scholarly journals Microbial predictors of environmental perturbations in coral reef ecosystems

2019 ◽  
Author(s):  
Bettina Glasl ◽  
David G. Bourne ◽  
Pedro R. Frade ◽  
Torsten Thomas ◽  
Britta Schaffelke ◽  
...  
Keyword(s):  
Coral Reef ◽  
Microbial Community ◽  
Microbial Communities ◽  
Community Assembly ◽  
Environmental Parameters ◽  
Diagnostic Value ◽  
Free Living ◽  
Environmental Pressures ◽  
Coral Reef Ecosystems ◽  
Community Data

AbstractIncorporation of microbial community data into environmental monitoring programs could improve prediction and management of environmental pressures. Coral reefs have experienced dramatic declines due to cumulative impacts of local and global stressors. Here we assess the utility of free-living (i.e. seawater and sediment) and host-associated (i.e. corals, sponges and macroalgae) microbiomes for diagnosing environmental perturbation based on their habitat-specificity, environmental sensitivity and uniformity. We show that the seawater microbiome has the greatest diagnostic value, with environmental parameters explaining 56% of the observed compositional variation and temporal successions being dominated by uniform community assembly patterns. Host-associated microbiomes, in contrast, were five-times less affected by the environment and their community assembly patterns were generally less uniform. Further, seawater microbial community data provided an accurate prediction on the environmental state, highlighting the diagnostic value of microorganisms and illustrating how long-term coral reef monitoring initiatives could be enhanced by incorporating assessments of microbial communities in seawater.ImportanceThe recent success in disease diagnostics based on the human microbiome has highlighted the utility of this approach for model systems. However, despite improved prediction and management of environmental pressures from the inclusion of microbial community data in monitoring programs, this approach has not previously been applied to coral reef ecosystems. Coral reefs are facing unprecedented pressure on a local and global scale, and sensitive and rapid markers for ecosystem stress are urgently needed to underpin effective management and restoration strategies. In this study, we performed the first assessment of the diagnostic value of multiple free-living and host-associated reef microbiomes to infer the environmental state of coral reef ecosystems. Our results reveal that free-living microbial communities have a higher potential to infer environmental parameters than host-associated microbial communities due to their higher determinacy and environmental sensitivity. We therefore recommend timely integration of microbial sampling into current coral reef monitoring initiatives.

scholarly journals Environmental parameters and microbial community profiles as indication towards microbial activities and diversity in aquaponic system compartments

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zala Schmautz ◽  
Carlos A. Espinal ◽  
Andrea M. Bohny ◽  
Fabio Rezzonico ◽  
Ranka Junge ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Profile Analysis ◽  
Operation Mode ◽  
Environmental Parameters ◽  
Plant Production ◽  
Microbial Activities ◽  
Anaerobic Processes ◽  
Abiotic Parameters ◽  
Aerobic And Anaerobic

Abstract Background An aquaponic system couples cultivation of plants and fish in the same aqueous medium. The system consists of interconnected compartments for fish rearing and plant production, as well as for water filtration, with all compartments hosting diverse microbial communities, which interact within the system. Due to the design, function and operation mode of the individual compartments, each of them exhibits unique biotic and abiotic conditions. Elucidating how these conditions shape microbial communities is useful in understanding how these compartments may affect the quality of the water, in which plants and fish are cultured. Results We investigated the possible relationships between microbial communities from biofilms and water quality parameters in different compartments of the aquaponic system. Biofilm samples were analyzed by total community profiling for bacterial and archaeal communities. The results implied that the oxygen levels could largely explain the main differences in abiotic parameters and microbial communities in each compartment of the system. Aerobic system compartments are highly biodiverse and work mostly as a nitrifying biofilter, whereas biofilms in the anaerobic compartments contain a less diverse community. Finally, the part of the system connecting the aerobic and anaerobic processes showed common conditions where both aerobic and anaerobic processes were observed. Conclusion Different predicted microbial activities for each compartment were found to be supported by the abiotic parameters, of which the oxygen saturation, total organic carbon and total nitrogen differentiated clearly between samples from the main aerobic loop and the anaerobic compartments. The latter was also confirmed using microbial community profile analysis.

scholarly journals Deterministic Selection Dominates Microbial Community Assembly in Termite Mounds Across a Large Spatial Area

2020 ◽  
Author(s):  
Qing-Lin Chen ◽  
Hang-Wei Hu ◽  
Zhen-Zhen Yan ◽  
Chao-Yu Li ◽  
Bao-Anh Thi Nguyen ◽  
...  
Keyword(s):  
Microbial Community ◽  
Stochastic Processes ◽  
Microbial Communities ◽  
Fungal Community ◽  
Community Assembly ◽  
Distance Decay ◽  
Termite Mounds ◽  
Deterministic Processes ◽  
Microbial Community Assembly

Abstract Background: Termites are ubiquitous insects in tropical and subtropical habitats, where they construct massive mounds from soil, their saliva and excreta. Termite mounds harbor an enormous amount of microbial inhabitants, which regulate multiple ecosystem functions such as mitigating methane emissions and increasing ecosystem resistance to climate change. However, we lack a mechanistic understanding about the role of termite mounds in modulating the microbial community assembly processes, which are essential to unravel the biological interactions of soil fauna and microorganisms, the major components of soil food webs. We conducted a large-scale survey across a >1500 km transect in northern Australia to investigate biogeographical patterns of bacterial and fungal community in 134 termite mounds and the relative importance of deterministic versus stochastic processes in microbial community assembly. Results: Microbial alpha (number of phylotypes) and beta (changes in bacterial and fungal community composition) significantly differed between termite mounds and surrounding soils. Microbial communities in termite mounds exhibited a significant distance-decay pattern, and fungal communities had a stronger distance-decay relationship (slope = -1.91) than bacteria (slope = -0.21). Based on the neutral community model (fitness < 0.7) and normalized stochasticity ratio index (NST) with a value below the 50% boundary point, deterministic selection, rather than stochastic forces, predominated the microbial community assembly in termite mounds. Deterministic processes exhibited significantly weaker impacts on bacteria (NST = 45.23%) than on fungi (NST = 33.72%), probably due to the wider habitat niche breadth and higher potential migration rate of bacteria. The abundance of antibiotic resistance genes (ARGs) was negatively correlated with bacterial/fungal biomass ratios, indicating that ARG content might be an important biotic factor that drove the biogeographic pattern of microbial communities in termite mounds. Conclusions: Deterministic processes play a more important role than stochastic processes in shaping the microbial community assembly in termite mounds, an unique habitat ubiquitously distributed in tropical and subtropical ecosystems. An improved understanding of the biogeographic patterns of microorganisms in termite mounds is crucial to decipher the role of soil faunal activities in shaping microbial community assembly, with implications for their mediated ecosystems functions and services.

Microbiota community assembly in wild rice (Oryza longistaminata) in response to drought stress shows phylogenetic conservation, stochasticity, and aboveground-belowground patterns

2020 ◽  
Author(s):  
xia ding ◽  
Xiaojue Peng ◽  
Zhichao Chen ◽  
Yingjie Li ◽  
Lihui Mao ◽  
...  
Keyword(s):  
Microbial Community ◽  
Drought Stress ◽  
Microbial Communities ◽  
Community Assembly ◽  
Wild Rice ◽  
Microbial Community Composition ◽  
Α Diversity ◽  
Oryza Longistaminata ◽  
Network Properties ◽  
Microbiome Assembly

Abstract Background Drought is a global environmental stress that limits crop yields. Microbial communities control many biogeochemical processes, and a predictive understanding of how crop microbial communities assemble in response to drought stress is central to addressing the challenges caused by drought. Little is known about the microbiome assembly processes in rice-ecosystems, particularly with regard to their environmental adaptation. Wild rice may serve as a source of superior drought tolerance candidate for rice breeding. There is an urgent need to explore wild rice resistance mechanisms to drought stress. Here, we evaluated the effect of drought stress on the microbial community recruitment and assembly in the endosphere (leaf, stem, and root) and rhizosphere of Oryza longistaminata. Results Species replacement was the dominant process shaping microbial community composition under drought stress. O. longistaminata recruited the phyla Actinobacteria and Fusobacteria, the genus Streptomyces, and phototrophic prokaryotes to improve its fitness. The host exerted strong effects on microbiome assembly, and the responses of the microbial community structure to the drought environment showed above- and belowground patterns. Drought reduced taxonomic α-diversity and destabilized co-occurrence network properties in the leaves and stems, but not in the roots and rhizosphere. Drought promoted the restructuring and strengthening of belowground network links to more strongly interconnect network properties. The drought response of the microbiome was phylogenetically conserved. Stochastic (neutral) processes acted on microbial community reassembly in response to drought stress across all four compartments. Conclusions Our results provide new insight into the mechanisms through which drought alters microbial community assembly in drought-tolerant wild rice and reveal a potential strategy for manipulating plant microbiomes to improve crop fitness.

scholarly journals Hill-based Dissimilarity Indices and Null Models for Analysis of Microbial Community Assembly

2020 ◽  
Author(s):  
Oskar Modin ◽  
Raquel Liebana ◽  
Soroush Saheb-Alam ◽  
Britt-Marie Wilén ◽  
Carolina Suarez ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Assembly ◽  
Null Model ◽  
Amplicon Sequencing ◽  
Null Models ◽  
Marker Genes ◽  
Experimental Systems ◽  
Microbial Community Assembly ◽  
The Impact

Abstract Background: High-throughput amplicon sequencing of marker genes, such as the 16S rRNA gene in Bacteria and Archaea, provides a wealth of information about the composition of microbial communities. To quantify differences between samples and draw conclusions about factors affecting community assembly, dissimilarity indices are typically used. However, results are subject to several biases and data interpretation can be challenging. The Jaccard and Bray-Curtis indices, which are often used to quantify taxonomic dissimilarity, are not necessarily the most logical choices. Instead, we argue that Hill-based indices, which make it possible to systematically investigate the impact of relative abundance on dissimilarity, should be used for robust analysis of data. In combination with a null model, mechanisms of microbial community assembly can be analyzed. Here, we also introduce a new software, qdiv, which enables rapid calculations of Hill-based dissimilarity indices in combination with null models.Results: Using amplicon sequencing data from two experimental systems, aerobic granular sludge (AGS) reactors and microbial fuel cells (MFC), we show that the choice of dissimilarity index can have considerable impact on results and conclusions. High dissimilarity between replicates because of random sampling effects make incidence-based indices less suited for identifying differences between groups of samples. Determining a consensus table based on count tables generated with different bioinformatic pipelines reduced the number of low-abundant, potentially spurious amplicon sequence variants (ASVs) in the data sets, which led to lower dissimilarity between replicates. Analysis with a combination of Hill-based indices and a null model allowed us to show that different ecological mechanisms acted on different fractions of the microbial communities in the experimental systems.Conclusions: Hill-based indices provide a rational framework for analysis of dissimilarity between microbial community samples. In combination with a null model, the effects of deterministic and stochastic community assembly factors on taxa of different relative abundances can be systematically investigated. Calculations of Hill-based dissimilarity indices in combination with a null model can be done in qdiv, which is freely available as a Python package (https://github.com/omvatten/qdiv). In qdiv, a consensus table can also be determined from several count tables generated with different bioinformatic pipelines.

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.

scholarly journals Colonization in the Photic Zone and Subsequent Changes during Sinking Determine Bacterial Community Composition in Marine Snow

2014 ◽  
Vol 81 (4) ◽  
pp. 1463-1471 ◽  
Author(s):  
Stefan Thiele ◽  
Bernhard M. Fuchs ◽  
Rudolf Amann ◽  
Morten H. Iversen
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Marine Snow ◽  
Free Living ◽  
Fluorescence Maximum

ABSTRACTDue to sampling difficulties, little is known about microbial communities associated with sinking marine snow in the twilight zone. A drifting sediment trap was equipped with a viscous cryogel and deployed to collect intact marine snow from depths of 100 and 400 m off Cape Blanc (Mauritania). Marine snow aggregates were fixed and washedin situto prevent changes in microbial community composition and to enable subsequent analysis using catalyzed reporter deposition fluorescencein situhybridization (CARD-FISH). The attached microbial communities collected at 100 m were similar to the free-living community at the depth of the fluorescence maximum (20 m) but different from those at other depths (150, 400, 550, and 700 m). Therefore, the attached microbial community seemed to be “inherited” from that at the fluorescence maximum. The attached microbial community structure at 400 m differed from that of the attached community at 100 m and from that of any free-living community at the tested depths, except that collected near the sediment at 700 m. The differences between the particle-associated communities at 400 m and 100 m appeared to be due to internal changes in the attached microbial community rather thande novocolonization, detachment, or grazing during the sinking of marine snow. The new sampling method presented here will facilitate future investigations into the mechanisms that shape the bacterial community within sinking marine snow, leading to better understanding of the mechanisms which regulate biogeochemical cycling of settling organic matter.

scholarly journals Coral symbiotic algae calcifyex hospitein partnership with bacteria

2015 ◽  
Vol 112 (19) ◽  
pp. 6158-6163 ◽  
Author(s):  
Jörg C. Frommlet ◽  
Maria L. Sousa ◽  
Artur Alves ◽  
Sandra I. Vieira ◽  
David J. Suggett ◽  
...  
Keyword(s):  
Life History ◽  
Coral Reef ◽  
Evolutionary History ◽  
Central Importance ◽  
Free Living ◽  
Algal Communities ◽  
Symbiotic Algae ◽  
Coral Reef Ecosystems ◽  
History Of

Dinoflagellates of the genusSymbiodiniumare commonly recognized as invertebrate endosymbionts that are of central importance for the functioning of coral reef ecosystems. However, the endosymbiotic phase withinSymbiodiniumlife history is inherently tied to a more cryptic free-living (ex hospite) phase that remains largely unexplored. Here we show that free-livingSymbiodiniumspp. in culture commonly form calcifying bacterial–algal communities that produce aragonitic spherulites and encase the dinoflagellates as endolithic cells. This process is driven bySymbiodiniumphotosynthesis but occurs only in partnership with bacteria. Our findings not only place dinoflagellates on the map of microbial–algal organomineralization processes but also point toward an endolithic phase in theSymbiodiniumlife history, a phenomenon that may provide new perspectives on the biology and ecology ofSymbiodiniumspp. and the evolutionary history of the coral–dinoflagellate symbiosis.

scholarly journals How sample heterogeneity can obscure the signal of microbial interactions

2019 ◽  
Author(s):  
David W. Armitage ◽  
Stuart E. Jones
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Species Interactions ◽  
Dynamic Models ◽  
Spatial Scales ◽  
Microbial Interactions ◽  
Vital Rates ◽  
Ecological Processes ◽  
Correlation Networks ◽  
Community Data

ABSTRACTMicrobial community data are commonly subjected to computational tools such as correlation networks, null models, and dynamic models, with the goal of identifying the ecological processes structuring microbial communities. Researchers applying these methods assume that the signs and magnitudes of species interactions and vital rates can be reliably parsed from observational data on species’ (relative) abundances. However, we contend that this assumption is violated when sample units contain any underlying spatial structure. Here, we show how three phenomena — Simpson’s paradox, context-dependence, and nonlinear averaging — can lead to erroneous conclusions about population parameters and species interactions when samples contain heterogeneous mixtures of populations or communities. At the root of this issue is the fundamental mismatch between the spatial scales of species interactions (micrometres) and those of typical microbial community samples (millimetres to centimetres). These issues can be overcome by measuring and accounting for spatial heterogeneity at very small scales, which will lead to more reliable inference of the ecological mechanisms structuring natural microbial communities.

scholarly journals Disturbance and recovery: a synthesis of microbial community reassembly following disturbance across realms

2021 ◽  
Author(s):  
Stephanie Jurburg ◽  
Shane Blowes ◽  
Ashley Shade ◽  
Nico Eisenhauer ◽  
Jonathan Chase
Keyword(s):  
Time Series ◽  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Community Assembly ◽  
Disturbance And Recovery ◽  
Microbial Community Assembly ◽  
Community Reassembly ◽  
Over Time

Disturbances alter the diversity and composition of microbial communities, but whether microbiomes from different environments exhibit similar degrees of resistance or rates of recovery has not been evaluated. Here, we synthesized 86 time series of disturbed mammalian, aquatic, and soil microbiomes to examine how the recovery of microbial richness and community composition differed after disturbance. We found no general patterns in compositional variance (i.e., dispersion) in any microbiomes over time. Only mammalian microbiomes consistently exhibited decreases in richness following disturbance. Importantly, they tended to recover this richness, but not their composition, over time. In contrast, aquatic microbiomes tended to diverge from their pre-disturbance composition following disturbance. By synthesizing microbiome responses across environments, our study aids in the reconciliation of disparate microbial community assembly frameworks, and highlights the role of the environment in microbial community reassembly following disturbance.

scholarly journals Metabolic dissimilarity determines the establishment of cross-feeding interactions in bacteria

2020 ◽  
Author(s):  
Samir Giri ◽  
Leonardo Oña ◽  
Silvio Waschina ◽  
Shraddha Shitut ◽  
Ghada Yousif ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Assembly ◽  
Bacterial Species ◽  
Exchange Interactions ◽  
Structure And Function ◽  
Phylogenetic Distance ◽  
And Function ◽  
Microbial Community Assembly ◽  
Feeding Interactions

AbstractThe exchange of metabolites among different bacterial genotypes is key for determining the structure and function of microbial communities. However, the factors that govern the establishment of these cross-feeding interactions remain poorly understood. While kin selection theory predicts that individuals should direct benefits preferentially to close relatives, the potential benefits resulting from a metabolic exchange may be larger for more distantly related species. Here we distinguish between these two possibilities by performing pairwise cocultivation experiments between auxotrophic recipients and 25 species of potential amino acid donors. Auxotrophic recipients were able to grow in the vast majority of pairs tested (78%), suggesting that metabolic cross-feeding interactions are readily established. Strikingly, both the phylogenetic distance between donor and recipient as well as the dissimilarity of their metabolic networks was positively associated with the growth of auxotrophic recipients. Finally, this result was corroborated in an in-silico analysis of a co-growth of species from a gut microbial community. Together, these findings suggest metabolic cross-feeding interactions are more likely to establish between strains that are metabolically more dissimilar. Thus, our work identifies a new rule of microbial community assembly, which can help predict, understand, and manipulate natural and synthetic microbial systems.SignificanceMetabolic cross-feeding is critical for determining the structure and function of natural microbial communities. However, the rules that determine the establishment of these interactions remain poorly understood. Here we systematically analyze the propensity of different bacterial species to engage in unidirectional cross-feeding interactions. Our results reveal that synergistic growth was prevalent in the vast majority of cases analyzed. Moreover, both phylogenetic and metabolic dissimilarity between donors and recipients favored a successful establishment of metabolite exchange interactions. This work identifies a new rule of microbial community assembly that can help predict, understand, and manipulate microbial communities for diverse applications.

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