scholarly journals Thermodynamic constraints on the assembly and diversity of microbial ecosystems are different near to and far from equilibrium

2021 ◽  
Vol 17 (12) ◽  
pp. e1009643
Author(s):  
Jacob Cook ◽  
Samraat Pawar ◽  
Robert G. Endres
Keyword(s):  
Free Energy ◽  
Microbial Communities ◽  
Community Dynamics ◽  
Time Frame ◽  
Community Diversity ◽  
Ecosystem Level ◽  
Energy Consuming ◽  
Interaction Types ◽  
Mechanistic Basis ◽  
Underlying Mechanisms

Non-equilibrium thermodynamics has long been an area of substantial interest to ecologists because most fundamental biological processes, such as protein synthesis and respiration, are inherently energy-consuming. However, most of this interest has focused on developing coarse ecosystem-level maximisation principles, providing little insight into underlying mechanisms that lead to such emergent constraints. Microbial communities are a natural system to decipher this mechanistic basis because their interactions in the form of substrate consumption, metabolite production, and cross-feeding can be described explicitly in thermodynamic terms. Previous work has considered how thermodynamic constraints impact competition between pairs of species, but restrained from analysing how this manifests in complex dynamical systems. To address this gap, we develop a thermodynamic microbial community model with fully reversible reaction kinetics, which allows direct consideration of free-energy dissipation. This also allows species to interact via products rather than just substrates, increasing the dynamical complexity, and allowing a more nuanced classification of interaction types to emerge. Using this model, we find that community diversity increases with substrate lability, because greater free-energy availability allows for faster generation of niches. Thus, more niches are generated in the time frame of community establishment, leading to higher final species diversity. We also find that allowing species to make use of near-to-equilibrium reactions increases diversity in a low free-energy regime. In such a regime, two new thermodynamic interaction types that we identify here reach comparable strengths to the conventional (competition and facilitation) types, emphasising the key role that thermodynamics plays in community dynamics. Our results suggest that accounting for realistic thermodynamic constraints is vital for understanding the dynamics of real-world microbial communities.

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 Temporally selective modification of the tomato rhizosphere and root microbiome by a dacitic tuff breccia (volcanic ash) containing minerals and trace elements.

2021 ◽  
Author(s):  
Elijah C. Mehlferber ◽  
Kent F. McCue ◽  
Jon E. Ferrel ◽  
Britt Koskella ◽  
Rajnish Khanna
Keyword(s):  
Microbial Communities ◽  
Volcanic Ash ◽  
Crop Productivity ◽  
Growth Stress ◽  
Microbial Composition ◽  
Nutrient Environment ◽  
Ash Deposit ◽  
Phosphorus And Potassium ◽  
Underlying Mechanisms ◽  
Functional Pathway

Abstract Food crops are grown with fertilizers containing nitrogen, phosphorus, and potassium (macronutrients), along with magnesium, calcium, boron, and zinc (micronutrients) at different ratios during their cultivation. Soil and plant associated microbes have been implicated to promote plant growth, stress tolerance, and productivity. However, the high degree of variability across agricultural environments makes it difficult to assess the possible influences of nutrient fertilizers on these microbial communities. Uncovering the underlying mechanisms could lead us to achieving consistently improved food quality and productivity with minimal environmental impacts. For this purpose, we tested a commercially available fertilizer (surface-mined 38-million-year-old volcanic ash deposit AZOMITE®), applied as a supplement to the normal fertilizer program to tomato plants grown in the greenhouse. We examined its impact on the composition of below-ground microbial communities, focusing on those members we identified as "core taxa" that were enriched in the rhizosphere and root endosphere compared to bulk soil, and appeared above their predicted neutral distribution levels in control and treated samples. This analysis revealed that Azomite had little effect on soil or rhizosphere microbial composition overall, but it had a significant, temporally selective influence on the rhizosphere and root associated core taxa. Changes in the composition of the core taxa were correlated to associated functional pathway enrichment of carbohydrate metabolism over shorter chain carbon metabolism, suggesting a conversion of available microbial nutrient source within the roots. This finding exemplifies how the nutrient environment can specifically alter the functional capacity of root-associated bacterial taxa, with potential to improve crop productivity.

scholarly journals Less Is More: Genome Reduction and the Emergence of Cooperation—Implications into the Coevolution of Microbial Communities

2019 ◽  
Vol 2019 ◽  
pp. 1-5 ◽  
Author(s):  
Emanuele Bosi ◽  
Flavia Mascagni
Keyword(s):  
Microbial Communities ◽  
Community Dynamics ◽  
Evolutionary Ecology ◽  
Genome Reduction ◽  
Biological Functions ◽  
Evolutionary Mechanisms ◽  
Less Is More ◽  
Ecological Patterns ◽  
Emergence Of Cooperation ◽  
Antagonistic Interactions

Organisms change to adapt to the environment in which they live, evolving with coresiding individuals. Classic Darwinism postulates the primal importance of antagonistic interactions and selfishness as a major driver of evolution, promoting an increase of genomic and organism complexities. Recently, advancements in evolutionary ecology reshaped this notion, showing how leakiness in biological functions favours the adaptive genome reduction, leading to the emergence of codependence patterns. Microbial communities are complex entities exerting a gargantuan influence on the environment and the biology of the eukaryotic hosts they are associated with. Notwithstanding, we are still far from a comprehension of the ecological and evolutionary mechanisms governing the community dynamics. Here, we review the implications of genome streamlining into the unfolding of codependence within microbial communities and how this translates to an understanding of ecological patterns underlying the emerging properties of the community.

scholarly journals Visualizing Microbial Community Dynamics via a Controllable Soil Environment

mSystems ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Arunima Bhattacharjee ◽  
Dusan Velickovic ◽  
Thomas W. Wietsma ◽  
Sheryl L. Bell ◽  
Janet K. Jansson ◽  
...  
Keyword(s):  
Soil Moisture ◽  
Microbial Community ◽  
Microbial Communities ◽  
Community Dynamics ◽  
Soil Microbial Communities ◽  
Soil Microbiome ◽  
Soil Core ◽  
Soil Microbial ◽  
Functional Relationships ◽  
Microbial Community Dynamics

ABSTRACT Understanding the basic biology that underpins soil microbiome interactions is required to predict the metaphenomic response to environmental shifts. A significant knowledge gap remains in how such changes affect microbial community dynamics and their metabolic landscape at microbially relevant spatial scales. Using a custom-built SoilBox system, here we demonstrated changes in microbial community growth and composition in different soil environments (14%, 24%, and 34% soil moisture), contingent upon access to reservoirs of nutrient sources. The SoilBox emulates the probing depth of a common soil core and enables determination of both the spatial organization of the microbial communities and their metabolites, as shown by confocal microscopy in combination with mass spectrometry imaging (MSI). Using chitin as a nutrient source, we used the SoilBox system to observe increased adhesion of microbial biomass on chitin islands resulting in degradation of chitin into N-acetylglucosamine (NAG) and chitobiose. With matrix-assisted laser desorption/ionization (MALDI)-MSI, we also observed several phospholipid families that are functional biomarkers for microbial growth on the chitin islands. Fungal hyphal networks bridging different chitin islands over distances of 27 mm were observed only in the 14% soil moisture regime, indicating that such bridges may act as nutrient highways under drought conditions. In total, these results illustrate a system that can provide unprecedented spatial information about interactions within soil microbial communities as a function of changing environments. We anticipate that this platform will be invaluable in spatially probing specific intra- and interkingdom functional relationships of microbiomes within soil. IMPORTANCE Microbial communities are key components of the soil ecosystem. Recent advances in metagenomics and other omics capabilities have expanded our ability to characterize the composition and function of the soil microbiome. However, characterizing the spatial metabolic and morphological diversity of microbial communities remains a challenge due to the dynamic and complex nature of soil microenvironments. The SoilBox system, demonstrated in this work, simulates an ∼12-cm soil depth, similar to a typical soil core, and provides a platform that facilitates imaging the molecular and topographical landscape of soil microbial communities as a function of environmental gradients. Moreover, the nondestructive harvesting of soil microbial communities for the imaging experiments can enable simultaneous multiomics analysis throughout the depth of the SoilBox. Our results show that by correlating molecular and optical imaging data obtained using the SoilBox platform, deeper insights into the nature of specific soil microbial interactions can be achieved.

scholarly journals Extreme climatic event drives range contraction of a habitat-forming species

2013 ◽  
Vol 280 (1754) ◽  
pp. 20122829 ◽  
Author(s):  
Dan A. Smale ◽  
Thomas Wernberg
Keyword(s):  
Structural Changes ◽  
Species Distributions ◽  
Ecological Change ◽  
Ecosystem Structure ◽  
Discrete Events ◽  
Marginal Populations ◽  
Range Contraction ◽  
Range Edge ◽  
Ecosystem Level ◽  
Underlying Mechanisms

Species distributions have shifted in response to global warming in all major ecosystems on the Earth. Despite cogent evidence for these changes, the underlying mechanisms are poorly understood and currently imply gradual shifts. Yet there is an increasing appreciation of the role of discrete events in driving ecological change. We show how a marine heat wave (HW) eliminated a prominent habitat-forming seaweed, Scytothalia dorycarpa , at its warm distribution limit, causing a range contraction of approximately 100 km (approx. 5% of its global distribution). Seawater temperatures during the HW exceeded the seaweed's physiological threshold and caused extirpation of marginal populations, which are unlikely to recover owing to life-history traits and oceanographic processes. Scytothalia dorycarpa is an important canopy-forming seaweed in temperate Australia, and loss of the species at its range edge has caused structural changes at the community level and is likely to have ecosystem-level implications. We show that extreme warming events, which are increasing in magnitude and frequency, can force step-wise changes in species distributions in marine ecosystems. As such, return times of these events have major implications for projections of species distributions and ecosystem structure, which have typically been based on gradual warming trends.

Interactions between zebra mussels (Dreissena polymorpha) and microbial communities

2000 ◽  
Vol 57 (3) ◽  
pp. 591-599 ◽  
Author(s):  
Marc E Frischer ◽  
Sandra A Nierzwicki-Bauer ◽  
Robert H Parsons ◽  
Kanda Vathanodorn ◽  
Kelli R Waitkus
Keyword(s):  
Microbial Communities ◽  
Zebra Mussel ◽  
Dreissena Polymorpha ◽  
Hudson River ◽  
Zebra Mussels ◽  
Community Diversity ◽  
Ecological Effect ◽  
Clearance Rates ◽  
Surrounding Water ◽  
The Impact

Zebra mussels (Dreissena polymorpha) have had an enormous impact on aquatic environments. However, little is known concerning their interactions with microbial communities. In these studies, the ability of zebra mussels to derive nutrition from bacterioplankton and their effect on microbial community diversity were investigated in samples from the Hudson River, New York, and in laboratory studies. Clear physiological responses to starvation were observed, including decreases in respiration rates, lipid content, and total weight, that were reversed after feeding zebra mussels a diet of bacteria. Clearance rates of bacteria were correlated with bacteria size (r2= 0.995), with the lowest clearance rates associated with small indigenous river bacteria (size = 0.03 ± 0.04 µm3, clearance rate = 0.08 ± 0.02 mL·mussel-1·min-1). Comparison of the diversity of microbial communities in zebra mussel tissue extract, detritus, and pseudofecal material associated with zebra mussel colonies, surrounding water, and sediment samples revealed distinct microbial assemblages associated with these environments. The overall ecological effect and importance of bacteria - zebra mussel interactions remains unclear, but these studies indicate that these interactions occur and should be included in our efforts to better understand the impact of zebra mussels on aquatic systems.

scholarly journals System Biology Modeling with Compositional Microbiome Data Reveals Personalized Gut Microbial Dynamics and Keystone Species

2018 ◽  
Author(s):  
Chenhao Li ◽  
Lisa Tucker-Kellogg ◽  
Niranjan Nagarajan
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Community Dynamics ◽  
Keystone Species ◽  
Microbial Interactions ◽  
Natural Environments ◽  
Sequencing Data ◽  
Predator Prey ◽  
Public Datasets ◽  
Microbiome Data

AbstractA growing body of literature points to the important roles that different microbial communities play in diverse natural environments and the human body. The dynamics of these communities is driven by a range of microbial interactions from symbiosis to predator-prey relationships, the majority of which are poorly understood, making it hard to predict the response of the community to different perturbations. With the increasing availability of high-throughput sequencing based community composition data, it is now conceivable to directly learn models that explicitly define microbial interactions and explain community dynamics. The applicability of these approaches is however affected by several experimental limitations, particularly the compositional nature of sequencing data. We present a new computational approach (BEEM) that addresses this key limitation in the inference of generalised Lotka-Volterra models (gLVMs) by coupling biomass estimation and model inference in an expectation maximization like algorithm (BEEM). Surprisingly, BEEM outperforms state-of-the-art methods for inferring gLVMs, while simultaneously eliminating the need for additional experimental biomass data as input. BEEM’s application to previously inaccessible public datasets (due to the lack of biomass data) allowed us for the first time to analyse microbial communities in the human gut on a per individual basis, revealing personalised dynamics and keystone species.

scholarly journals Corynebacterium Comparative Genomics Reveals a Role for Cobamide Sharing in the Skin Microbiome

2020 ◽  
Author(s):  
Mary Hannah Swaney ◽  
Lindsay R Kalan
Keyword(s):  
Comparative Genomics ◽  
Microbial Communities ◽  
Community Dynamics ◽  
De Novo ◽  
Skin Barrier ◽  
Skin Microbiome ◽  
Bacterial Phyla ◽  
Host Interactions ◽  
Complex Interactions ◽  
Associated Species

ABSTRACTThe human skin microbiome is a key player in human health, with diverse functions ranging from defense against pathogens to education of the immune system. Recent studies have begun unraveling the complex interactions within skin microbial communities, shedding light on the invaluable role that skin microorganisms have in maintaining a healthy skin barrier. While the Corynebacterium genus is a dominant taxon of the skin microbiome, relatively little is known how skin-associated Corynebacteria contribute to microbe-microbe and microbe-host interactions on the skin. Here, we performed a comparative genomics analysis of 71 Corynebacterium species from diverse ecosystems, which revealed functional differences between host- and environment-associated species. In particular, host-associated species were enriched for de novo biosynthesis of cobamides, which are a class of cofactor essential for metabolism in organisms across the tree of life but are produced by a limited number of prokaryotes. Because cobamides have been hypothesized to mediate community dynamics within microbial communities, we analyzed skin metagenomes for Corynebacterium cobamide producers, which revealed a positive correlation between cobamide producer abundance and microbiome diversity, a trait associated with skin health. We also provide the first metagenome-based assessment of cobamide biosynthesis and utilization in the skin microbiome, showing that both dominant and low abundant skin taxa encode for the de novo biosynthesis pathway and that cobamide-dependent enzymes are encoded by phylogenetically diverse taxa across the major bacterial phyla on the skin. Taken together, our results support a role for cobamide sharing within skin microbial communities, which we hypothesize mediates community dynamics.

scholarly journals Short-Term Plant Community Responses to Warming and Defoliation in a Northern Temperate Grassland

ISRN Ecology ◽  
2011 ◽  
Vol 2011 ◽  
pp. 1-8 ◽  
Author(s):  
Eliza S. Deutsch ◽  
Edward W. Bork ◽  
James F. Cahill ◽  
Scott X. Chang
Keyword(s):  
Plant Community ◽  
Community Dynamics ◽  
Plant Biomass ◽  
Temperate Grassland ◽  
Community Diversity ◽  
Native Plant ◽  
Short Term ◽  
Canadian Prairies ◽  
Growing Seasons ◽  
Second Year

Little is known about the short-term impacts of warming on native plant community dynamics in the northern Canadian prairies. This study examined the immediate effects of elevated temperature and defoliation on plant community diversity, composition, and biomass within a native rough fescue (Festuca hallii (Vasey) Piper) grassland over two growing seasons. We used open-top chambers to simulate climate change and defoliated vegetation in midsummer of the first year to simulate biomass loss associated with periodic ungulate grazing. Warming marginally increased plant species diversity and changed community composition shortly after treatment, but effects were not apparent the second year, and there were no apparent impacts on plant biomass. Nonetheless, warming may have impacted community diversity indirectly through reduced soil moisture content, a pattern that persisted into the second year. Overall, this northern temperate grassland demonstrated limited community-level changes to warming even in the presence of defoliation.

scholarly journals Bacterial Communities in Concrete Reflect Its Composite Nature and Change with Weathering

mSystems ◽  
2021 ◽  
Vol 6 (3) ◽  
Author(s):  
E. Anders Kiledal ◽  
Jessica L. Keffer ◽  
Julia A. Maresca
Keyword(s):  
Microbial Communities ◽  
Community Composition ◽  
Extreme Environment ◽  
Community Diversity ◽  
Bioindicator Species ◽  
Large Aggregate ◽  
Concrete Cylinders ◽  
Composite Nature ◽  
Outdoor Weathering ◽  
Very High

ABSTRACT Concrete is an extreme but common environment and is home to microbial communities adapted to alkaline, saline, and oligotrophic conditions. Microbes inside the concrete that makes up buildings or roads have received little attention despite their ubiquity and capacity to interact with the concrete. Because concrete is a composite of materials which have their own microbial communities, we hypothesized that the microbial communities of concrete reflect those of the concrete components and that these communities change as the concrete ages. Here, we used a 16S amplicon study to show how microbial communities change over 2 years of outdoor weathering in two sets of concrete cylinders, one prone to the concrete-degrading alkali-silica reaction (ASR) and the other having the risk of the ASR mitigated. After identifying and removing taxa that were likely laboratory or reagent contaminants, we found that precursor materials, particularly the large aggregate (gravel), were the probable source of ∼50 to 60% of the bacteria observed in the first cylinders from each series. Overall, community diversity decreased over 2 years, with temporarily increased diversity in warmer summer months. We found that most of the concrete microbiome was composed of Proteobacteria, Firmicutes, and Actinobacteria, although community composition changed seasonally and over multiyear time scales and was likely influenced by environmental deposition. Although the community composition between the two series was not significantly different overall, several taxa, including Arcobacter, Modestobacter, Salinicoccus, Rheinheimera, Lawsonella, and Bryobacter, appear to be associated with ASR. IMPORTANCE Concrete is the most-used building material in the world and a biologically extreme environment, with a microbiome composed of bacteria that likely come from concrete precursor materials, aerosols, and environmental deposition. These microbes, though seeded from a variety of materials, are all subject to desiccation, heating, starvation, high salinity, and very high pH. Microbes that survive and even thrive under these conditions can potentially either degrade concrete or contribute to its repair. Thus, understanding which microbes survive in concrete, under what conditions, and for how long has potential implications for biorepair of concrete. Further, methodological pipelines for analyzing concrete microbial communities can be applied to concrete from a variety of structures or with different types of damage to identify bioindicator species that can be used for structural health monitoring and service life prediction.

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