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 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 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.

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

scholarly journals Mapping metabolic activity at single cell resolution in intact volcanic fumarole sediment

2020 ◽  
Vol 367 (1) ◽  
Author(s):  
Jeffrey J Marlow ◽  
Isabella Colocci ◽  
Sean P Jungbluth ◽  
Nils Moritz Weber ◽  
Amy Gartman ◽  
...  
Keyword(s):  
Structure Function ◽  
Microbial Communities ◽  
Metabolic Activity ◽  
Point Sources ◽  
Emergent Properties ◽  
Spatial Relationships ◽  
Environmental Regime ◽  
Novel Approach ◽  
Stable Conditions ◽  
Metabolite Exchange

ABSTRACT Interactions among microorganisms and their mineralogical substrates govern the structure, function and emergent properties of microbial communities. These interactions are predicated on spatial relationships, which dictate metabolite exchange and access to key substrates. To quantitatively assess links between spatial relationships and metabolic activity, this study presents a novel approach to map all organisms, the metabolically active subset and associated mineral grains, all while maintaining spatial integrity of an environmental microbiome. We applied this method at an outgassing fumarole of Vanuatu's Marum Crater, one of the largest point sources of several environmentally relevant gaseous compounds, including H2O, CO2 and SO2. With increasing distance from the sediment-air surface and from mineral grain outer boundaries, organism abundance decreased but the proportion of metabolically active organisms often increased. These protected niches may provide more stable conditions that promote consistent metabolic activity of a streamlined community. Conversely, exterior surfaces accumulate more organisms that may cover a wider range of preferred conditions, implying that only a subset of the community will be active under any particular environmental regime. More broadly, the approach presented here allows investigators to see microbial communities ‘as they really are’ and explore determinants of metabolic activity across a range of microbiomes.

scholarly journals Spatial heterogeneity of the shorebird gastrointestinal microbiome

2020 ◽  
Vol 7 (1) ◽  
pp. 191609
Author(s):  
Kirsten Grond ◽  
Hannah Guilani ◽  
Sarah M. Hird
Keyword(s):  
Microbial Communities ◽  
Large Intestine ◽  
Alpha Diversity ◽  
Source Tracking ◽  
Similar Species ◽  
Gastrointestinal Microbiome ◽  
Semipalmated Sandpiper ◽  
Microbial Ecosystems ◽  
Genus Richness ◽  
Intestine Microbiome

The gastrointestinal tract (GIT) consists of connected structures that vary in function and physiology, and different GIT sections potentially provide different habitats for microorganisms. Birds possess unique GIT structures, including the oesophagus, proventriculus, gizzard, small intestine, caeca and large intestine. To understand birds as hosts of microbial ecosystems, we characterized the microbial communities in six sections of the GIT of two shorebird species, the Dunlin and Semipalmated Sandpiper, identified potential host species effects on the GIT microbiome and used microbial source tracking to determine microbial origin throughout the GIT. The upper three GIT sections had higher alpha diversity and genus richness compared to the lower sections, and microbial communities in the upper GIT showed no clustering. The proventriculus and gizzard microbiomes primarily originated from upstream sections, while the majority of the large intestine microbiome originated from the caeca. The heterogeneity of the GIT sections shown in our study urges caution in equating data from faeces or a single GIT component to the entire GIT microbiome but confirms that ecologically similar species may share many attributes in GIT microbiomes.

scholarly journals Disruption of cross-feeding interactions by invading taxa can cause invasional meltdown in microbial communities

2020 ◽  
Vol 287 (1927) ◽  
pp. 20192945 ◽  
Author(s):  
Cristina M. Herren
Keyword(s):  
Microbial Communities ◽  
Biotic Interactions ◽  
Invasion Risk ◽  
Invasional Meltdown ◽  
Native Community ◽  
Exchange Networks ◽  
Composition And Structure ◽  
Metabolite Exchange ◽  
Successful Invader ◽  
The Impact

The strength of biotic interactions within an ecological community affects the susceptibility of the community to invasion by introduced taxa. In microbial communities, cross-feeding is a widespread type of biotic interaction that has the potential to affect community assembly and stability. Yet, there is little understanding of how the presence of cross-feeding within a community affects invasion risk. Here, I develop a metabolite-explicit model where native microbial taxa interact through both cross-feeding and competition for metabolites. I use this model to study how the strength of biotic interactions, especially cross-feeding, influence whether an introduced taxon can join the community. I found that stronger cross-feeding and competition led to much lower invasion risk, as both types of biotic interactions lead to greater metabolite scarcity for the invader. I also evaluated the impact of a successful invader on community composition and structure. The effect of invaders on the native community was greatest at intermediate levels of cross-feeding; at this ‘critical’ level of cross-feeding, successful invaders generally cause decreased diversity, decreased productivity, greater metabolite availability, and decreased quantities of metabolites exchanged among taxa. Furthermore, these changes resulting from a successful primary invader made communities further susceptible to future invaders. The increase in invasion risk was greatest when the network of metabolite exchange between taxa was minimally redundant. Thus, this model demonstrates a case of invasional meltdown that is mediated by initial invaders disrupting the metabolite exchange networks of the native community.

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 Communities that thrive in extreme conditions captured from a freshwater lake

2016 ◽  
Vol 12 (9) ◽  
pp. 20160562 ◽  
Author(s):  
Etienne Low-Décarie ◽  
Gregor F. Fussmann ◽  
Alex J. Dumbrell ◽  
Graham Bell
Keyword(s):  
Microbial Communities ◽  
Extreme Environments ◽  
Freshwater Lake ◽  
Extreme Conditions ◽  
Acidic Ph ◽  
Algae And Bacteria ◽  
Functional Attribute

Organisms that can grow in extreme conditions would be expected to be confined to extreme environments. However, we were able to capture highly productive communities of algae and bacteria capable of growing in acidic (pH 2), basic (pH 12) and saline (40 ppt) conditions from an ordinary freshwater lake. Microbial communities may thus include taxa that are highly productive in conditions that are far outside the range of conditions experienced in their host ecosystem. The organisms we captured were not obligate extremophiles, but were capable of growing in both extreme and benign conditions. The ability to grow in extreme conditions may thus be a common functional attribute in microbial communities.

scholarly journals Microbial Potlatch: Cell-level adaptation of leakiness of metabolites leads to resilient symbiosis among diverse cells

2020 ◽  
Author(s):  
Jumpei F Yamagishi ◽  
Nen Saito ◽  
Kunihiko Kaneko
Keyword(s):  
Growth Rate ◽  
Microbial Communities ◽  
Cell Level ◽  
Frequency Dependent ◽  
Symbiotic Relationships ◽  
Microbial Species ◽  
Nutrient Limitations ◽  
Environmental Perturbations ◽  
Microbial Ecosystems ◽  
Diverse Species

AbstractMicrobial communities display extreme diversity, facilitated by the secretion of chemicals that can create new niches. However, it is unclear why cells often secrete even essential metabolites after evolution. By noting that cells can enhance their own growth rate by leakage of essential metabolites, we show that such leaker cells can benefit from coexistence with cells that consume the leaked chemicals in the environment. This leads to an unusual form of mutualism between “leaker” and “consumer” cells, resulting in frequency-dependent coexistence of multiple microbial species, as supported by extensive simulations. Remarkably, such symbiotic relationships generally evolve when each species adapts its leakiness to optimize its own growth rate under crowded conditions and nutrient limitations, leading to ecosystems with diverse species exchanging many metabolites with each other. In addition, such ecosystems are resilient against structural and environmental perturbations. Thus, we present a new basis for diverse, complex microbial ecosystems.

scholarly journals A conceptual framework for the phylogenetically constrained assembly of microbial communities

Microbiome ◽  
2019 ◽  
Vol 7 (1) ◽  
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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