal succession on the spring leaves highly correlated with the disease occurrence in the orchards and with the temperature and precipitation variation from spring to summer. Of the pathogen-associated fungal groups, an increase in the relative abundance of Mycosphaerellaceae, hosting the causal agent of citrus greasy spot, correlated with the occurrence of the disease, while the relative abundance of Diaporthaceae, hosting the causal agent of melanose, was extremely low during the fungal succession. These results confirm that the two kinds of pathogen-associated fungal groups share different lifestyles on citrus, and also suggest that the study of temporal fungal succession in microbial communities can add to our understanding of the epidemiology of potential plant pathogens.

Ecological succession and the balance between stochastic and deterministic processes are two major themes within microbial ecology, but these conceptual domains have mostly developed independent of each other. Here we provide a framework that integrates shifts in community assembly processes with microbial primary succession to better understand mechanisms governing the stochastic/deterministic balance. Synthesizing previous work, we devised a conceptual model that links ecosystem development to alternative hypotheses related to shifts in ecological assembly processes. Conceptual model hypotheses were tested by coupling spatiotemporal data on soil bacterial communities with environmental conditions in a salt marsh chronosequence spanning 105 years of succession. Analyses within successional stages showed community composition to be initially governed by stochasticity, but as succession proceeded, there was a progressive increase in deterministic selection correlated with increasing sodium concentration. Analyses of community turnover among successional stages--which provide a larger spatiotemporal scale relative to within stage analyses--revealed that changes in the concentration of soil organic matter were the main predictor of the type and relative influence of determinism. Taken together, these results suggest scale-dependency in the mechanisms underlying selection. To better understand mechanisms governing these patterns, we developed an ecological simulation model that revealed how changes in selective environments cause shifts in the stochastic/deterministic balance. Finally, we propose an extended--and experimentally testable--conceptual model integrating ecological assembly processes with primary and secondary succession. This framework provides a priori hypotheses for future experiments, thereby facilitating a systematic approach to understand assembly and succession in microbial communities across ecosystems.