Modeling of the Coral Microbiome: the Influence of Temperature and Microbial Network

ABSTRACT Host-associated microbial communities are shaped by extrinsic and intrinsic factors to the holobiont organism. Environmental factors and microbe-microbe interactions act simultaneously on the microbial community structure, making the microbiome dynamics challenging to predict. The coral microbiome is essential to the health of coral reefs and sensitive to environmental changes. Here, we develop a dynamic model to determine the microbial community structure associated with the surface mucus layer (SML) of corals using temperature as an extrinsic factor and microbial network as an intrinsic factor. The model was validated by comparing the predicted relative abundances of microbial taxa to the relative abundances of microbial taxa from the sample data. The SML microbiome from Pseudodiploria strigosa was collected across reef zones in Bermuda, where inner and outer reefs are exposed to distinct thermal profiles. A shotgun metagenomics approach was used to describe the taxonomic composition and the microbial network of the coral SML microbiome. By simulating the annual temperature fluctuations at each reef zone, the model output is statistically identical to the observed data. The model was further applied to six scenarios that combined different profiles of temperature and microbial network to investigate the influence of each of these two factors on the model accuracy. The SML microbiome was best predicted by model scenarios with the temperature profile that was closest to the local thermal environment, regardless of the microbial network profile. Our model shows that the SML microbiome of P. strigosa in Bermuda is primarily structured by seasonal fluctuations in temperature at a reef scale, while the microbial network is a secondary driver. IMPORTANCE Coral microbiome dysbiosis (i.e., shifts in the microbial community structure or complete loss of microbial symbionts) caused by environmental changes is a key player in the decline of coral health worldwide. Multiple factors in the water column and the surrounding biological community influence the dynamics of the coral microbiome. However, by including only temperature as an external factor, our model proved to be successful in describing the microbial community associated with the surface mucus layer (SML) of the coral P. strigosa. The dynamic model developed and validated in this study is a potential tool to predict the coral microbiome under different temperature conditions.

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Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale

10.21203/rs.3.rs-600995/v1 ◽

2021 ◽

Author(s):

Laís Farias Oliveira Lima ◽

Amanda Alker ◽

Bhavya Papudeshi ◽

Megan Morris ◽

Robert Edwards ◽

...

Keyword(s):

Microbial Community ◽

Nutrient Cycling ◽

Ecosystem Functioning ◽

Environmental Changes ◽

Coral Host ◽

Shotgun Metagenomics ◽

Patch Reefs ◽

Coral Microbiome ◽

Gene Functions ◽

Coral Health

Abstract Background The coral holobiont is comprised of a highly diverse microbial community that provides key services to corals such as protection against pathogens and nutrient cycling. The coral surface mucus layer (SML) microbiome is very sensitive to external changes and tied to ecosystem functioning, as it constitutes the direct interface between the coral host and the environment. The functional profile of microbial genes in the coral SML is underexplored and the use of shotgun metagenomics is relatively rare among coral microbiome studies. Here we investigate whether the bacterial taxonomic and functional profiles in the coral SML are shaped by the local reef zone and explore their role in coral health and ecosystem functioning. Results The analysis was conducted using metagenomes and metagenome assemble genomes (MAGs) associated with the coral Pseudodiploria strigosa and the water column from two naturally distinct reef environments in Bermuda: inner patch reefs exposed to a fluctuating thermal regime and the more stable outer reefs . Our results showed that the microbial community structure is simultaneously selected by the host medium (i.e., coral SML versus water) and the local environment (i.e., inner reefs versus outer reefs), both at taxonomic and functional levels. The coral SML microbiome from inner reefs provides more gene functions that are involved in nutrient cycling (e.g., photosynthesis, phosphorus metabolism, sulfur assimilation) and that are related to higher levels of microbial activity, competition, and stress response, such as dimethylsulfoniopropionate (DMSP) breakdown. In contrast, the coral SML microbiome from outer reefs contained genes indicative of a carbohydrate-rich mucus composition found in corals exposed to less stressful temperatures and showed high proportions of microbial gene functions that play a potential role in coral disease, such as degradation of lignin-derived compounds and sulfur oxidation. Conclusion The fluctuating environment in the inner patch reefs of Bermuda could be driving a more beneficial coral SML microbiome; potentially increasing holobiont resilience to environmental changes and disease. Our results reveal microbial taxa and functions selected at reef scale in the coral SML microbiome that can leverage disease management, microbiome engineering, and microbial eco-evolutionary theories.

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Large shifts among eukaryotes, bacteria, and archaea define the vertical organization of a lake sediment

10.1101/057117 ◽

2016 ◽

Author(s):

Christian Wurzbacher ◽

Andrea Fuchs ◽

Katrin Attermeyer ◽

Katharina Frindte ◽

Hans-Peter Grossart ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

Environmental Changes ◽

Microbial Community Composition ◽

Environmental Parameters ◽

Global Trends ◽

Water Columns ◽

And Function ◽

Microbial Hotspots

AbstractSediments are depositional areas where particles sink from water columns, but they are also microbial hotspots that play an important role in biogeochemical cycles. Unfortunately, the importance of both processes in structuring microbial community composition has not been assessed. We surveyed all organismic signals of the last ca. 170 years of sediment by metabarcoding, identifying global trends for eukaryotes, bacteria, archaea, and monitored 40 sediment parameters. We linked the microbial community structure to ongoing and historical environmental parameters and defined three distinct sediment horizons. This not only expands our knowledge of freshwater sediments, but also has profound implications for understanding the microbial community structure and function of sediment communities in relation to future, present, and past environmental changes.

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A practical introduction to microbial community sequencing

Open Life Sciences ◽

10.2478/s11535-013-0155-8 ◽

2013 ◽

Vol 8 (5) ◽

pp. 399-409 ◽

Cited By ~ 1

Author(s):

Dominika Chmolowska

Keyword(s):

Community Structure ◽

Microbial Community ◽

Sample Preparation ◽

Community Ecology ◽

Microbial Community Structure ◽

Shotgun Metagenomics ◽

Genetic Tool ◽

Amplicon Library ◽

Microbial Community Ecology ◽

Sample Preparation Procedure

AbstractThe use of molecular methods is gaining popularity throughout the field of microbial community ecology studies thanks to their flexibility of application, which ranges from community structure to function and trait determination. Nonetheless, there are environmental microbiologists, who are new in the field and are just starting to get to grips with the genetic tool box. It is for them that this practitioner’s mini-review was compiled. The methods available for microbial community structure analysis are discussed, after which, the reader is introduced to sequencing, as this tool is the most appropriate and has seen the greatest development in recent years. A focus on the practical aspects of the methodology is maintained throughout. The sample preparation procedure from extraction to sequencing is described. Different applications and considerations of sequencing are briefly explained, including clone library sequencing vs. amplicon library sequencing, shotgun-metagenomics vs. metatranscriptomics and the ‘double RNA approach’.

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Reintroduction of Decomposed Straw To Maize Fields Resulted In Soil Microbial Community Change And Increased Corn Production

10.21203/rs.3.rs-1166069/v1 ◽

2021 ◽

Author(s):

Yang Zhou ◽

Weihui Xu ◽

Wenjing Chen ◽

Yunlong Hu ◽

Zhigang Wang

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

Soil Microbial Community ◽

Maize Yield ◽

Soil Enzyme ◽

Soil Microbial Community Structure ◽

Soil Microbial ◽

Maize Growth ◽

Relative Abundances

Abstract Purpose Returning decomposed straw to crop fields could address many agricultural shortcomings. In this study, the soil microbial community, soil nutrients, soil enzyme activities and maize yield were investigated after returning decomposed straw to the field. Methods To investigate the effects of returning decomposed straw to field on soil microorganisms and maize growth, field experiments were carried out to measure soil nutrient content, soil enzyme activity and maize yield, and the soil microbial community structure was measured by 16SRNA and ITS amplicon sequencing technology.Results The results showed that the contents of total nitrogen (TN), nitrate nitrogen (NN), total phosphorus (TP), available phosphorus (AP) and pH were significantly increased, and the contents of ammonium nitrogen (AN) and available kalium were decreased in both the rotary tillage (SR) and mulching (SM) treatments. The bacterial and fungal community structures in bulk and rhizosphere soils were clearly changed under SR and SM. The relative abundances of bacterial genera related to soil denitrification, such as Skermanella, Blastococcus, Geodermatophilus and Asanoa, were significantly increased. The relative abundances of Conexibacter, Streptomyces and Trichoderma, which bacteria that has shown to inhibit plant diseases, were increased. In addition, the relative abundances of growth-promoting bacteria, such as Arthrobacter and Mesorhizobium, were also significantly increased. Moreover, adding decomposed straw back to the field promoted the absorption of nutrients by maize, and resulted in higher yield of maize.Conclusions Our findings suggest positive responses of soil microbial community structure and maize growth to decomposition straw returning.

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