Mechanism of differential expression of β-glucosidase genes in functional microbial communities in response to carbon catabolite repression

Abstract Background β-Glucosidase is the rate-limiting enzyme of cellulose degradation. It has been stipulated and established that β-glucosidase-producing microbial communities differentially regulate the expression of glucose/non-glucose tolerant β-glucosidase genes. However, it is still unknown if this differential expression of functional microbial community happens accidentally or as a general regulatory mechanism, and of what biological significance it has. To investigate the composition and function of microbial communities and how they respond to different carbon metabolism pressures and the transcriptional regulation of functional genes, the different carbon metabolism pressure was constructed by setting up the static chamber during composting. Results The composition and function of functional microbial communities demonstrated different behaviors under the carbon metabolism pressure. Functional microbial community up-regulated glucose tolerant β-glucosidase genes expression to maintain the carbon metabolism rate by enhancing the transglycosylation activity of β-glucosidase to compensate for the decrease of hydrolysis activity under carbon catabolite repression (CCR). Micrococcales play a vital role in the resistance of functional microbial community under CCR. The transcription regulation of GH1 family β-glucosidase genes from Proteobacteria showed more obvious inhibition than other phyla under CCR. Conclusion Microbial functional communities differentially regulate the expression of glucose/non-glucose tolerant β-glucosidase genes under CCR, which is a general regulatory mechanism, not accidental. Furthermore, the differentially expressed β-glucosidase gene exhibited species characteristics at the phylogenetic level.

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β-Glucosidase genes differentially expressed during composting

Biotechnology for Biofuels ◽

10.1186/s13068-020-01813-w ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Xinyue Zhang ◽

Bo Ma ◽

Jiawen Liu ◽

Xiehui Chen ◽

Shanshan Li ◽

...

Keyword(s):

Microbial Communities ◽

Environmental Changes ◽

Cellulose Degradation ◽

Degradation Mechanism ◽

Degradation Process ◽

Global Scale ◽

Expression Of Genes ◽

Glucose Tolerant ◽

Cooling Phase ◽

And Function

Abstract Background Cellulose degradation by cellulase is brought about by complex communities of interacting microorganisms, which significantly contribute to the cycling of carbon on a global scale. β-Glucosidase (BGL) is the rate-limiting enzyme in the cellulose degradation process. Thus, analyzing the expression of genes involved in cellulose degradation and regulation of BGL gene expression during composting will improve the understanding of the cellulose degradation mechanism. Based on our previous research, we hypothesized that BGL-producing microbial communities differentially regulate the expression of glucose-tolerant BGL and non-glucose-tolerant BGL to adapt to the changes in cellulose degradation conditions. Results To confirm this hypothesis, the structure and function of functional microbial communities involved in cellulose degradation were investigated by metatranscriptomics and a DNA library search of the GH1 family of BGLs involved in natural and inoculated composting. Under normal conditions, the group of non-glucose-tolerant BGL genes exhibited higher sensitivity to regulation than the glucose-tolerant BGL genes, which was suppressed during the composting process. Compared with the expression of endoglucanase and exoglucanase, the functional microbial communities exhibited a different transcriptional regulation of BGL genes during the cooling phase of natural composting. BGL-producing microbial communities upregulated the expression of glucose-tolerant BGL under carbon catabolite repression due to the increased glucose concentration, whereas the expression of non-glucose-tolerant BGL was suppressed. Conclusion Our results support the hypothesis that the functional microbial communities use multiple strategies of varying effectiveness to regulate the expression of BGL genes to facilitate adaptation to environmental changes.

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Predation by protists influences the temperature response of microbial communities

10.1101/2021.04.08.439073 ◽

2021 ◽

Author(s):

Jennifer D Rocca ◽

Andrea Yammine ◽

Marie Simonin ◽

Jean Gibert

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Biomass ◽

Microbial Communities ◽

Microbial Community Structure ◽

Temperature Response ◽

Global Carbon Cycle ◽

Structure And Function ◽

And Function ◽

Global Carbon

Temperature strongly influences microbial community structure and function, which in turn contributes to the global carbon cycle that can fuel further warming. Recent studies suggest that biotic interactions amongst microbes may play an important role in determining the temperature responses of these communities. However, how microbial predation regulates these communities under future climates is still poorly understood. Here we assess whether predation by one of the most important bacterial consumers globally, protists, influences the temperature response of a freshwater microbial community structure and function. To do so, we exposed these microbial communities to two cosmopolitan species of protists at two different temperatures, in a month-long microcosm experiment. While microbial biomass and respiration increased with temperature due to shifts in microbial community structure, these responses changed over time and in the presence of protist predators. Protists influenced microbial biomass and function through effects on community structure, and predation actually reduced microbial respiration rate at elevated temperature. Indicator species and threshold indicator taxa analyses showed that these predation effects were mostly determined by phylum-specific bacterial responses to protist density and cell size. Our study supports previous findings that temperature is an important driver of microbial communities, but also demonstrates that predation can mediate these responses to warming, with important consequences for the global carbon cycle and future warming.

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Mussels and Local Conditions Interact to Influence Microbial Communities in Mussel Beds

Frontiers in Microbiology ◽

10.3389/fmicb.2021.790554 ◽

2022 ◽

Vol 12 ◽

Author(s):

Edward Higgins ◽

Thomas B. Parr ◽

Caryn C. Vaughn

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Microbial Community Composition ◽

Canopy Cover ◽

Freshwater Mussel ◽

Local Conditions ◽

Individual Organism ◽

Mussel Shells ◽

Landscape Scales ◽

And Function

Microbiomes are increasingly recognized as widespread regulators of function from individual organism to ecosystem scales. However, the manner in which animals influence the structure and function of environmental microbiomes has received considerably less attention. Using a comparative field study, we investigated the relationship between freshwater mussel microbiomes and environmental microbiomes. We used two focal species of unionid mussels, Amblema plicata and Actinonaias ligamentina, with distinct behavioral and physiological characteristics. Mussel microbiomes, those of the shell and biodeposits, were less diverse than both surface and subsurface sediment microbiomes. Mussel abundance was a significant predictor of sediment microbial community composition, but mussel species richness was not. Our data suggest that local habitat conditions which change dynamically along streams, such as discharge, water turnover, and canopy cover, work in tandem to influence environmental microbial community assemblages at discreet rather than landscape scales. Further, mussel burrowing activity and mussel shells may provide habitat for microbial communities critical to nutrient cycling in these systems.

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A conceptual framework for the phylogenetically constrained assembly of microbial communities

Microbiome ◽

10.1186/s40168-019-0754-y ◽

2019 ◽

Vol 7 (1) ◽

Cited By ~ 5

Author(s):

Daniel Aguirre de Cárcer

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Assembly ◽

Phylogenetic Signal ◽

A Priori ◽

Amplicon Sequencing ◽

Bioinformatic Analysis ◽

Microbial Ecosystems ◽

And Function ◽

Microbial Community Assembly

Abstract Microbial communities play essential and preponderant roles in all ecosystems. Understanding the rules that govern microbial community assembly will have a major impact on our ability to manage microbial ecosystems, positively impacting, for instance, human health and agriculture. Here, I present a phylogenetically constrained community assembly principle grounded on the well-supported facts that deterministic processes have a significant impact on microbial community assembly, that microbial communities show significant phylogenetic signal, and that microbial traits and ecological coherence are, to some extent, phylogenetically conserved. From these facts, I derive a few predictions which form the basis of the framework. Chief among them is the existence, within most microbial ecosystems, of phylogenetic core groups (PCGs), defined as discrete portions of the phylogeny of varying depth present in all instances of the given ecosystem, and related to specific niches whose occupancy requires a specific phylogenetically conserved set of traits. The predictions are supported by the recent literature, as well as by dedicated analyses. Integrating the effect of ecosystem patchiness, microbial social interactions, and scale sampling pitfalls takes us to a comprehensive community assembly model that recapitulates the characteristics most commonly observed in microbial communities. PCGs’ identification is relatively straightforward using high-throughput 16S amplicon sequencing, and subsequent bioinformatic analysis of their phylogeny, estimated core pan-genome, and intra-group co-occurrence should provide valuable information on their ecophysiology and niche characteristics. Such a priori information for a significant portion of the community could be used to prime complementing analyses, boosting their usefulness. Thus, the use of the proposed framework could represent a leap forward in our understanding of microbial community assembly and function.

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Soil and sediment microbial structure and function in intermittent stream corridors after a decade of catchment succession

10.5194/egusphere-egu2020-4952 ◽

2020 ◽

Author(s):

Jose Schreckinger ◽

Aline Frossard ◽

Linda Gerull ◽

Mark O. Gessner ◽

Michael Mutz

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Vegetation Cover ◽

Structure And Function ◽

Grass Species ◽

Microbial Structure ◽

Small Streams ◽

Northeastern Germany ◽

And Function ◽

Soil And Sediment

<p>Large-scale resource exploitation by open-cast mining severely alters landscapes and impairs key ecosystem properties such as soil and sediment structure and function. Understanding the ecological recovery processes starting from an initially bare landscape generated by destructive land-use is extremely limited. Here we took advantage of a 6-ha experimental catchment to assess microbial community structure and function in soils and stream sediments after 3 and 13 years of catchment succession. The catchment (Chicken Creek) was created in 2005 by depositing quaternary sands from a lignite mine forefield in northeastern Germany and has since been left to develop under undisturbed conditions. In the initial stage, 3 years after catchment construction, rills and small streams had formed and the sparse vegetation cover mainly consisted of forbs. Over the next 10 years, the geomorphology, hydrology, and vegetation structure underwent a major transformation. A nearly full vegetation cover established, including various tree, shrub and grass species. Increased evaporation lowered the shallow groundwater table and led to stream intermittency. These changes were accompanied by large modifications in the structure and function of the microbial communities in sediments and soils. Initially, microbial structure and function were strikingly disconnected, whereas linkages had established 10 years later, although some functions still remained disconnected. Potential enzymatic activities increased vastly over the course of 10 years and also became much less variable across seasons. Cyanobacteria, predominant in soils and sediments during the early successional stage, declined to become a minor component of the microbial community. Moreover, despite distinct flow intermittency of the streams, microbial structure and function distinctly differed between sediments and adjacent soils. These results demonstrate a rapid succession of microbial communities during a decade of ecosystem development, suggesting that undisturbed succession is a feasible catchment restoration strategy.</p>

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Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology

Frontiers in Microbiology ◽

10.3389/fmicb.2021.642422 ◽

2021 ◽

Vol 12 ◽

Author(s):

Lauren M. Lui ◽

Erica L.-W. Majumder ◽

Heidi J. Smith ◽

Hans K. Carlson ◽

Frederick von Netzer ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Microbial Ecology ◽

High Throughput Sequencing ◽

Spatial Scales ◽

Data Types ◽

Modeling Framework ◽

Rapid Acquisition ◽

Mechanistic Understanding ◽

And Function

Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.

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Microbial community composition interacts with local abiotic conditions to drive colonization resistance in human gut microbiome samples

10.1101/2020.08.18.255695 ◽

2020 ◽

Author(s):

Michael Baumgartner ◽

Katia R Pfrunder-Cardozo ◽

Alex R Hall

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Microbial Community Composition ◽

Nutrient Status ◽

Taxonomic Composition ◽

Colonization Resistance ◽

Abiotic Conditions ◽

E Coli ◽

And Function

AbstractBiological invasions can alter ecosystem stability and function, and predicting what happens when a new species or strain arrives remains a major challenge in ecology. In the mammalian gastrointestinal tract, susceptibility of the resident microbial community to invasion by pathogens has important implications for host health. However, at the community level, it is unclear whether susceptibility to invasion depends mostly on resident community composition (which microbes are present), or also on local abiotic conditions (such as nutrient status). Here, we used a gut microcosm system to disentangle some of the drivers of susceptibility to invasion in microbial communities sampled from humans. We found resident microbial communities inhibited an invading E. coli strain, compared to community-free control treatments, sometimes excluding the invader completely (colonization resistance). These effects were stronger at later time points, coinciding with shifts in microbial community composition and nutrient availability. By separating these two components (microbial community and abiotic environment), we found taxonomic composition played a crucial role in suppressing invasion, but this depended critically on local abiotic conditions (adapted communities were more suppressive in nutrient-depleted conditions). This helps predict when resident communities will be most susceptible to invasion, with implications for optimizing treatments based around microbiota management.

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Metabolic dissimilarity determines the establishment of cross-feeding interactions in bacteria

10.1101/2020.10.09.333336 ◽

2020 ◽

Cited By ~ 1

Author(s):

Samir Giri ◽

Leonardo Oña ◽

Silvio Waschina ◽

Shraddha Shitut ◽

Ghada Yousif ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Assembly ◽

Bacterial Species ◽

Exchange Interactions ◽

Structure And Function ◽

Phylogenetic Distance ◽

And Function ◽

Microbial Community Assembly ◽

Feeding Interactions

AbstractThe exchange of metabolites among different bacterial genotypes is key for determining the structure and function of microbial communities. However, the factors that govern the establishment of these cross-feeding interactions remain poorly understood. While kin selection theory predicts that individuals should direct benefits preferentially to close relatives, the potential benefits resulting from a metabolic exchange may be larger for more distantly related species. Here we distinguish between these two possibilities by performing pairwise cocultivation experiments between auxotrophic recipients and 25 species of potential amino acid donors. Auxotrophic recipients were able to grow in the vast majority of pairs tested (78%), suggesting that metabolic cross-feeding interactions are readily established. Strikingly, both the phylogenetic distance between donor and recipient as well as the dissimilarity of their metabolic networks was positively associated with the growth of auxotrophic recipients. Finally, this result was corroborated in an in-silico analysis of a co-growth of species from a gut microbial community. Together, these findings suggest metabolic cross-feeding interactions are more likely to establish between strains that are metabolically more dissimilar. Thus, our work identifies a new rule of microbial community assembly, which can help predict, understand, and manipulate natural and synthetic microbial systems.SignificanceMetabolic cross-feeding is critical for determining the structure and function of natural microbial communities. However, the rules that determine the establishment of these interactions remain poorly understood. Here we systematically analyze the propensity of different bacterial species to engage in unidirectional cross-feeding interactions. Our results reveal that synergistic growth was prevalent in the vast majority of cases analyzed. Moreover, both phylogenetic and metabolic dissimilarity between donors and recipients favored a successful establishment of metabolite exchange interactions. This work identifies a new rule of microbial community assembly that can help predict, understand, and manipulate microbial communities for diverse applications.

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Metabolic tuning of a stable microbial community in the surface oligotrophic Indian Ocean revealed by integrated meta-omics

Marine Life Science & Technology ◽

10.1007/s42995-021-00119-6 ◽

2022 ◽

Author(s):

Zhang-Xian Xie ◽

Ke-Qiang Yan ◽

Ling-Fen Kong ◽

Ying-Bao Gai ◽

Tao Jin ◽

...

Keyword(s):

Microbial Community ◽

Indian Ocean ◽

Microbial Communities ◽

Fine Tuning ◽

Metabolic Potential ◽

Environmental Forcing ◽

Metabolic Functions ◽

Microbial Response ◽

The Stability ◽

And Function

AbstractUnderstanding the mechanisms, structuring microbial communities in oligotrophic ocean surface waters remains a major ecological endeavor. Functional redundancy and metabolic tuning are two mechanisms that have been proposed to shape microbial response to environmental forcing. However, little is known about their roles in the oligotrophic surface ocean due to less integrative characterization of community taxonomy and function. Here, we applied an integrated meta-omics-based approach, from genes to proteins, to investigate the microbial community of the oligotrophic northern Indian Ocean. Insignificant spatial variabilities of both genomic and proteomic compositions indicated a stable microbial community that was dominated by Prochlorococcus, Synechococcus, and SAR11. However, fine tuning of some metabolic functions that are mainly driven by salinity and temperature was observed. Intriguingly, a tuning divergence occurred between metabolic potential and activity in response to different environmental perturbations. Our results indicate that metabolic tuning is an important mechanism for sustaining the stability of microbial communities in oligotrophic oceans. In addition, integrated meta-omics provides a powerful tool to comprehensively understand microbial behavior and function in the ocean.

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Oil and Gas Wastewater Components Alter Streambed Microbial Community Structure and Function

Frontiers in Microbiology ◽

10.3389/fmicb.2021.752947 ◽

2021 ◽

Vol 12 ◽

Author(s):

Denise M. Akob ◽

Adam C. Mumford ◽

Andrea Fraser ◽

Cassandra R. Harris ◽

William H. Orem ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

West Virginia ◽

Hydraulic Fracturing ◽

Microbial Communities ◽

Microbial Community Structure ◽

Oil And Gas ◽

Structure And Function ◽

Underground Injection ◽

And Function

The widespread application of directional drilling and hydraulic fracturing technologies expanded oil and gas (OG) development to previously inaccessible resources. A single OG well can generate millions of liters of wastewater, which is a mixture of brine produced from the fractured formations and injected hydraulic fracturing fluids (HFFs). With thousands of wells completed each year, safe management of OG wastewaters has become a major challenge to the industry and regulators. OG wastewaters are commonly disposed of by underground injection, and previous research showed that surface activities at an Underground Injection Control (UIC) facility in West Virginia affected stream biogeochemistry and sediment microbial communities immediately downstream from the facility. Because microbially driven processes can control the fate and transport of organic and inorganic components of OG wastewater, we designed a series of aerobic microcosm experiments to assess the influence of high total dissolved solids (TDS) and two common HFF additives—the biocide 2,2-dibromo-3-nitrilopropionamide (DBNPA) and ethylene glycol (an anti-scaling additive)—on microbial community structure and function. Microcosms were constructed with sediment collected upstream (background) or downstream (impacted) from the UIC facility in West Virginia. Exposure to elevated TDS resulted in a significant decrease in aerobic respiration, and microbial community analysis following incubation indicated that elevated TDS could be linked to the majority of change in community structure. Over the course of the incubation, the sediment layer in the microcosms became anoxic, and addition of DBNPA was observed to inhibit iron reduction. In general, disruptions to microbial community structure and function were more pronounced in upstream and background sediment microcosms than in impacted sediment microcosms. These results suggest that the microbial community in impacted sediments had adapted following exposure to OG wastewater releases from the site. Our findings demonstrate the potential for releases from an OG wastewater disposal facility to alter microbial communities and biogeochemical processes. We anticipate that these studies will aid in the development of useful models for the potential impact of UIC disposal facilities on adjoining surface water and shallow groundwater.

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