scholarly journals Nutritional Composition and Microbial Communities of Two Non-alcoholic Traditional Fermented Beverages from Zambia: A Study of Mabisi and Munkoyo

Nutrients ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 1628 ◽  
Author(s):  
Justin Chileshe ◽  
Joost van den Heuvel ◽  
Ray Handema ◽  
Bas J Zwaan ◽  
Elise F. Talsma ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Raw Materials ◽  
Microbial Community Composition ◽  
Nutritional Composition ◽  
Fermented Foods ◽  
Microbial Composition ◽  
Specific Product ◽  
Traditional Fermented Foods

Traditional fermented foods and beverages are common in many countries, including Zambia. While the general (nutritional) benefits of fermented foods are widely recognised, the nutritional composition of most traditional fermented foods is unknown. Furthermore, fermentation is known to add nutritional value to raw materials, mainly by adding B-vitamins and removing anti-nutritional factors. In the case of traditional fermentation, the composition of microbial communities responsible for fermentation varies from producer to producer and this may also be true for the nutritional composition. Here, we characterized the nutrient profile and microbial community composition of two traditional fermented foods: milk-based Mabisi and cereal-based Munkoyo. We found that the two products are different with respect to their nutritional parameters and their microbial compositions. Mabisi was found to have higher nutritional values for crude protein, fat, and carbohydrates than Munkoyo. The microbial community composition was also different for the two products, while both communities were dominated by lactic acid bacteria. Our analyses showed that variations in nutritional composition, defined as the amount of consumption that would contribute to the estimated average requirement (EAR), might be explained by variations in microbial community composition. Consumption of Mabisi appeared to contribute more than Munkoyo to the EAR and its inclusion in food-based recommendations is warranted. Our results show the potential of traditional fermented foods such as Mabisi and Munkoyo to add value to current diets and suggests that variations in microbial composition between specific product samples can result in variations in nutritional composition.

scholarly journals Spatial Diversity in Bacterial Communities across Barren and Vegetated, Native and Invasive, Coastal Dune Microhabitats

Diversity ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 525
Author(s):  
Brianna L. Boss ◽  
Bianca R. Charbonneau ◽  
Javier A. Izquierdo
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Plant Species ◽  
Bacterial Communities ◽  
Environmental Gradients ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Spatial Diversity ◽  
Microbial Composition

The microbial community composition of coastal dunes can vary across environmental gradients, with the potential to impact erosion and deposition processes. In coastal foredunes, invasive plant species establishment can create and alter environmental gradients, thereby altering microbial communities and other ecogeomorphic processes with implications for storm response and management and conservation efforts. However, the mechanisms of these processes are poorly understood. To understand how changing microbial communities can alter these ecogeomorphic dynamics, one must first understand how soil microbial communities vary as a result of invasion. Towards this goal, bacterial communities were assessed spatially along foredune microhabitats, specifically in barren foredune toe and blowout microhabitats and in surrounding vegetated monocultures of native Ammophila breviligulata and invasive Carex kobomugi. Across dune microhabitats, microbial composition was more dissimilar in barren dune toe and blowout microhabitats than among the two plant species, but it did not appear that it would favor the establishment of one plant species over the other. However, the subtle differences between the microbial community composition of two species could ultimately aid in the success of the invasive species by reducing the proportions of bacterial genera associated exclusively with A. breviligulata. These results suggest that arrival time may be crucial in fostering microbiomes that would further the continued establishment and spread of either plant species.

scholarly journals Spatial gradients in the characteristics of soil-carbon fractions are associated with abiotic features but not microbial communities

2019 ◽  
Vol 16 (19) ◽  
pp. 3911-3928 ◽  
Author(s):  
Aditi Sengupta ◽  
Julia Indivero ◽  
Cailene Gunn ◽  
Malak M. Tfaily ◽  
Rosalie K. Chu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Organic Compounds ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Water Soluble ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Organic C ◽  
Shallow Soils

Abstract. Coastal terrestrial–aquatic interfaces (TAIs) are dynamic zones of biogeochemical cycling influenced by salinity gradients. However, there is significant heterogeneity in salinity influences on TAI soil biogeochemical function. This heterogeneity is perhaps related to unrecognized mechanisms associated with carbon (C) chemistry and microbial communities. To investigate this potential, we evaluated hypotheses associated with salinity-associated shifts in organic C thermodynamics; biochemical transformations; and nitrogen-, phosphorus-, and sulfur-containing heteroatom organic compounds in a first-order coastal watershed on the Olympic Peninsula of Washington, USA. In contrast to our hypotheses, thermodynamic favorability of water-soluble organic compounds in shallow soils decreased with increasing salinity (43–867 µS cm−1), as did the number of inferred biochemical transformations and total heteroatom content. These patterns indicate lower microbial activity at higher salinity that is potentially constrained by accumulation of less-favorable organic C. Furthermore, organic compounds appeared to be primarily marine- or algae-derived in forested floodplain soils with more lipid-like and protein-like compounds, relative to upland soils that had more lignin-, tannin-, and carbohydrate-like compounds. Based on a recent simulation-based study, we further hypothesized a relationship between C chemistry and the ecological assembly processes governing microbial community composition. Null modeling revealed that differences in microbial community composition – assayed using 16S rRNA gene sequencing – were primarily the result of limited exchange of organisms among communities (i.e., dispersal limitation). This results in unstructured demographic events that cause community composition to diverge stochastically, as opposed to divergence in community composition being due to deterministic selection-based processes associated with differences in environmental conditions. The strong influence of stochastic processes was further reflected in there being no statistical relationship between community assembly processes (e.g., the relative influence of stochastic assembly processes) and C chemistry (e.g., heteroatom content). This suggests that microbial community composition does not have a mechanistic or causal linkage to C chemistry. The salinity-associated gradient in C chemistry was, therefore, likely influenced by a combination of spatially structured inputs and salinity-associated metabolic responses of microbial communities that were independent of community composition. We propose that impacts of salinity on coastal soil biogeochemistry need to be understood in the context of C chemistry, hydrologic or depositional dynamics, and microbial physiology, while microbial composition may have less influence.

scholarly journals Antarctic Water Tracks: Microbial Community Responses to Variation in Soil Moisture, pH, and Salinity

2021 ◽  
Vol 12 ◽  
Author(s):  
Scott F. George ◽  
Noah Fierer ◽  
Joseph S. Levy ◽  
Byron Adams
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Environmental Conditions ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Vapor Flow ◽  
Arid Soils ◽  
Opposite Pattern ◽  
Dry Valley

Ice-free soils in the McMurdo Dry Valleys select for taxa able to cope with challenging environmental conditions, including extreme chemical water activity gradients, freeze-thaw cycling, desiccation, and solar radiation regimes. The low biotic complexity of Dry Valley soils makes them well suited to investigate environmental and spatial influences on bacterial community structure. Water tracks are annually wetted habitats in the cold-arid soils of Antarctica that form briefly each summer with moisture sourced from snow melt, ground ice thaw, and atmospheric deposition via deliquescence and vapor flow into brines. Compared to neighboring arid soils, water tracks are highly saline and relatively moist habitats. They represent a considerable area (∼5–10 km2) of the Dry Valley terrestrial ecosystem, an area that is expected to increase with ongoing climate change. The goal of this study was to determine how variation in the environmental conditions of water tracks influences the composition and diversity of microbial communities. We found significant differences in microbial community composition between on- and off-water track samples, and across two distinct locations. Of the tested environmental variables, soil salinity was the best predictor of community composition, with members of the Bacteroidetes phylum being relatively more abundant at higher salinities and the Actinobacteria phylum showing the opposite pattern. There was also a significant, inverse relationship between salinity and bacterial diversity. Our results suggest water track formation significantly alters dry soil microbial communities, likely influencing subsequent ecosystem functioning. We highlight how Dry Valley water tracks could be a useful model system for understanding the potential habitability of transiently wetted environments found on the surface of Mars.

Soil microbial communities in microaggregates are less affected by top-down effects of collembolans than those in macroaggregates

2021 ◽  
Author(s):  
Amandine Erktan ◽  
MD Ekramul Haque ◽  
Jérôme Cortet ◽  
Paul Henning Krogh ◽  
Stefan Scheu
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Trophic Interactions ◽  
Phospholipid Fatty Acid ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Trophic Levels ◽  
Soil Matrix ◽  
Fungal Abundance

<p>Trophic regulation of microbial communities is receiving growing interest in soil ecology. Most studies investigated the effect of higher trophic levels on microbial communities at the bulk soil level. However, microbes are not equally accessible to consumers. They may be hidden in small pores and thus protected from consumers, suggesting that trophic regulation may depend on the localization of microbes within the soil matrix. As microaggregates (< 250 µm) usually are more stable than macroaggregates (> 250 µm) and embedded in the latter, we posit that they will be less affected by trophic regulations than larger aggregates. We quantified the effect of four contrasting species of collembolans (Ceratophysella denticulata, Protaphorura fimata, Folsomia candida, Sinella curviseta) on the microbial community composition in macro- (250 µm – 2mm) and microaggregates (50 – 250 µm). To do so, we re-built consumer-prey systems comprising remaining microbial background (post-autoclaving), fungal prey (Chaetomium globosum), and collembolan species (added as single species or combined). After three months, we quantified microbial community composition using phospholipid fatty acid markers (PLFAs). We found that the microbial communities in macroaggregates were more affected by the addition of collembolans than the communities in microaggregates. In particular, the fungal-to-bacterial (F:B) ratio significantly decreased in soil macroaggregates in the presence of collembolans. In the microaggregates, the F:B ratio remained lower and unaffected by collembolan inoculation. Presumably, fungal hyphae were more abundant in macroaggregates because they offered more habitat space for them, and the collembolans reduced fungal abundance because they consumed them. On the contrary, microaggregates presumably contained microbial communities protected from consumers. In addition, collembolans increased the formation of macroaggregates but did not influence their stability, despite their negative effect on fungal abundance, a well-known stabilizing agent. Overall, we show that trophic interactions between microbial communities and collembolans depend on the aggregate size class considered and, in return, soil macroaggregation is affected by these trophic interactions.</p>

scholarly journals Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence

2019 ◽  
Vol 85 (7) ◽  
Author(s):  
Alexander Burkert ◽  
Thomas A. Douglas ◽  
Mark P. Waldrop ◽  
Rachel Mackelprang
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Community Composition ◽  
Environmental Conditions ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Subzero Temperatures ◽  
Dormant Cells

ABSTRACTPermafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions, such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods, such as metagenomics and 16S rRNA gene sequencing. However, these methods do not distinguish among active, dead, and dormant cells. This is of particular concern in ancient permafrost, where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this, we applied (i) LIVE/DEAD differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19,000, 27,000, and 33,000 years old). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools, how they are influenced by soil physicochemical properties, and whether they change over geologic time. We found evidence that cells capable of forming endospores are not necessarily dormant and that members of the classBacilliwere more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of theClostridia, which were more likely to persist as vegetative cells in our older samples. We also found that removing exogenous “relic” DNA preserved within permafrost did not significantly alter microbial community composition. These results link the live, dead, and dormant microbial communities to physicochemical characteristics and provide insights into the survival of microbial communities in ancient permafrost.IMPORTANCEPermafrost soils store more than half of Earth’s soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171–179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains.

scholarly journals PSI-10 Establishing a foundation to harvest the potential of the microbiome in poultry production

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 293-294
Author(s):  
Camila S Marcolla ◽  
Benjamin Willing
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Community Composition ◽  
Relative Abundance ◽  
Microbial Community Composition ◽  
Alpha Diversity ◽  
Poultry Production ◽  
Microbiota Composition ◽  
Microbial Composition ◽  
The Impact

Abstract This study aimed to characterize poultry microbiota composition in commercial farms using 16S rRNA sequencing. Animals raised in sanitized environments have lower survival rates when facing pathogenic challenges compared to animals naturally exposed to commensal organisms. We hypothesized that intensive rearing practices inadvertently impair chicken exposure to microbes and the establishment of a balanced gut microbiota. We compared gut microbiota composition of broilers (n = 78) and layers (n = 20) from different systems, including commercial intensive farms with and without in-feed antibiotics, organic free-range farms, backyard-raised chickens and chickens in an experimental farm. Microbial community composition of conventionally raised broilers was significantly different from antibiotic-free broilers (P = 0.012), from broilers raised outdoors (P = 0.048) and in an experimental farm (P = 0.006) (Fig1). Significant community composition differences were observed between antibiotic-fed and antibiotic-free chickens (Fig2). Antibiotic-free chickens presented higher alpha-diversity, higher relative abundance of Deferribacteres, Fusobacteria, Bacteroidetes and Actinobacteria, and lower relative abundance of Firmicutes, Clostridiales and Enterobacteriales than antibiotic-fed chickens (P < 0.001) (Fig3). Microbial community composition significantly changed as birds aged. In experimental farm, microbial community composition was significant different for 7, 21 and 35 day old broilers (P < 0.001), and alpha diversity increased from 7 to 21d (P < 0.024), but not from 21 to 35d; whereas, in organic systems, increases in alpha-diversity were observed from 7d to 21d, and from 21d to 35d (P < 0.05). Broilers and layers raised together showed no differences in microbiota composition and alpha diversity (P > 0.8). It is concluded that production practices consistently impact microbial composition, and that antibiotics significantly reduces microbial diversity. We are now exploring the impact of differential colonization in a controlled setting, to determine the impact of the microbes associated with extensively raised chickens. This study will support future research and the development of methods to isolate and introduce beneficial microbes to commercial systems.

scholarly journals Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Vanessa L. Brisson ◽  
Jennifer E. Schmidt ◽  
Trent R. Northen ◽  
John P. Vogel ◽  
Amélie C. M. Gaudin
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Microbial Community Analysis ◽  
Agricultural System ◽  
Community Members ◽  
Genetic Groups ◽  
Maize Domestication ◽  
Rhizosphere Microbial Community

Abstract Maize domestication and breeding have resulted in drastic and well documented changes in aboveground traits, but belowground effects on root system functioning and rhizosphere microbial communities remain poorly understood, despite their critical importance for nutrient and water acquisition. We investigated the rhizosphere microbial community composition and structure of ten Zea mays accessions along an evolutionary transect (two teosinte, three inbred maize lines, and five modern maize hybrids) grown in nutrient depleted soil from a low input agricultural system. Microbial community analysis revealed significant differences in community composition between soil compartments (proximal vs. distal rhizosphere) and between plant genetic groups (teosinte, inbred, and modern hybrid). Only a small portion of the microbial community was differentially selected across plant genetic groups: 3.7% of prokaryotic community members and 4.9% of fungal community members were significantly associated with a specific plant genetic group. Indicator species analysis showed the greatest differentiation between modern hybrids and the other two plant genetic groups. Co-occurrence network analysis revealed that microbial co-occurrence patterns of the inbred maize lines’ rhizosphere were significantly more similar to those of the teosintes than to the modern hybrids. Our results suggest that advances in hybrid development significantly impacted rhizosphere microbial communities and network assembly.

scholarly journals Effects of Actinomycete Secondary Metabolites on Sediment Microbial Communities

2016 ◽  
Vol 83 (4) ◽  
Author(s):  
Nastassia V. Patin ◽  
Michelle Schorn ◽  
Kristen Aguinaldo ◽  
Tommie Lincecum ◽  
Bradley S. Moore ◽  
...  
Keyword(s):  
Microbial Community ◽  
Secondary Metabolites ◽  
Microbial Communities ◽  
Community Composition ◽  
Marine Sediments ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Next Generation ◽  
Content Type ◽  
Predatory Bacteria

ABSTRACT Marine sediments harbor complex microbial communities that remain poorly studied relative to other biomes such as seawater. Moreover, bacteria in these communities produce antibiotics and other bioactive secondary metabolites, yet little is known about how these compounds affect microbial community structure. In this study, we used next-generation amplicon sequencing to assess native microbial community composition in shallow tropical marine sediments. The results revealed complex communities comprised of largely uncultured taxa, with considerable spatial heterogeneity and known antibiotic producers comprising only a small fraction of the total diversity. Organic extracts from cultured strains of the sediment-dwelling actinomycete genus Salinispora were then used in mesocosm studies to address how secondary metabolites shape sediment community composition. We identified predatory bacteria and other taxa that were consistently reduced in the extract-treated mesocosms, suggesting that they may be the targets of allelopathic interactions. We tested related taxa for extract sensitivity and found general agreement with the culture-independent results. Conversely, several taxa were enriched in the extract-treated mesocosms, suggesting that some bacteria benefited from the interactions. The results provide evidence that bacterial secondary metabolites can have complex and significant effects on sediment microbial communities. IMPORTANCE Ocean sediments represent one of Earth's largest and most poorly studied biomes. These habitats are characterized by complex microbial communities where competition for space and nutrients can be intense. This study addressed the hypothesis that secondary metabolites produced by the sediment-inhabiting actinomycete Salinispora arenicola affect community composition and thus mediate interactions among competing microbes. Next-generation amplicon sequencing of mesocosm experiments revealed complex communities that shifted following exposure to S. arenicola extracts. The results reveal that certain predatory bacteria were consistently less abundant following exposure to extracts, suggesting that microbial metabolites mediate competitive interactions. Other taxa increased in relative abundance, suggesting a benefit from the extracts themselves or the resulting changes in the community. This study takes a first step toward assessing the impacts of bacterial metabolites on sediment microbial communities. The results provide insight into how low-abundance organisms may help structure microbial communities in ocean sediments.

scholarly journals Microbial Communities Show Parallels at Sites with Distinct Litter and Soil Characteristics

2011 ◽  
Vol 77 (21) ◽  
pp. 7560-7567 ◽  
Author(s):  
Marketa Sagova-Mareckova ◽  
Marek Omelka ◽  
Ladislav Cermak ◽  
Zdenek Kamenik ◽  
Jana Olsovska ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Soil Ph ◽  
Soil Chemistry ◽  
High Performance ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Carbon Sources ◽  
Soil Extracts

ABSTRACTPlant and microbial community composition in connection with soil chemistry determines soil nutrient cycling. The study aimed at demonstrating links between plant and microbial communities and soil chemistry occurring among and within four sites: two pine forests with contrasting soil pH and two grasslands of dissimilar soil chemistry and vegetation. Soil was characterized by C and N content, particle size, and profiles of low-molecular-weight compounds determined by high-performance liquid chromatography (HPLC) of soil extracts. Bacterial and actinobacterial community composition was assessed by terminal restriction fragment length polymorphism (T-RFLP) and cloning followed by sequencing. Abundances of bacteria, fungi, and actinobacteria were determined by quantitative PCR. In addition, a pool of secondary metabolites was estimated byermresistance genes coding for rRNA methyltransferases. The sites were characterized by a stable proportion of C/N within each site, while on a larger scale, the grasslands had a significantly lower C/N ratio than the forests. A Spearman's test showed that soil pH was correlated with bacterial community composition not only among sites but also within each site. Bacterial, actinobacterial, and fungal abundances were related to carbon sources while T-RFLP-assessed microbial community composition was correlated with the chemical environment represented by HPLC profiles. Actinobacteria community composition was the only studied microbial characteristic correlated to all measured factors. It was concluded that the microbial communities of our sites were influenced primarily not only by soil abiotic characteristics but also by dominant litter quality, particularly, by percentage of recalcitrant compounds.

scholarly journals Application of Methods for Identifying Broiler Chicken Gut Bacterial Species Linked with Increased Energy Metabolism

2007 ◽  
Vol 74 (3) ◽  
pp. 783-791 ◽  
Author(s):  
Valeria A. Torok ◽  
Kathy Ophel-Keller ◽  
Maylene Loo ◽  
Robert J. Hughes
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Bacterial Species ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Metabolizable Energy ◽  
Principal Coordinates ◽  
Improved Performance ◽  
Gut Microbial Community

ABSTRACT A high-throughput microbial profiling tool based on terminal restriction fragment length polymorphism was developed to monitor the poultry gut microbiota in response to dietary manipulations. Gut microbial communities from the duodena, jejuna, ilea, and ceca of 48 birds fed either a barley control diet or barley diet supplemented with exogenous enzymes for degrading nonstarch polysaccharide were characterized by using multivariate statistical methods. Analysis of samples showed that gut microbial communities varied significantly among gut sections, except between the duodenum and jejunum. Significant diet-associated differences in gut microbial communities were detected within the ileum and cecum only. The dissimilarity in bacterial community composition between diets was 73 and 66% within the ileum and cecum, respectively. Operational taxonomic units, representing bacterial species or taxonomically related groups, contributing to diet-associated differences were identified. Several bacterial species contributed to differences between diet-related gut microbial community composition, with no individual bacterial species contributing more than 1 to 5% of the total. Using canonical analysis of principal coordinates biplots, we correlated differences in gut microbial community composition within the ileum and cecum to improved performance, as measured by apparent metabolizable energy. This is the first report that directly links differences in the composition of the gut microbial community with improved performance, which implies that the presence of specific beneficial and/or absence of specific detrimental bacterial species may contribute to the improved performance in these birds.

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