Study on Microbial Community Succession and Functional Analysis during Biodegradation of Mushroom Residue.
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ABSTRACT:
SUBMITTER: Wang C
PROVIDER: S-EPMC8292071 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundPlastics now pollute marine environments across the globe. On entering these environments, plastics are rapidly colonised by a diverse community of microorganisms termed the plastisphere. Members of the plastisphere have a myriad of diverse functions typically found in any biofilm but, additionally, a number of marine plastisphere studies have claimed the presence of plastic-biodegrading organisms, although with little mechanistic verification. Here, we obtained a microbial community from marine plastic debris and analysed the community succession across 6 weeks of incubation with different polyethylene terephthalate (PET) products as the sole carbon source, and further characterised the mechanisms involved in PET degradation by two bacterial isolates from the plastisphere.ResultsWe found that all communities differed significantly from the inoculum and were dominated by Gammaproteobacteria, i.e. Alteromonadaceae and Thalassospiraceae at early time points, Alcanivoraceae at later time points and Vibrionaceae throughout. The large number of encoded enzymes involved in PET degradation found in predicted metagenomes and the observation of polymer oxidation by FTIR analyses both suggested PET degradation was occurring. However, we were unable to detect intermediates of PET hydrolysis with metabolomic analyses, which may be attributed to their rapid depletion by the complex community. To further confirm the PET biodegrading potential within the plastisphere of marine plastic debris, we used a combined proteogenomic and metabolomic approach to characterise amorphous PET degradation by two novel marine isolates, Thioclava sp. BHET1 and Bacillus sp. BHET2. The identification of PET hydrolytic intermediates by metabolomics confirmed that both isolates were able to degrade PET. High-throughput proteomics revealed that whilst Thioclava sp. BHET1 used the degradation pathway identified in terrestrial environment counterparts, these were absent in Bacillus sp. BHET2, indicating that either the enzymes used by this bacterium share little homology with those characterised previously, or that this bacterium uses a novel pathway for PET degradation.ConclusionsOverall, the results of our multi-OMIC characterisation of PET degradation provide a significant step forwards in our understanding of marine plastic degradation by bacterial isolates and communities and evidences the biodegrading potential extant in the plastisphere of marine plastic debris. Video abstract.
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Project description:The evolutional trajectory of gut microbial colonization from birth has been shown to prime for health later in life. Here, we combined cultivation-independent 16S rRNA gene sequencing and metaproteomics to investigate the functional maturation of gut microbiota in faecal samples from full-term healthy infants collected at 6 and 18 months of age. Phylogenetic analysis of the metaproteomes showed that Bifidobacterium provided the highest number of distinct protein groups. Considerable divergences between taxa abundance and protein phylogeny were observed at all taxonomic ranks. Age had a profound effect on early microbiota where compositional and functional complexity of less dissimilar communities increased with time. Comparisons of the relative abundances of proteins revealed the transition of taxon-associated saccharolytic and carbon metabolism strategies from catabolic pathways of milk and mucin-derived monosaccharides feeding acetate/propanoate synthesis to complex food sugars fuelling butyrate production. Furthermore, co-occurrence network analysis uncovered two anti-correlated modules of functional taxa. A low-connected Bifidobacteriaceae-centred guild of facultative anaerobes was succeeded by a rich club of obligate anaerobes densely interconnected around Lachnospiraceae, underpinning their pivotal roles in microbial ecosystem assemblies. Our findings establish a framework to visualize whole microbial community metabolism and ecosystem succession dynamics, proposing opportunities for microbiota-targeted health-promoting strategies early in life.
2018-07-16 | PXD009056 | Pride
Project description:The ecological mechanisms driving community succession are widely debated, particularly for microorganisms. While successional soil microbial communities are known to undergo predictable changes in structure concomitant with shifts in a variety of edaphic properties, the causal mechanisms underlying these patterns are poorly understood. Thus, to specifically isolate how nutrients--important drivers of plant succession--affect soil microbial succession, we established a full factorial nitrogen (N) and phosphorus (P) fertilization plot experiment in recently deglaciated (?3 years since exposure), unvegetated soils of the Puca Glacier forefield in Southeastern Peru. We evaluated soil properties and examined bacterial community composition in plots before and one year after fertilization. Fertilized soils were then compared to samples from three reference successional transects representing advancing stages of soil development ranging from 5 years to 85 years since exposure. We found that a single application of +NP fertilizer caused the soil bacterial community structure of the three-year old soils to most resemble the 85-year old soils after one year. Despite differences in a variety of soil edaphic properties between fertilizer plots and late successional soils, bacterial community composition of +NP plots converged with late successional communities. Thus, our work suggests a mechanism for microbial succession whereby changes in resource availability drive shifts in community composition, supporting a role for nutrient colimitation in primary succession. These results suggest that nutrients alone, independent of other edaphic factors that change with succession, act as an important control over soil microbial community development, greatly accelerating the rate of succession.
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Project description:The succession of microbial community structure and function is a central ecological topic, as microbes drive the Earth's biogeochemical cycles. To elucidate the response and mechanistic underpinnings of soil microbial community structure and metabolic potential relevant to natural forest succession, we compared soil microbial communities from three adjacent natural forests: a coniferous forest (CF), a mixed broadleaf forest (MBF) and a deciduous broadleaf forest (DBF) on Shennongjia Mountain in central China. In contrary to plant communities, the microbial taxonomic diversity of the DBF was significantly (P?<?0.05) higher than those of CF and MBF, rendering their microbial community compositions markedly different. Consistently, microbial functional diversity was also highest in the DBF. Furthermore, a network analysis of microbial carbon and nitrogen cycling genes showed the network for the DBF samples was relatively large and tight, revealing strong couplings between microbes. Soil temperature, reflective of climate regimes, was important in shaping microbial communities at both taxonomic and functional gene levels. As a first glimpse of both the taxonomic and functional compositions of soil microbial communities, our results suggest that microbial community structure and function potentials will be altered by future environmental changes, which have implications for forest succession.
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Project description:Ecosystem dynamics in monomictic lakes are characterized by seasonal thermal mixing and stratification. These physical processes bring about seasonal variations in nutrients and organic matter fluxes, affecting the biogeochemical processes that occur in the water column. Physical and chemical dynamics are generally reflected in seasonal structural changes in the phytoplankton and bacterio-plankton community. In this study, we analyzed, using 16S rRNA amplicon sequencing, the structure of the bacterial community associated with large particles (>20 ?m) in Lake Kinneret (Sea of Galilee, Israel), and its associations to phytoplankton populations. The study was carried out during late winter and early spring, a highly dynamic period in terms of thermal mixing, nutrient availability, and shifts in phytoplankton composition. Structural changes in the bacterioplankton population corresponded with limnological variations in the lake. In terms of the entire heterotrophic community, the structural patterns of particle-associated bacteria were mainly correlated with abiotic factors such as pH, ammonia, water temperature and nitrate. However, analysis of microbial taxon-specific correlations with phytoplankton species revealed a strong potential link between specific bacterial populations and the presence of different phytoplankton species, such as the cyanobacterium Microcystis, as well as the dinoflagellates Peridinium and Peridiniopsis. We found that Brevundimonas, a common freshwater genus, and Bdellovibrio, a well-known Gram-negative bacteria predator, were positively associated to Microcystis, suggesting a potentially important role of these three taxa in the microbial ecology of the lake. Our results show that the dynamics of environmental abiotic conditions, rather than specific phytoplankton assemblages, are the main factors positively correlated with changes in the community structure as a whole. Nevertheless, some specific bacteria may interact and be linked with specific phytoplankton, which may potentially control the dynamic patterns of the microbial community.
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Project description:This study evaluated the effects of three commercial dispersants (Finasol OSR 52, Slickgone NS, Superdispersant 25) and three biosurfactants (rhamnolipid, trehalolipid, sophorolipid) in crude-oil seawater microcosms. We analysed the crucial early bacterial response (1 and 3 days). In contrast, most analyses miss this key period and instead focus on later time points after oil and dispersant addition. By focusing on the early stage, we show that dispersants and biosurfactants, which reduce the interfacial surface tension of oil and water, significantly increase the abundance of hydrocarbon-degrading bacteria, and the rate of hydrocarbon biodegradation, within 24 h. A succession of obligate hydrocarbonoclastic bacteria (OHCB), driven by metabolite niche partitioning, is demonstrated. Importantly, this succession has revealed how the OHCB Oleispira, hitherto considered to be a psychrophile, can dominate in the early stages of oil-spill response (1 and 3 days), outcompeting all other OHCB, at the relatively high temperature of 16 °C. Additionally, we demonstrate how some dispersants or biosurfactants can select for specific bacterial genera, especially the biosurfactant rhamnolipid, which appears to provide an advantageous compatibility with Pseudomonas, a genus in which some species synthesize rhamnolipid in the presence of hydrocarbons.
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Project description:In composting system, the composition of microbial communities is determined by the constant change in the physicochemical parameters. This study explored the dynamics of bacterial and fungal communities during cow manure and corn straw composting using high throughput sequencing technology. The relationships between physicochemical parameters and microbial community composition and abundance were also evaluated. The sequencing results revealed the major phyla included Proteobacteria, Bacteroidetes, Firmicutes, Chloroflexi and Actinobacteria, Ascomycota, and Basidiomycota. Linear discriminant analysis effect size (LEfSe) illustrated that Actinomycetales and Sordariomycetes were the indicators of bacteria and fungi in the maturation phase, respectively. Mantel test showed that NO3 --N, NH4 +-N, TN, C/N, temperature and moisture content significantly influenced bacterial community composition while only TN and moisture content had a significant effect on fungal community structure. Structural equation model (SEM) indicated that TN, NH4 +-N, NO3 --N and pH had a significant effect on fungal abundance while TN and temperature significantly affected bacterial abundance. Our finding increases the understanding of microbial community succession in cow manure and corn straw composting under natural conditions.
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Project description:The microbial composition and environmental factors can take a great influence on community succession during the solid-state fermentation (SSF) of Maotai-flavor Baijiu. In this paper, high-throughput sequencing was used to reveal the dominant microorganisms and the evolution process of microbial community structure in the initial fermentation of Maotai-flavor Baijiu. The correlation analysis was carried out for the relationship between physicochemical factors and fermented microbes. The results showed that microorganisms were obviously enriched and the diversity of bacteria and fungi showed a downward trend during the heap fermentation process of Maotai-flavor Baijiu. However, the diversity of fungi in the pit fermentation process increased. Generally, Lactobacillus, Pichia, and Saccharomyces were the dominant microorganisms in the initial fermentation of Maotai-flavor Baijiu. According to the redundancy analysis, we found that reducing sugar was the key driving factor for microbial succession in the heap fermentation, while acidity, alcohol, and temperature were the main driving forces in pit fermentation. This study revealed the microbial succession and its related environmental factors in the initial fermentation of Maotai-flavor Baijiu, which will enrich our knowledge of the mechanism of solid-state liquor fermentation.
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Project description:The quality of traditional Chinese soy sauce is determined by microbial communities and their inter-related metabolic roles in the fermentation tank. In this study, traditional Chinese soy sauce brine samples were obtained periodically to monitor the transitions of the microbial population and functional properties during the 6 months of fermentation process. Whole genome shotgun method revealed that the fermentation brine was dominated by the bacterial genus Weissella and later dominated by the fungal genus Candida. Metabolic reconstruction of the metagenome sequences demonstrated a characteristic profile of heterotrophic fermentation of proteins and carbohydrates. This was supported by the detection of ethanol with stable decrease of pH values. To the best of our knowledge, this is the first study that explores the temporal changes in microbial successions over a period of 6 months, through metagenome shotgun sequencing in traditional Chinese soy sauce fermentation and the biological processes therein.
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Project description:Microorganisms play a critical role in the decomposition of organic matter, which contributes to energy and nutrient transformation in every ecosystem. Yet, little is known about the functional activity of epinecrotic microbial communities associated with carrion. The objective of this study was to provide a description of the carrion associated microbial community functional activity using differential carbon source use throughout decomposition over seasons, between years and when microbial communities were isolated from eukaryotic colonizers (e.g., necrophagous insects). Additionally, microbial communities were identified at the phyletic level using high throughput sequencing during a single study. We hypothesized that carrion microbial community functional profiles would change over the duration of decomposition, and that this change would depend on season, year and presence of necrophagous insect colonization. Biolog EcoPlates™ were used to measure the variation in epinecrotic microbial community function by the differential use of 29 carbon sources throughout vertebrate carrion decomposition. Pyrosequencing was used to describe the bacterial community composition in one experiment to identify key phyla associated with community functional changes. Overall, microbial functional activity increased throughout decomposition in spring, summer and winter while it decreased in autumn. Additionally, microbial functional activity was higher in 2011 when necrophagous arthropod colonizer effects were tested. There were inconsistent trends in the microbial function of communities isolated from remains colonized by necrophagous insects between 2010 and 2011, suggesting a greater need for a mechanistic understanding of the process. These data indicate that functional analyses can be implemented in carrion studies and will be important in understanding the influence of microbial communities on an essential ecosystem process, carrion decomposition.
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