Sonny T. M. Lee

Successive shifts in the microbial community of the surface mucus layer and tissues of the coral Acropora muricata under thermal stress

The coral mucus may harbor commensal bacteria that inhibit growth of pathogens. Therefore, there is a need to understand the dynamics of bacterial communities between the coral mucus and tissues. Nubbins of Acropora muricata were subjected to increasing water temperatures of 26°C-33°C, to simultaneously explore the bacterial diversity in coral mucus and tissues by 16S rRNA gene amplicon sequencing. Photochemical efficiency of symbiotic dinoflagellates within the corals declined above 31°C. Both the mucus and tissues of healthy A. muricata were dominated by γ-Proteobacteria, but under thermal stress there was a shift towards bacteria from the Verrucomicrobiaceae and α-Proteobacteria. Members of Cyanobacteria, Flavobacteria and Sphingobacteria also become more prominent at higher temperatures. The relative abundance of Vibrio spp. in the coral mucus increased at 29°C, but at 31°C, there was a drop in the relative abundance of Vibrio spp. in the mucus, with a reciprocal increase in the tissues. On the other hand, during bleaching, the relative abundance of Endozoicomonas spp. decreased in the tissues with a reciprocal increase in the mucus. This is the first systematic experiment that shows the potential for a bacterial community shift between the coral surface mucus and tissues in a thermally stressed coral.

Mucus Sugar Content Shapes the Bacterial Community Structure in Thermally Stressed Acropora muricata

It has been proposed that the chemical composition of a coral’s mucus can influence the associated bacterial community. However, information on this topic is rare, and non-existent for corals that are under thermal stress. This study therefore compared the carbohydrate composition of mucus in the coral Acropora muricata when subjected to increasing thermal stress from 26 to 31°C, and determined whether this composition correlated with any changes in the bacterial community. Results showed that, at lower temperatures, the main components of mucus were N-acetyl glucosamine and C6 sugars, but these constituted a significantly lower proportion of the mucus in thermally stressed corals. The change in the mucus composition coincided with a shift from a γ-Proteobacteria- to a Verrucomicrobiae- and α-Proteobacteria-dominated community in the coral mucus. Bacteria in the class Cyanobacteria also started to become prominent in the mucus when the coral was thermally stressed. The increase in the relative abundance of the Verrucomicrobiae at higher temperature was strongly associated with a change in the proportion of fucose, glucose, and mannose in the mucus. Increase in the relative abundance of α-Proteobacteria were associated with GalNAc and glucose, while the drop in relative abundance of γ-Proteobacteria at high temperature coincided with changes in fucose and mannose. Cyanobacteria were highly associated with arabinose and xylose. Changes in mucus composition and the bacterial community in the mucus layer occurred at 29°C, which were prior to visual signs of coral bleaching at 31°C. A compositional change in the coral mucus, induced by thermal stress could therefore be a key factor leading to a shift in the associated bacterial community. This, in turn, has the potential to impact the physiological function of the coral holobiont.

Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

BackgroundFecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection and shows promise for treating other medical conditions associated with intestinal dysbioses. However, we lack a sufficient understanding of which microbial populations successfully colonize the recipient gut, and the widely used approaches to study the microbial ecology of FMT experiments fail to provide enough resolution to identify populations that are likely responsible for FMT-derived benefits.MethodsWe used shotgun metagenomics together with assembly and binning strategies to reconstruct metagenome-assembled genomes (MAGs) from fecal samples of a single FMT donor. We then used metagenomic mapping to track the occurrence and distribution patterns of donor MAGs in two FMT recipients.ResultsOur analyses revealed that 22% of the 92 highly complete bacterial MAGs that we identified from the donor successfully colonized and remained abundant in two recipients for at least 8xa0weeks. Most MAGs with a high colonization rate belonged to the order Bacteroidales. The vast majority of those that lacked evidence of colonization belonged to the order Clostridiales, and colonization success was negatively correlated with the number of genes related to sporulation. Our analysis of 151 publicly available gut metagenomes showed that the donor MAGs that colonized both recipients were prevalent, and the ones that colonized neither were rare across the participants of the Human Microbiome Project. Although our dataset showed a link between taxonomy and the colonization ability of a given MAG, we also identified MAGs that belong to the same taxon with different colonization properties, highlighting the importance of an appropriate level of resolution to explore the functional basis of colonization and to identify targets for cultivation, hypothesis generation, and testing in model systems.ConclusionsThe analytical strategy adopted in our study can provide genomic insights into bacterial populations that may be critical to the efficacy of FMT due to their success in gut colonization and metabolic properties, and guide cultivation efforts to investigate mechanistic underpinnings of this procedure beyond associations.

Nitrogen-Fixing Populations Of Planctomycetes And Proteobacteria Are Abundant In The Surface Ocean

Nitrogen fixation in the surface ocean impacts the global climate by regulating the microbial primary productivity and the sequestration of carbon through the biological pump. Cyanobacterial populations have long been thought to represent the main suppliers of the bio-available nitrogen in this habitat. However, recent molecular surveys of nitrogenase reductase gene revealed the existence of rare non-cyanobacterial populations that can also fix nitrogen. Here, we characterize for the first time the genomic content of some of these heterotrophic bacterial diazotrophs (HBDs) inhabiting the open surface ocean waters. They represent new lineages within Planctomycetes and Proteobacteria, a phylum never linked to nitrogen fixation prior to this study. HBDs were surprisingly abundant in the Pacific Ocean and the Atlantic Ocean northwest, conflicting with decades of PCR surveys. The abundance and widespread occurrence of non-cyanobacterial diazotrophs in the surface ocean emphasizes the need to re-evaluate their role in the nitrogen cycle and primary productivity.

Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes

Nitrogen fixation in the surface ocean impacts global marine nitrogen bioavailability and thus microbial primary productivity. Until now, cyanobacterial populations have been viewed as the main suppliers of bioavailable nitrogen in this habitat. Although PCR amplicon surveys targeting the nitrogenase reductase gene have revealed the existence of diverse non-cyanobacterial diazotrophic populations, subsequent quantitative PCR surveys suggest that they generally occur in low abundance. Here, we use state-of-the-art metagenomic assembly and binning strategies to recover nearly one thousand non-redundant microbial population genomes from the TARA Oceans metagenomes. Among these, we provide the first genomic evidence for non-cyanobacterial diazotrophs inhabiting surface waters of the open ocean, which correspond to lineages within the Proteobacteria and, most strikingly, the Planctomycetes. Members of the latter phylum are prevalent in aquatic systems, but have never been linked to nitrogen fixation previously. Moreover, using genome-wide quantitative read recruitment, we demonstrate that the discovered diazotrophs were not only widespread but also remarkably abundant (up to 0.3% of metagenomic reads for a single population) in both the Pacific Ocean and the Atlantic Ocean northwest. Our results extend decades of PCR-based gene surveys, and substantiate the importance of heterotrophic bacteria in the fixation of nitrogen in the surface ocean.Recovery of population genomes from surface ocean samples identified non-cyanobacterial diazotrophs that were widespread and abundant, including Proteobacteria and Planctomycetes, indicating their importance for nitrogen fixation in this environment.

Water flow buffers shifts in bacterial community structure in heat-stressed Acropora muricata

Deterioration of coral health and associated change in the coral holobiont’s bacterial community are often a result of different environmental stressors acting synergistically. There is evidence that water flow is important for a coral’s resistance to elevated seawater temperature, but there is no information on how water flow affects the coral-associated bacterial community under these conditions. In a laboratory cross-design experiment, Acropora muricata nubbins were subjected to interactive effects of seawater temperature (27u2009°C to 31u2009°C) and water flow (0.20u2009m s−1 and 0.03u2009m s−1). In an in situ experiment, water flow manipulation was conducted with three colonies of A. muricata during the winter and summer, by partially enclosing each colony in a clear plastic mesh box. 16S rRNA amplicon pyrosequencing showed an increase in the relative abundance of Flavobacteriales and Rhodobacterales in the laboratory experiment, and Vibrio spp. in the in situ experiment when corals were exposed to elevated temperature and slow water flow. In contrast, corals that were exposed to faster water flow under laboratory and in situ conditions had a stable bacterial community. These findings indicate that water flow plays an important role in the maintenance of specific coral-bacteria associations during times of elevated thermal stress.

Baseline seabed habitat and biotope mapping for a proposed marine reserve

Seabed mapping can quantify the extent of benthic habitats that comprise marine ecosystems, and assess the impact of fisheries on an ecosystem. In this study, the distribution of seabed habitats in a proposed no-take Marine Reserve along the northeast coast of Great Barrier Island, New Zealand, was mapped using underwater video combined with bathymetry and substratum data. As a result of the boundary extending to the 12 nautical mile Territorial Limit, it would have been the largest coastal Marine Reserve in the country. Recreational and commercial fisheries occur in the region and would be expected to affect species’ abundance. The seabed of the study area and adjacent coastal waters has been trawled up to five times per year. Benthic communities were grouped by multivariate cluster analysis into four biotope classes; namely (1) shallow water macroalgae Ecklonia sp. and Ulva sp. on rocky substrata (Eck.Ulv); and deeper (2) diverse epifauna of sponges and bryozoans on rocky substrata (Por.Bry), (3) brittle star Amphiura sp. and sea anemone Edwardsia sp. on muddy sand (Amph.Edw), and (4) hydroids on mud (Hyd). In biotopes Por.Bry, Amph.Edw and Hyd, there where boulders and rocks were present, and diverse sponge, bryozoan and coral communities. Fifty species were recorded in the deep water survey including significant numbers of the shallow-water hexactinellid glass sponges Symplectella rowi Dendy, 1924 and Rossella ijimai Dendy, 1924, the giant pipe demosponge Isodictya cavicornuta Dendy, 1924, black corals, and locally endemic gorgonians. The habitats identified in the waters to the northeast of Great Barrier Island are likely to be representative of similar depth ranges in northeast New Zealand. This study provides a baseline of the benthic habitats so that should the area become a Marine Reserve, any habitat change might be related to protection from fishing activities and impacts, such as recovery of epifauna following cessation of trawling. The habitat map may also be used to stratify future sampling that would aim to collect and identify epifauna and infauna for identification, and thus better describe the biodiversity of the area.

Long-Term Survey Is Necessary to Reveal Various Shifts of Microbial Composition in Corals

The coral holobiont is the assemblage of coral host and its microbial symbionts, which functions as a unit and is responsive to host species and environmental factors. Although monitoring surveys have been done to determine bacteria associated with coral, none have persisted for >1 year. Therefore, potential variations in minor or dominant community members that occur over extended intervals have not been characterized. In this study, 16S rRNA gene amplicon pyrosequencing was used to investigate the relationship between bacterial communities in healthy Stylophora pistillata in tropical and subtropical Taiwan over 2 years, apparently one of the longest surveys of coral-associated microbes. Dominant bacterial genera in S. pistillata had disparate changes in different geographical setups, whereas the constitution of minor bacteria fluctuated in abundance over time. We concluded that dominant bacteria (Acinetobacter, Propionibacterium, and Pseudomonas) were stable in composition, regardless of seasonal and geographical variations, whereas Endozoicomonas had a geographical preference. In addition, by combining current data with previous studies, we concluded that a minor bacteria symbiont, Ralstonia, was a keystone species in coral. Finally, we concluded that long-term surveys for coral microbial communities were necessary to detect compositional shifts, especially for minor bacterial members in corals.

High-resolution tracking of microbial colonization in Fecal Microbiota Transplantation experiments via metagenome-assembled genomes

Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection and shows promise for treating other medical conditions associated with intestinal dysbioses. However, we lack a sufficient understanding of which microbial populations successfully colonize the recipient gut, and the widely used approaches to study the microbial ecology of FMT experiments fail to provide enough resolution to identify populations that are likely responsible for FMT-derived benefits. Here we used shotgun metagenomics to reconstruct 97 metagenome-assembled genomes (MAGs) from fecal samples of a single donor and followed their distribution in two FMT recipients to identify microbial populations with different colonization properties. Our analysis of the occurrence and distribution patterns post-FMT revealed that 22% of the MAGs transferred from the donor to both recipients and remained abundant in their guts for at least eight weeks. Most MAGs that successfully colonized the recipient gut belonged to the order Bacteroidales. The vast majority of those that lacked evidence of colonization belonged to the order Clostridiales and colonization success was negatively correlated with the number of genes related to sporulation. Although our dataset showed a link between taxonomy and the ability of a MAG to colonize the recipient gut, we also identified MAGs with different colonization properties that belong to the same taxon, highlighting the importance of genome-resolved approaches to explore the functional basis of colonization and to identify targets for cultivation, hypothesis generation, and testing in model systems for mechanistic insights.

Transcriptomic response in Acropora muricata under acute temperature stress follows preconditioned seasonal temperature fluctuations

ObjectiveGlobal climate change has resulted in the decline of health and condition of various coral reefs worldwide. Here, we describe expression profiles of Acropora muricata collected during opposing seasons in Otsuki, Kochi, Japan to define the capacity of corals to cope with changing environmental conditions. Coral communities in Otsuki experience large temperature fluctuations between the winter (~xa016xa0°C) and summer (~xa027xa0°C).ResultsCoral nubbins that were collected in the summer showed no change in photochemical efficiency when exposed to thermal or cold stress, while winter samples showed a decrease in photochemical health when subjected to thermal stress. Under cold stress, corals that were collected in the summer showed an up-regulation of actin-related protein and serine/threonine protein kinase, while corals collected during the winter did not show any cellular stress. On the other hand, under thermal stress, the most notable change was the up-regulation of phosphoenolpyruvate carboxykinase in corals that were collected during the winter season. Our observations in the differential genes expressed under temperature-derived stress suggest that A. muricata from Kochi may maintain physiological resilience due to the frequently encountered environmental stress, and this may play a role in the coral’s thermal tolerance.