scholarly journals Beneath the surface: community assembly and functions of the coral skeleton microbiome

Microbiome ◽  
2019 ◽  
Vol 7 (1) ◽  
Author(s):  
Francesco Ricci ◽  
Vanessa Rossetto Marcelino ◽  
Linda L. Blackall ◽  
Michael Kühl ◽  
Mónica Medina ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Assembly ◽  
Dispersal Limitation ◽  
Priority Effects ◽  
Coral Host ◽  
Chemical Gradients ◽  
Physico Chemical ◽  
Archaeal Species ◽  
Coral Holobiont ◽  
Coral Health

AbstractCoral microbial ecology is a burgeoning field, driven by the urgency of understanding coral health and slowing reef loss due to climate change. Coral resilience depends on its microbiota, and both the tissue and the underlying skeleton are home to a rich biodiversity of eukaryotic, bacterial and archaeal species that form an integral part of the coral holobiont. New techniques now enable detailed studies of the endolithic habitat, and our knowledge of the skeletal microbial community and its eco-physiology is increasing rapidly, with multiple lines of evidence for the importance of the skeletal microbiota in coral health and functioning. Here, we review the roles these organisms play in the holobiont, including nutritional exchanges with the coral host and decalcification of the host skeleton. Microbial metabolism causes steep physico-chemical gradients in the skeleton, creating micro-niches that, along with dispersal limitation and priority effects, define the fine-scale microbial community assembly. Coral bleaching causes drastic changes in the skeletal microbiome, which can mitigate bleaching effects and promote coral survival during stress periods, but may also have detrimental effects. Finally, we discuss the idea that the skeleton may function as a microbial reservoir that can promote recolonization of the tissue microbiome following dysbiosis and help the coral holobiont return to homeostasis.

scholarly journals Beneath the surface: community assembly and functions of the coral skeleton microbiome

2019 ◽  
Author(s):  
Francesco Ricci ◽  
Vanessa Rossetto Marcelino ◽  
Linda Blackall ◽  
Michael Kühl ◽  
Monica Medina ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Assembly ◽  
Dispersal Limitation ◽  
Coral Host ◽  
Chemical Gradients ◽  
Physico Chemical ◽  
Archaeal Species ◽  
Coral Holobiont ◽  
Coral Health ◽  
Microbial Community Assembly

Coral microbial ecology is a burgeoning field, driven by the urgency of understanding coral health and slowing reef loss due to climate change. Coral resilience depends on its microbiota, and both the tissue and the underlying skeleton are home to a rich biodiversity of eukaryotic, bacterial and archaeal species that form an integral part of the coral holobiont. New techniques now enable detailed studies of the endolithic habitat, and our knowledge of the skeletal microbial community and its eco-physiology is increasing rapidly, with multiple lines of evidence for the importance of the skeletal microbiota in coral health and functioning. Here, we review the roles these organisms play in the holobiont, including nutritional exchanges with the coral host and decalcification of the host skeleton. Microbial metabolism causes steep physico-chemical gradients in the skeleton, creating micro-niches that, along with dispersal limitation and priority affects, define the fine-scale microbial community assembly. Coral bleaching causes drastic changes in the skeletal microbiome, which can mitigate bleaching effects and promote coral survival during stress periods, but may also have detrimental effects. Finally, we discuss the idea that the skeleton may function as a microbial reservoir that can promote recolonization of the tissue microbiome following dysbiosis and help the coral holobiont return to homeostasis.

scholarly journals Ecosystem size-induced environmental fluctuations affect the temporal dynamics of community assembly mechanisms

2022 ◽  
Author(s):  
Raven L Bier ◽  
Máté Vass ◽  
Anna J Székely ◽  
Silke Langenheder
Keyword(s):  
Community Assembly ◽  
Temporal Dynamics ◽  
Bacterial Community Composition ◽  
Dispersal Limitation ◽  
Priority Effects ◽  
Environmental Fluctuation ◽  
Species Sorting ◽  
Ecosystem Size ◽  
Environmental Fluctuations ◽  
Over Time

Understanding processes that determine community membership and abundance is important for many fields from theoretical community ecology to conservation. However, spatial community studies are often conducted only at a single timepoint despite the known influence of temporal variability on community assembly processes. Here we used a spatiotemporal study to determine how environmental fluctuation differences induced by mesocosm volumes (larger volumes were more stable) influence assembly processes of aquatic bacterial metacommunities along a press disturbance gradient. By combining path analysis and network approaches, we found mesocosm size categories had distinct relative influences of assembly process and environmental factors that determined spatiotemporal bacterial community composition, including dispersal and species sorting by conductivity. These processes depended on, but were not affected proportionately by, mesocosm size. Low fluctuation, large mesocosms primarily developed through the interplay of species sorting that became more important over time and transient priority effects as evidenced by more time-delayed associations. High fluctuation, small mesocosms had regular disruptions to species sorting and greater importance of ecological drift and dispersal limitation indicated by lower richness and higher taxa replacement. Together, these results emphasize that environmental fluctuations influence ecosystems over time and its impacts are modified by biotic properties intrinsic to ecosystem size.

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

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.

scholarly journals Spatial gradients in soil-carbon character of a coastal forested floodplain are associated with abiotic features, but not microbial communities

2019 ◽  
Author(s):  
Aditi Sengupta ◽  
Julia Indivero ◽  
Cailene Gunn ◽  
Malak M. Tfaily ◽  
Rosalie K. Chu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Organic Compounds ◽  
Community Composition ◽  
Community Assembly ◽  
Dispersal Limitation ◽  
Water Soluble ◽  
Microbial Composition ◽  
Organic C ◽  
Shallow Soils

Abstract. Coastal terrestrial-aquatic interfaces (TAIs) are dynamic zones of biogeochemical cycling influenced by salinity gradients. However, there is significant heterogeneity in salinity influences on TAI soil biogeochemical function. This heterogeneity is perhaps related to unrecognized mechanisms associated with carbon (C) chemistry and microbial communities. To investigate this potential, we evaluated hypotheses associated with salinity-associated shifts in organic C thermodynamics, biochemical transformations, and heteroatom content in a first-order coastal watershed in the Olympic Peninsula of Washington state, USA. In contrast to our hypotheses, thermodynamic favorability of water soluble organic compounds in shallow soils decreased with increasing salinity, as did the number of inferred biochemical transformations and total heteroatom content. These patterns indicate lower microbial activity at higher salinity that is potentially constrained by accumulation of less favorable organic C. Furthermore, organic compounds appeared to be primarily marine/algal-derived in forested floodplain soils with more lipid-like and protein-like compounds, relative to upland soils that had more lignin-, tannin-, and carbohydrate-like compounds. Based on a recent simulation-based study, we further hypothesized a relationship between microbial community assembly processes and C chemistry. Null modelling revealed strong influences of dispersal limitation over microbial composition, which may be due to limited hydrologic connectivity within the clay-rich soils. Dispersal limitation indicated stochastically assembled communities, which was further reflected in the lack of an association between community assembly processes and C chemistry. This suggests a disconnect between microbial community composition and C biogeochemistry, thereby indicating that the salinity-associated gradient in C chemistry was driven by a combination of spatially-structured inputs and salinity-associated metabolic responses of microbial communities that were independent of community composition. We propose that impacts of salinity on coastal soil biogeochemistry need to be understood in the context of C chemistry, hydrologic/depositional dynamics, and microbial physiology, while microbial composition may have less influence.

scholarly journals Seasonal Variations in the Culturable Mycobiome of Acropora loripes along a Depth Gradient

2020 ◽  
Vol 8 (8) ◽  
pp. 1139
Author(s):  
Nofar Lifshitz ◽  
Lena Hazanov ◽  
Maoz Fine ◽  
Oded Yarden
Keyword(s):  
Environmental Conditions ◽  
Fungal Diversity ◽  
Gulf Of Aqaba ◽  
Coral Host ◽  
Depth Gradient ◽  
Coral Holobiont ◽  
Colony Forming Units ◽  
Coral Health ◽  
Fungal Colony ◽  
Apparently Healthy

Coral associated fungi are widespread, highly diverse and are part and parcel of the coral holobiont. To study how environmental conditions prevailing near the coral-host may affect fungal diversity, the culturable (isolated on potato dextrose agar) mycobiome associated with Acropora loripes colonies was seasonally sampled along a depth gradient in the Gulf of Aqaba. Fragments were sampled from both apparently healthy coral colonies as well as those exhibiting observable lesions. Based on phylogenetic analysis of 197 fungal sequences, Ascomycota were the most prevalent (91.9%). The abundance of fungi increased with increasing water depth, where corals sampled at 25 m yielded up to 70% more fungal colony forming units (CFUs) than those isolated at 6 m. Fungal diversity at 25 m was also markedly higher, with over 2-fold more fungal families represented. Diversity was also higher in lesioned coral samples, when compared to apparently healthy colonies. In winter, concurrent with water column mixing and increased levels of available nutrients, at the shallow depths, Saccharomytacea and Sporidiobolacea were more prevalent, while in spring and fall Trichocomacea (overall, the most prevalent family isolated throughout this study) were the most abundant taxa isolated at these depths as well as at deeper sampling sites. Our results highlight the dynamic nature of the culturable coral mycobiome and its sensitivity to environmental conditions and coral health.

Conservation and Restoration of Grasslands

2018 ◽  
Author(s):  
Brian J. Wilsey
Keyword(s):  
Community Assembly ◽  
Woody Plants ◽  
Woody Plant ◽  
Priority Effects ◽  
Woody Plant Encroachment ◽  
Humpty Dumpty ◽  
Alternate States ◽  
Density And Biomass ◽  
Acid Test ◽  
Stocking Rates

Conservation programs alter herbivore stocking rates and find and protect the remaining areas that have not been plowed or converted to crops. Restoration is an ‘Acid Test’ for ecology. If we fully understand how grassland systems function and assemble after disturbance, then it should be easy to restore them after they have been degraded or destroyed. Alternatively, the idea that restorations will not be equivalent to remnants has been termed the ‘Humpty Dumpty’ hypothesis—once lost, it cannot be put back together again. Community assembly may follow rules, and if these rules are uncovered, then we may be able to accurately predict final species composition after assembly. Priority effects are sometimes found depending on species arrival orders, and they can result in alternate states. Woody plant encroachment is the increase in density and biomass of woody plants, and it is strongly affecting grassland C and water cycles.

scholarly journals Multi-domain probiotic consortium as an alternative to chemical remediation of oil spills at coral reefs and adjacent sites

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Denise P. Silva ◽  
Helena D. M. Villela ◽  
Henrique F. Santos ◽  
Gustavo A. S. Duarte ◽  
José Roberto Ribeiro ◽  
...  
Keyword(s):  
Microbial Community ◽  
Coral Reefs ◽  
Environmental Changes ◽  
Oil Spills ◽  
Anthropogenic Activities ◽  
Oil Contamination ◽  
Negative Effects ◽  
Corexit 9500 ◽  
Coral Health ◽  
The Impact

Abstract Background Beginning in the last century, coral reefs have suffered the consequences of anthropogenic activities, including oil contamination. Chemical remediation methods, such as dispersants, can cause substantial harm to corals and reduce their resilience to stressors. To evaluate the impacts of oil contamination and find potential alternative solutions to chemical dispersants, we conducted a mesocosm experiment with the fire coral Millepora alcicornis, which is sensitive to environmental changes. We exposed M. alcicornis to a realistic oil-spill scenario in which we applied an innovative multi-domain bioremediator consortium (bacteria, filamentous fungi, and yeast) and a chemical dispersant (Corexit® 9500, one of the most widely used dispersants), to assess the effects on host health and host-associated microbial communities. Results The selected multi-domain microbial consortium helped to mitigate the impacts of the oil, substantially degrading the polycyclic aromatic and n-alkane fractions and maintaining the physiological integrity of the corals. Exposure to Corexit 9500 negatively impacted the host physiology and altered the coral-associated microbial community. After exposure, the abundances of certain bacterial genera such as Rugeria and Roseovarius increased, as previously reported in stressed or diseased corals. We also identified several bioindicators of Corexit 9500 in the microbiome. The impact of Corexit 9500 on the coral health and microbial community was far greater than oil alone, killing corals after only 4 days of exposure in the flow-through system. In the treatments with Corexit 9500, the action of the bioremediator consortium could not be observed directly because of the extreme toxicity of the dispersant to M. alcicornis and its associated microbiome. Conclusions Our results emphasize the importance of investigating the host-associated microbiome in order to detect and mitigate the effects of oil contamination on corals and the potential role of microbial mitigation and bioindicators as conservation tools. Chemical dispersants were far more damaging to corals and their associated microbiome than oil, and should not be used close to coral reefs. This study can aid in decision-making to minimize the negative effects of oil and dispersants on coral reefs.

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