scholarly journals Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities

mSystems ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Manuel Kleiner
Keyword(s):  
Gene Expression ◽  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Large Scale ◽  
Molecular Level ◽  
Carbon Sources ◽  
Community Members ◽  
Insight Into

ABSTRACT Metaproteomics is the large-scale identification and quantification of proteins from microbial communities and thus provides direct insight into the phenotypes of microorganisms on the molecular level. Initially, metaproteomics was mainly used to assess the “expressed” metabolism and physiology of microbial community members. However, recently developed metaproteomic tools allow quantification of per-species biomass to determine community structure, in situ carbon sources of community members, and the uptake of labeled substrates by community members. In this perspective, I provide a brief overview of the questions that we can currently address, as well as new metaproteomics-based approaches that we and others are developing to address even more questions in the study of microbial communities and plant and animal microbiota. I also highlight some areas and technologies where I anticipate developments and potentially major breakthroughs in the next 5 years and beyond.

In Situ Gene Expression in Mixed-Culture Biofilms: Evidence of Metabolic Interactions between Community Members

1998 ◽  
Vol 64 (2) ◽  
pp. 721-732 ◽  
Author(s):  
Søren Møller ◽  
Claus Sternberg ◽  
Jens Bo Andersen ◽  
Bjarke Bak Christensen ◽  
Juan Luis Ramos ◽  
...  
Keyword(s):  
Gene Expression ◽  
Microbial Communities ◽  
Pure Culture ◽  
Fluorescent Protein ◽  
Confocal Laser ◽  
Specific Gene ◽  
Community Members ◽  
Metabolic Interactions ◽  
Green Fluorescent

ABSTRACT Microbial communities growing in laboratory-based flow chambers were investigated in order to study compartmentalization of specific gene expression. Among the community members studied, the focus was in particular on Pseudomonas putida and a strain of anAcinetobacter sp., and the genes studied are involved in the biodegradation of toluene and related aromatic compounds. The upper-pathway promoter (Pu) and themeta-pathway promoter (Pm) from the TOL plasmid were fused independently to the gene coding for the green fluorescent protein (GFP), and expression from these promoters was studied inP. putida, which was a dominant community member. Biofilms were cultured in flow chambers, which in combination with scanning confocal laser microscopy allowed direct monitoring of promoter activity with single-cell spatial resolution. Expression from thePu promoter was homogeneously induced by benzyl alcohol in both community and pure-culture biofilms, while the Pmpromoter was induced in the mixed community but not in a pure-culture biofilm. By sequentially adding community members, induction ofPm was shown to be a consequence of direct metabolic interactions between an Acinetobacter species and P. putida. Furthermore, in fixed biofilm samples organism identity was determined and gene expression was visualized at the same time by combining GFP expression with in situ hybridization with fluorescence-labeled 16S rRNA targeting probes. This combination of techniques is a powerful approach for investigating structure-function relationships in microbial communities.

Composition and Physiological Profiling of Sprout-Associated Microbial Communities

2002 ◽  
Vol 65 (12) ◽  
pp. 1903-1908 ◽  
Author(s):  
ANABELLE MATOS ◽  
JAY L. GARLAND ◽  
WILLIAM F. FETT
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Carbon Sources ◽  
The Other ◽  
Independent Effect ◽  
Patterns Of Utilization ◽  
Plate Counts ◽  
Alfalfa Sprouts

The native microfloras of various types of sprouts (alfalfa, clover, sunflower, mung bean, and broccoli sprouts) were examined to assess the relative effects of sprout type and inoculum factors (i.e., sprout-growing facility, seed lot, and inoculation with sprout-derived inocula) on the microbial community structure of sprouts. Sprouts were sonicated for 7 min or hand shaken with glass beads for 2 min to recover native microfloras from the surface, and the resulting suspensions were diluted and plated. The culturable fraction was characterized by the density (log CFU/g), richness (e.g., number of types of bacteria), and diversity (e.g., microbial richness and evenness) of colonies on tryptic soy agar plates incubated for 48 h at 30°C. The relative similarity between sprout-associated microbial communities was assessed with the use of community-level physiological profiles (CLPPs) based on patterns of utilization of 95 separate carbon sources. Aerobic plate counts of 7.96 ± 0.91 log CFU/g of sprout tissue (fresh weight) were observed, with no statistically significant differences in microbial cell density, richness, or diversity due to sprout type, sprout-growing facility, or seed lot. CLPP analyses revealed that the microbial communities associated with alfalfa and clover sprouts are more similar than those associated with the other sprout types tested. Variability among sprout types was more extensive than any differences between microbial communities associated with alfalfa and clover sprouts from different sprout-growing facilities and seed lots. These results indicate that the subsequent testing of biocontrol agents should focus on similar organisms for alfalfa and clover, but alternative types may be most suitable for the other sprout types tested. The inoculation of alfalfa sprouts with communities derived from various sprout types had a significant, source-independent effect on microbial community structure, indicating that the process of inoculation alters the dynamics of community development regardless of the types of organisms involved.

scholarly journals Colonization Habitat Controls Biomass, Composition, and Metabolic Activity of Attached Microbial Communities in the Columbia River Hyporheic Corridor

2017 ◽  
Vol 83 (16) ◽  
Author(s):  
Noah Stern ◽  
Matthew Ginder-Vogel ◽  
James C. Stegen ◽  
Evan Arntzen ◽  
David W. Kennedy ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Organic Carbon ◽  
Microbial Communities ◽  
River Water ◽  
Hyporheic Zone ◽  
Columbia River ◽  
Fluid Source ◽  
Hydrologic Exchange

ABSTRACT Hydrologic exchange plays a critical role in biogeochemical cycling within the hyporheic zone (the interface between river water and groundwater) of riverine ecosystems. Such exchange may set limits on the rates of microbial metabolism and impose deterministic selection on microbial communities that adapt to dynamically changing dissolved organic carbon (DOC) sources. This study examined the response of attached microbial communities (in situ colonized sand packs) from groundwater, hyporheic, and riverbed habitats within the Columbia River hyporheic corridor to “cross-feeding” with either groundwater, river water, or DOC-free artificial fluids. Our working hypothesis was that deterministic selection during in situ colonization would dictate the response to cross-feeding, with communities displaying maximal biomass and respiration when supplied with their native fluid source. In contrast to expectations, the major observation was that the riverbed colonized sand had much higher biomass and respiratory activity, as well as a distinct community structure, compared with those of the hyporheic and groundwater colonized sands. 16S rRNA gene amplicon sequencing revealed a much higher proportion of certain heterotrophic taxa as well as significant numbers of eukaryotic algal chloroplasts in the riverbed colonized sand. Significant quantities of DOC were released from riverbed sediment and colonized sand, and separate experiments showed that the released DOC stimulated respiration in the groundwater and piezometer colonized sand. These results suggest that the accumulation and degradation of labile particulate organic carbon (POC) within the riverbed are likely to release DOC, which may enter the hyporheic corridor during hydrologic exchange, thereby stimulating microbial activity and imposing deterministic selective pressure on the microbial community composition. IMPORTANCE The influence of river water-groundwater mixing on hyporheic zone microbial community structure and function is an important but poorly understood component of riverine biogeochemistry. This study employed an experimental approach to gain insight into how such mixing might be expected to influence the biomass, respiration, and composition of hyporheic zone microbial communities. Colonized sands from three different habitats (groundwater, river water, and hyporheic) were “cross-fed” with either groundwater, river water, or DOC-free artificial fluids. We expected that the colonization history would dictate the response to cross-feeding, with communities displaying maximal biomass and respiration when supplied with their native fluid source. By contrast, the major observation was that the riverbed communities had much higher biomass and respiration, as well as a distinct community structure compared with those of the hyporheic and groundwater colonized sands. These results highlight the importance of riverbed microbial metabolism in organic carbon processing in hyporheic corridors.

Microbial communities and their interactions in biofilm systems: an overview

2004 ◽  
Vol 49 (11-12) ◽  
pp. 327-336 ◽  
Author(s):  
S. Wuertz ◽  
S. Okabe ◽  
M. Hausner
Keyword(s):  
Microbial Community ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Microbial Communities ◽  
Enrichment Culture ◽  
Community Analysis ◽  
Microbial Populations ◽  
Community Members ◽  
Biofilm Architecture

Several important advances have been made in the study of biofilm microbial populations relating to their spatial structure (or architecture), their community structure, and their dependence on physicochemical parameters. With the knowledge that hydrodynamic forces influence biofilm architecture came the realization that metabolic processes may be enhanced if certain spatial structures can be forced. An example is the extent of plasmid-mediated horizontal gene transfer in biofilms. Recent in situ work in defined model systems has shown that the biofilm architecture plays a role for genetic transfer by bacterial conjugation in determining how far the donor cells can penetrate the biofilm. Open channels and pores allow for more efficient donor transport and hence more frequent cell collisions leading to rapid spread of the genes by horizontal gene transfer. Such insight into the physical environment of biofilms can be utilized for bioenhancement of catabolic processes by introduction of mobile genetic elements into an existing microbial community. If the donor organisms themselves persist, bioaugmentation can lead to successful establishment of newly introduced species and may be a more successful strategy than biostimulation (the addition of nutrients or specific carbon sources to stimulate the authochthonous population) as shown for an enrichment culture of nitrifying bacteria added to rotating disk biofilm reactors using fluorescent in situ hybridization (FISH) and microelectrode measurements of NH4+, NO2-, NO3-, and O2. However, few studies have been carried out on full-scale systems. Bioaugmentation and bioenhancement are most successful if a constant selective pressure can be maintained favoring the promulgation of the added enrichment culture. Overall, knowledge gain about microbial community interactions in biofilms continues to be driven by the availability of methods for the rapid analysis of microbial communities and their activities. Molecular tools can be grouped into those suitable for ex situ and in situ community analysis. Non-spatial community analysis, in the sense of assessing changes in microbial populations as a function of time or environmental conditions, relies on general fingerprinting methods, like DGGE and T-RFLP, performed on nucleic acids extracted from biofilm. These approaches have been most useful when combined with gene amplification, cloning and sequencing to assemble a phylogenetic inventory of microbial species. It is expected that the use of oligonucleotide microarrays will greatly facilitate the analysis of microbial communities and their activities in biofilms. Structure-activity relationships can be explored using incorporation of 13C-labeled substrates into microbial DNA and RNA to identify metabolically active community members. Finally, based on the DNA sequences in a biofilm, FISH probes can be designed to verify the abundance and spatial location of microbial community members. This in turn allows for in situ structure/function analysis when FISH is combined with microsensors, microautoradiography, and confocal laser scanning microscopy with advanced image analysis.

scholarly journals The exchange of vitamin B1 and its biosynthesis intermediates in synthetic microbial communities shapes the community composition and reveals complexities of nutrient sharing

2021 ◽  
Author(s):  
Rupali R. M. Sathe ◽  
Ryan W. Paerl ◽  
Amrita B. Hazra
Keyword(s):  
Microbial Communities ◽  
Large Scale ◽  
General Pattern ◽  
Carbon Sources ◽  
Vibrio Anguillarum ◽  
Vitamin B1 ◽  
Individual Species ◽  
Community Members ◽  
E Coli ◽  
The Media

AbstractMicrobial communities occupy diverse niches in nature, and exchanges of metabolites such as carbon sources, amino acids, and vitamins occur routinely among the community members. While large-scale metagenomic and metabolomic studies shed some light on these exchanges, the contribution of individual species and the molecular details of specific interactions are difficult to track. Here, we explore the molecular picture of vitamin B1 (thiamin) metabolism occurring in synthetic communities of Escherichia coli thiamin auxotrophs which engage in the exchange of thiamin and its biosynthesis intermediates. In E. coli, the two parts of thiamin – the 4-amino-5-hydroxymethyl-2-methylpyrimidine and the 4-methyl-5-(2-hydroxyethyl)thiazole – are synthesized by separate pathways using enzymes ThiC and ThiG, respectively, and are then joined by ThiE to form thiamin. We observed that even though E. coli ΔthiC, ΔthiE, and ΔthiG mutants are thiamin auxotrophs, co-cultures of ΔthiC-ΔthiE and ΔthiC-ΔthiG grow in a thiamin-deficient minimal medium, whereas the ΔthiE-ΔthiG co-culture does not. Analysis of the exchange of thiamin and its intermediates in Vibrio anguillarum co-cultures, and in mixed co-cultures of V. anguillarum and E. coli revealed that the general pattern of thiamin metabolism and exchange among microbes is conserved across species. Specifically, the microorganisms exchange HMP and thiamin easily among themselves but not THZ. Furthermore, we observe that the availability of exogenous thiamin in the media affects whether these strains interact with each other or grow independently. This underscores the importance of the exchange of essential metabolites as a defining factor in building and modulating synthetic or natural microbial communities.

scholarly journals A Long-Standing Complex Tropical Dipole Shapes Marine Microbial Biogeography

2018 ◽  
Vol 84 (18) ◽  
Author(s):  
Wei Yan ◽  
Rui Zhang ◽  
Nianzhi Jiao
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Large Scale ◽  
Community Dynamics ◽  
Anticyclonic Eddy ◽  
Cyclonic Eddy ◽  
Content Type ◽  
Microbial Community Dynamics ◽  
Biogeographic Provinces

ABSTRACTMicrobial population size, production, diversity, and community structure are greatly influenced by the surrounding physicochemical conditions, such as large-scale biogeographic provinces and water masses. An oceanic mesoscale dipole consists of a cyclonic eddy and an anticyclonic eddy. Dipoles occur frequently in the ocean and usually last from a few days to several months; they have significant impacts on local and global oceanic biological, ecological, and geochemical processes. To better understand how dipoles shape microbial communities, we examined depth-resolved distributions of microbial communities across a dipole in the South China Sea. Our data demonstrated that the dipole had a substantial influence on microbial distributions, community structure, and functional groups both vertically and horizontally. Large alpha and beta diversity differences were observed between anticyclonic and cyclonic eddies in surface and subsurface layers, consistent with distribution changes of major bacterial groups in the dipole. The dipole created uplift, downward transport, enrichment, depletion, and horizontal transport effects. We also found that the edge of the dipole might induce strong subduction, indicated by the presence ofProchlorococcusandSynechococcusin deep waters. Our findings suggest that dipoles, with their unique characteristics, might act as a driver for microbial community dynamics.IMPORTANCEOceanic dipoles, which consist of a cyclonic eddy and an anticyclonic eddy together, are among the most contrasted phenomena in the ocean. Dipoles generate strong vertical mixing and horizontal advection, inducing biological responses. This study provides vertical profiles of microbial abundance, diversity, and community structure in a mesoscale dipole. We identify the links between the physical oceanography and microbial oceanography and demonstrate that the dipole, with its unique features, could act as a driver for microbial community dynamics, which may have large impacts on both the local and global marine biogeochemical cycles.

scholarly journals Metagenome-assembled genomes infer potential microbial metabolism in alkaline sulphidic tailings

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Wenjun Li ◽  
Xiaofang Li
Keyword(s):  
Community Structure ◽  
Mine Tailings ◽  
Fluorescent In Situ Hybridization ◽  
High Throughput Sequencing ◽  
Microbial Consortia ◽  
Metabolic Reconstruction ◽  
Metal Release ◽  
Community Members ◽  
Oxidative Stresses

Abstract Background Mine tailings are hostile environment. It has been well documented that several microbes can inhabit such environment, and metagenomic reconstruction has successfully pinpointed their activities and community structure in acidic tailings environments. We still know little about the microbial metabolic capacities of alkaline sulphidic environment where microbial processes are critically important for the revegetation. Microbial communities therein may not only provide soil functions, but also ameliorate the environment stresses for plants’ survival. Results In this study, we detected a considerable amount of viable bacterial and archaeal cells using fluorescent in situ hybridization in alkaline sulphidic tailings from Mt Isa, Queensland. By taking advantage of high-throughput sequencing and up-to-date metagenomic binning technology, we reconstructed the microbial community structure and potential coupled iron and nitrogen metabolism pathways in the tailings. Assembly of 10 metagenome-assembled genomes (MAGs), with 5 nearly complete, was achieved. From this, detailed insights into the community metabolic capabilities was derived. Dominant microbial species were seen to possess powerful resistance systems for osmotic, metal and oxidative stresses. Additionally, these community members had metabolic capabilities for sulphide oxidation, for causing increased salinity and metal release, and for leading to N depletion. Conclusions Here our results show that a considerable amount of microbial cells inhabit the mine tailings, who possess a variety of genes for stress response. Metabolic reconstruction infers that the microbial consortia may actively accelerate the sulphide weathering and N depletion therein.

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