scholarly journals Closed microbial communities self-organize to persistently cycle carbon

2021 ◽  
Vol 118 (45) ◽  
pp. e2013564118
Author(s):  
Luis Miguel de Jesús Astacioa ◽  
Kaumudi H. Prabhakara ◽  
Zeqian Li ◽  
Harry Mickalide ◽  
Seppe Kuehn
Keyword(s):  
Microbial Communities ◽  
Carbon Cycling ◽  
Critical Role ◽  
Microbial Consortia ◽  
Ecosystem Structure ◽  
Bacterial Consortia ◽  
Self Organized ◽  
Microbial Ecosystems ◽  
Emergent Feature ◽  
Ecosystem Organization

Cycles of nutrients (N, P, etc.) and resources (C) are a defining emergent feature of ecosystems. Cycling plays a critical role in determining ecosystem structure at all scales, from microbial communities to the entire biosphere. Stable cycles are essential for ecosystem persistence because they allow resources and nutrients to be regenerated. Therefore, a central problem in ecology is understanding how ecosystems are organized to sustain robust cycles. Addressing this problem quantitatively has proved challenging because of the difficulties associated with manipulating ecosystem structure while measuring cycling. We address this problem using closed microbial ecosystems (CES), hermetically sealed microbial consortia provided with only light. We develop a technique for quantifying carbon cycling in hermetically sealed microbial communities and show that CES composed of an alga and diverse bacterial consortia self-organize to robustly cycle carbon for months. Comparing replicates of diverse CES, we find that carbon cycling does not depend strongly on the taxonomy of the bacteria present. Moreover, despite strong taxonomic differences, self-organized CES exhibit a conserved set of metabolic capabilities. Therefore, an emergent carbon cycle enforces metabolic but not taxonomic constraints on ecosystem organization. Our study helps establish closed microbial communities as model ecosystems to study emergent function and persistence in replicate systems while controlling community composition and the environment.

scholarly journals Facility-Specific “House” Microbiome Drives Microbial Landscapes of Artisan Cheesemaking Plants

2013 ◽  
Vol 79 (17) ◽  
pp. 5214-5223 ◽  
Author(s):  
Nicholas A. Bokulich ◽  
David A. Mills
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Microbial Consortia ◽  
True Nature ◽  
Specific Product ◽  
Site Specific ◽  
Content Type ◽  
Microbial Ecosystems ◽  
Spatial Diversification ◽  
Regional Product

ABSTRACTCheese fermentations involve the growth of complex microbial consortia, which often originate in the processing environment and drive the development of regional product qualities. However, the microbial milieus of cheesemaking facilities are largely unexplored and the true nature of the fermentation-facility relationship remains nebulous. Thus, a high-throughput sequencing approach was employed to investigate the microbial ecosystems of two artisanal cheesemaking plants, with the goal of elucidating how the processing environment influences microbial community assemblages. Results demonstrate that fermentation-associated microbes dominated most surfaces, primarilyDebaryomycesandLactococcus, indicating that establishment of these organisms on processing surfaces may play an important role in microbial transfer, beneficially directing the course of sequential fermentations. Environmental organisms detected in processing environments dominated the surface microbiota of washed-rind cheeses maturing in both facilities, demonstrating the importance of the processing environment for populating cheese microbial communities, even in inoculated cheeses. Spatial diversification within both facilities reflects the functional adaptations of microbial communities inhabiting different surfaces and the existence of facility-specific “house” microbiota, which may play a role in shaping site-specific product characteristics.

scholarly journals The Persistence Potential of Mobile Genetic Elements

2020 ◽  
Author(s):  
Teng Wang ◽  
Lingchong You
Keyword(s):  
Gene Flow ◽  
Microbial Communities ◽  
Quantitative Data ◽  
Critical Role ◽  
Mobile Genetic Elements ◽  
Microbial Consortia ◽  
Modeling Framework ◽  
Combinatorial Explosion ◽  
Genetic Elements ◽  
Quantitative Understanding

AbstractMobile genetic elements (MGEs), such as plasmids, phages, and transposons, play a critical role in mediating the transfer and maintenance of diverse traits and functions in microbial communities. This role depends on the ability of MGEs to persist. For a community consisting of multiple populations transferring multiple MGEs, however, the conditions underlying the persistence of these MGEs are poorly understood. Computationally, this difficulty arises from the combinatorial explosion associated with describing the gene flow in a complex community using the conventional modeling framework. Here, we describe an MGE-centric framework that makes it computationally feasible to analyze such transfer dynamics. Using this framework, we derive the persistence potential: a general, heuristic metric that predicts the persistence and abundance of any MGEs. We validate the metric with engineered microbial consortia transferring mobilizable plasmids and quantitative data available in the literature. Our modeling framework and the resulting metric have implications for developing a quantitative understanding of natural microbial communities and guiding the engineering of microbial consortia.

scholarly journals Closed microbial communities self-organize to persistently cycle carbon

2020 ◽  
Author(s):  
Luis Miguel de Jesús Astacio ◽  
Kaumudi H. Prabhakara ◽  
Zeqian Li ◽  
Harry Mickalide ◽  
Seppe Kuehn
Keyword(s):  
Microbial Communities ◽  
Metabolic Profiling ◽  
Emergent Property ◽  
Nutrient Cycles ◽  
Challenging Problem ◽  
Self Organized ◽  
Microbial Ecosystems ◽  
Metabolite Exchange ◽  
Algae And Bacteria ◽  
A New Technique

Nutrient cycling is an emergent property of ecosystems at all scales, from microbial communities to the entire biosphere. Understanding how nutrient cycles emerge from the collective metabolism of ecosystems is a challenging problem. Here we use closed microbial ecosystems (CES), hermetically sealed consortia that sustain nutrient cycles when provided with only light, to learn how microbial communities cycle carbon. A new technique for quantifying carbon exchange shows that CES comprised of an alga and diverse bacteria self-organize to robustly cycle carbon. Comparing a library of CES, we find that carbon cycling does not depend strongly on the taxonomy of the bacteria present. Metabolic profiling reveals functional redundancy across CES: despite strong taxonomic differences, self-organized CES exhibit a conserved set of metabolic capabilities.SummaryClosed microbial communities of algae and bacteria self-organize to robustly cycle carbon via emergent metabolite exchange.

scholarly journals Compost-Induced Suppression of Pythium Damping-Off Is Mediated by Fatty-Acid-Metabolizing Seed-Colonizing Microbial Communities

2003 ◽  
Vol 69 (1) ◽  
pp. 452-460 ◽  
Author(s):  
Mary E. McKellar ◽  
Eric B. Nelson
Keyword(s):  
Fatty Acid ◽  
Linoleic Acid ◽  
Microbial Communities ◽  
Pythium Ultimum ◽  
Disease Suppression ◽  
Microbial Consortia ◽  
Damping Off ◽  
Bacterial Consortia ◽  
Seed Colonization

ABSTRACT Leaf composts were studied for their suppressive effects on Pythium ultimum sporangium germination, cottonseed colonization, and the severity of Pythium damping-off of cotton. A focus of the work was to assess the role of fatty-acid-metabolizing microbial communities in disease suppression. Suppressiveness was expressed within the first few hours of seed germination as revealed by reduced P. ultimum sporangium germination, reduced seed colonization, and reduced damping-off in transplant experiments. These reductions were not observed when cottonseeds were sown in a conducive leaf compost. Microbial consortia recovered from the surface of cottonseeds during the first few hours of germination in suppressive compost (suppressive consortia) induced significant levels of damping-off suppression, whereas no suppression was induced by microbial consortia recovered from cottonseeds germinated in conducive compost (conducive consortia). Suppressive consortia rapidly metabolized linoleic acid, whereas conducive consortia did not. Furthermore, populations of fatty-acid-metabolizing bacteria and actinobacteria were higher in suppressive consortia than in conducive consortia. Individual bacterial isolates varied in their ability to metabolize linoleic acid and protect seedlings from damping-off. Results indicate that communities of compost-inhabiting microorganisms colonizing cottonseeds within the first few hours after sowing in a Pythium-suppressive compost play a major role in the suppression of P. ultimum sporangium germination, seed colonization, and damping-off. Results further indicate that fatty acid metabolism by these seed-colonizing bacterial consortia can explain the Pythium suppression observed.

scholarly journals Allelochemicals Produced by Brown Macroalgae of the Lobophora Genus Are Active against Coral Larvae and Associated Bacteria, Supporting Pathogenic Shifts to Vibrio Dominance

2016 ◽  
Vol 83 (1) ◽  
Author(s):  
Kathleen M. Morrow ◽  
Katrina Bromhall ◽  
Cherie A. Motti ◽  
Colin B. Munn ◽  
David G. Bourne
Keyword(s):  
Microbial Communities ◽  
Larval Settlement ◽  
Critical Role ◽  
Significant Shift ◽  
Ecosystem Structure ◽  
Competitive Balance ◽  
Coral Larvae ◽  
Associated Bacteria ◽  
Content Type ◽  
Coral Holobiont

ABSTRACT Pervasive environmental stressors on coral reefs are attributed with shifting the competitive balance in favor of alternative dominants, such as macroalgae. Previous studies have demonstrated that macroalgae compete with corals via a number of mechanisms, including the production of potent primary and secondary metabolites that can influence coral-associated microbial communities. The present study investigates the effects of the Pacific brown macroalga Lobophora sp. (due to the shifting nature of the Lobophora species complex, it will be referred to here as Lobophora sp.) on coral bacterial isolates, coral larvae, and the microbiome associated with the coral Porites cylindrica. Crude aqueous and organic macroalgal extracts were found to inhibit the growth of coral-associated bacteria. Extracts and fractions were also shown to inhibit coral larval settlement and cause mortality at concentrations lower (<0.3 mg · ml−1) than calculated natural concentrations (4.4 mg · ml−1). Microbial communities associated with coral tissues exposed to aqueous (e.g., hydrophilic) crude extracts demonstrated a significant shift to Vibrio dominance and a loss of sequences related to the putative coral bacterial symbiont, Endozoicomonas sp., based on 16S rRNA amplicon sequencing. This study contributes to growing evidence that macroalgal allelochemicals, dissolved organic material, and native macroalgal microbial assemblages all play a role in shifting the microbial equilibrium of the coral holobiont away from a beneficial state, contributing to a decline in coral fitness and a shift in ecosystem structure. IMPORTANCE Diverse microbial communities associate with coral tissues and mucus, providing important protective and nutritional services, but once disturbed, the microbial equilibrium may shift from a beneficial state to one that is detrimental or pathogenic. Macroalgae (e.g., seaweeds) can physically and chemically interact with corals, causing abrasion, bleaching, and overall stress. This study contributes to a growing body of evidence suggesting that macroalgae play a critical role in shifting the coral holobiont equilibrium, which may promote the invasion of opportunistic pathogens and cause coral mortality, facilitating additional macroalgal growth and invasion in the reef. Thus, macroalgae not only contribute to a decline in coral fitness but also influence coral reef ecosystem structure.

scholarly journals CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial Ecosystems

2021 ◽  
Vol 9 (4) ◽  
pp. 816
Author(s):  
Matthew G. Links ◽  
Tim J. Dumonceaux ◽  
E. Luke McCarthy ◽  
Sean M. Hemmingsen ◽  
Edward Topp ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Dna Sequences ◽  
Pcr Amplification ◽  
Shotgun Sequencing ◽  
Natural Ecosystems ◽  
Gene Markers ◽  
Microbial Profile ◽  
Microbial Ecosystems ◽  
Pcr Targeting

Background. The molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with “universal” PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. Methods. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. Results. The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health. Conclusions: cpn60-based hybridization enriched for taxonomically informative DNA sequences from complex mixtures. In synthetic and natural microbial ecosystems, CaptureSeq provided sequences from prokaryotes and eukaryotes simultaneously, with quantitatively reliable read abundances. CaptureSeq provides an alternative to PCR amplification of taxonomic markers with deep community coverage while minimizing amplification biases.

Invasive plant-derived dissolved organic matter alters microbial communities and carbon cycling in soils

2021 ◽  
pp. 108191
Author(s):  
Morgan Luce McLeod ◽  
Lorinda Bullington ◽  
Cory C. Cleveland ◽  
Johannes Rousk ◽  
Ylva Lekberg
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Microbial Communities ◽  
Carbon Cycling ◽  
Invasive Plant

scholarly journals Insights into Bacterial Community Involved in Bioremediation of Aged Oil-Contaminated Soil in Arid Environment

2021 ◽  
Vol 17 ◽  
pp. 117693432110168
Author(s):  
Rita Rahmeh ◽  
Abrar Akbar ◽  
Vinod Kumar ◽  
Hamad Al-Mansour ◽  
Mohamed Kishk ◽  
...  
Keyword(s):  
Oil Spills ◽  
Critical Role ◽  
Arid Environment ◽  
Total Petroleum Hydrocarbons ◽  
Microbial Consortia ◽  
Soil Microbial ◽  
Taxonomic Profiling ◽  
Degradation Pattern ◽  
Polycyclic Aromatic ◽  
Global Concern

Soil contamination by hydrocarbons due to oil spills has become a global concern and it has more implications in oil producing regions. Biostimulation is considered as one of the promising remediation techniques that can be adopted to enhance the rate of degradation of crude oil. The soil microbial consortia play a critical role in governing the biodegradation of total petroleum hydrocarbons (TPHs), in particular polycyclic aromatic hydrocarbons (PAHs). In this study, the degradation pattern of TPHs and PAHs of Kuwait soil biopiles was measured at three-month intervals. Then, the microbial consortium associated with oil degradation at each interval was revealed through 16S rRNA based next generation sequencing. Rapid degradation of TPHs and most of the PAHs was noticed at the first 3 months of biostimulation with a degradation rate of pyrene significantly higher compared to other PAHs counterparts. The taxonomic profiling of individual stages of remediation revealed that, biostimulation of the investigated soil favored the growth of Proteobacteria, Alphaprotobacteria, Chloroflexi, Chlorobi, and Acidobacteria groups. These findings provide a key step towards the restoration of oil-contaminated lands in the arid environment.

Effects of Community Versus Single Strain Inoculants on the Biocontrol of Salmonella and Microbial Community Dynamics in Alfalfa Sprouts†

2005 ◽  
Vol 68 (1) ◽  
pp. 40-48 ◽  
Author(s):  
ANABELLE MATOS ◽  
JAY L. GARLAND
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Dynamics ◽  
Community Level ◽  
Microbial Consortia ◽  
Single Strain ◽  
Acridine Orange Staining ◽  
Physiological Profiles ◽  
Alfalfa Sprouts ◽  
Alfalfa Seeds

Potential biological control inoculants, Pseudomonas fluorescens 2-79 and microbial communities derived from market sprouts or laboratory-grown alfalfa sprouts, were introduced into alfalfa seeds with and without a Salmonella inoculum. We examined their ability to inhibit the growth of this foodborne pathogen and assess the relative effects of the inoculants on the alfalfa microbial community structure and function. Alfalfa seeds contaminated with a Salmonella cocktail were soaked for 2 h in bacterial suspensions from each inoculant tested. Inoculated alfalfa seeds were grown for 7 days and sampled during days 1, 3, and 7. At each sampling, alfalfa sprouts were sonicated for 7 min to recover microflora from the surface, and the resulting suspensions were diluted and plated on selective and nonselective media. Total bacterial counts were obtained using acridine orange staining, and the percentage culturability was calculated. Phenotypic potential of sprout-associated microbial communities inoculated with biocontrol treatments was assessed using community-level physiological profiles based on patterns of use of 95 separate carbon sources in Biolog plates. Community-level physiological profiles were also determined using oxygen-sensitive fluorophore in BD microtiter plates to examine functional patterns in these communities. No significant differences in total and mesophilic aerobe microbial cell density or microbial richness resulting from the introduction of inoculants on alfalfa seeds with and without Salmonella were observed. P. fluorescens 2-79 exhibited the greatest reduction in the growth of Salmonella early during alfalfa growth (4.22 log at day 1), while the market sprout inoculum had the reverse effect, resulting in a maximum log reduction (5.48) of Salmonella on day 7. Community-level physiological profiles analyses revealed that market sprout communities peaked higher and faster compared with the other inoculants tested. These results suggest that different modes of actions of single versus microbial consortia biocontrol treatments may be involved.

scholarly journals Synthetic microbial ecosystems: an exciting tool to understand and apply microbial communities

2013 ◽  
Vol 16 (6) ◽  
pp. 1472-1481 ◽  
Author(s):  
Karen De Roy ◽  
Massimo Marzorati ◽  
Pieter Van den Abbeele ◽  
Tom Van de Wiele ◽  
Nico Boon
Keyword(s):  
Microbial Communities ◽  
Microbial Ecosystems
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