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The gut of geographically disparate Ciona intestinalis harbors a core microbiota. PLoS One 2014; 9:e93386. [PMID: 24695540 PMCID: PMC3973685 DOI: 10.1371/journal.pone.0093386] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 03/04/2014] [Indexed: 02/07/2023] Open
Abstract
It is now widely understood that all animals engage in complex interactions with bacteria (or microbes) throughout their various life stages. This ancient exchange can involve cooperation and has resulted in a wide range of evolved host-microbial interdependencies, including those observed in the gut. Ciona intestinalis, a filter-feeding basal chordate and classic developmental model that can be experimentally manipulated, is being employed to help define these relationships. Ciona larvae are first exposed internally to microbes upon the initiation of feeding in metamorphosed individuals; however, whether or not these microbes subsequently colonize the gut and whether or not Ciona forms relationships with specific bacteria in the gut remains unknown. In this report, we show that the Ciona gut not only is colonized by a complex community of bacteria, but also that samples from three geographically isolated populations reveal striking similarity in abundant operational taxonomic units (OTUs) consistent with the selection of a core community by the gut ecosystem.
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Tout J, Jeffries TC, Webster NS, Stocker R, Ralph PJ, Seymour JR. Variability in microbial community composition and function between different niches within a coral reef. MICROBIAL ECOLOGY 2014; 67:540-552. [PMID: 24477921 DOI: 10.1007/s00248-013-0362-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 12/26/2013] [Indexed: 06/03/2023]
Abstract
To explore how microbial community composition and function varies within a coral reef ecosystem, we performed metagenomic sequencing of seawater from four niches across Heron Island Reef, within the Great Barrier Reef. Metagenomes were sequenced from seawater samples associated with (1) the surface of the coral species Acropora palifera, (2) the surface of the coral species Acropora aspera, (3) the sandy substrate within the reef lagoon and (4) open water, outside of the reef crest. Microbial composition and metabolic function differed substantially between the four niches. The taxonomic profile showed a clear shift from an oligotroph-dominated community (e.g. SAR11, Prochlorococcus, Synechococcus) in the open water and sandy substrate niches, to a community characterised by an increased frequency of copiotrophic bacteria (e.g. Vibrio, Pseudoalteromonas, Alteromonas) in the coral seawater niches. The metabolic potential of the four microbial assemblages also displayed significant differences, with the open water and sandy substrate niches dominated by genes associated with core house-keeping processes such as amino acid, carbohydrate and protein metabolism as well as DNA and RNA synthesis and metabolism. In contrast, the coral surface seawater metagenomes had an enhanced frequency of genes associated with dynamic processes including motility and chemotaxis, regulation and cell signalling. These findings demonstrate that the composition and function of microbial communities are highly variable between niches within coral reef ecosystems and that coral reefs host heterogeneous microbial communities that are likely shaped by habitat structure, presence of animal hosts and local biogeochemical conditions.
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Affiliation(s)
- Jessica Tout
- Plant Functional Biology and Climate Change Cluster, University of Technology, Sydney, NSW, Australia,
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53
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Affiliation(s)
- Keith Clay
- Department of Biology; Indiana University; Bloomington IN USA
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54
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Frydenborg BR, Krediet CJ, Teplitski M, Ritchie KB. Temperature-dependent inhibition of opportunistic Vibrio pathogens by native coral commensal bacteria. MICROBIAL ECOLOGY 2014; 67:392-401. [PMID: 24370863 DOI: 10.1007/s00248-013-0334-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 11/18/2013] [Indexed: 06/03/2023]
Abstract
Bacteria living within the surface mucus layer of corals compete for nutrients and space. A number of stresses affect the outcome of this competition. The interactions between native microorganisms and opportunistic pathogens largely determine the coral holobiont's overall health and fitness. In this study, we tested the hypothesis that commensal bacteria isolated from the mucus layer of a healthy elkhorn coral, Acropora palmata, are capable of inhibition of opportunistic pathogens, Vibrio shiloi AK1 and Vibrio coralliilyticus. These vibrios are known to cause disease in corals and their virulence is temperature dependent. Elevated temperature (30 °C) increased the cell numbers of one commensal and both Vibrio pathogens in monocultures. We further tested the hypothesis that elevated temperature favors pathogenic organisms by simultaneously increasing the fitness of vibrios and decreasing the fitness of commensals by measuring growth of each species within a co-culture over the course of 1 week. In competition experiments between vibrios and commensals, the proportion of Vibrio spp. increased significantly under elevated temperature. We finished by investigating several temperature-dependent mechanisms that could influence co-culture differences via changes in competitive fitness. The ability of Vibrio spp. to utilize glycoproteins found in A. palmata mucus increased or remained stable when exposed to elevated temperature, while commensals' tended to decrease utilization. In both vibrios and commensals, protease activity increased at 30 °C, while chiA expression increased under elevated temperatures for Vibrio spp. These results provide insight into potential mechanisms through which elevated temperature may select for pathogenic bacterial dominance and lead to disease or a decrease in coral fitness.
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Affiliation(s)
- Beck R Frydenborg
- Microbiology and Cell Science Department, University of Florida-IFAS, Gainesville, FL, 32611, USA
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55
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Boutin S, Audet C, Derome N. Probiotic treatment by indigenous bacteria decreases mortality without disturbing the natural microbiota of Salvelinus fontinalis. Can J Microbiol 2013; 59:662-70. [PMID: 24102219 DOI: 10.1139/cjm-2013-0443] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Next-generation sequencing is revealing the complex interactive networks of host-bacteria interactions, as it is now possible to screen in detail the microbiota harbored by a host. This study investigated the influence of a probiotic treatment on the survival and microbiota of brook charr (Salvelinus fontinalis), focusing on its disturbance of the natural microbiota (dysbiosis). The results indicated that an indigenous probiotic strain (identified as Rhodococcus sp.) colonized neither the fish skin mucus nor the water following the probiotic treatment. Instead, the probiotic strain was detected only in the biofilm of the test tank. Nevertheless, a substantial beneficial effect of the probiotic treatment was observed: the population of the pathogen Flavobacterium psychrophilum decreased in the treated tank water. This study clearly shows that the indigenous strain chosen for the probiotic treatment did not disturb the natural fish skin mucus microbiota but acted directly through the production system to control the growth of the pathogen and, as a consequence, to enhance fish survival.
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Affiliation(s)
- Sébastien Boutin
- a Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, 1030 Avenue de la Médecine, Québec, QC G1V 0A6, Canada
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56
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16SrDNA Pyrosequencing of the Mediterranean Gorgonian Paramuricea clavata Reveals a Link among Alterations in Bacterial Holobiont Members, Anthropogenic Influence and Disease Outbreaks. PLoS One 2013; 8:e67745. [PMID: 23840768 PMCID: PMC3694090 DOI: 10.1371/journal.pone.0067745] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 05/21/2013] [Indexed: 01/11/2023] Open
Abstract
Mass mortality events of benthic invertebrates in the Mediterranean Sea are becoming an increasing concern with catastrophic effects on the coastal marine environment. Sea surface temperature anomalies leading to physiological stress, starvation and microbial infections were identified as major factors triggering animal mortality. However the highest occurrence of mortality episodes in particular geographic areas and occasionally in low temperature deep environments suggest that other factors play a role as well. We conducted a comparative analysis of bacterial communities associated with the purple gorgonian Paramuricea clavata, one of the most affected species, collected at different geographic locations and depth, showing contrasting levels of anthropogenic disturbance and health status. Using massive parallel 16SrDNA gene pyrosequencing we showed that the bacterial community associated with healthy P. clavata in pristine locations was dominated by a single genus Endozoicomonas within the order Oceanospirillales which represented ∼90% of the overall bacterial community. P. clavata samples collected in human impacted areas and during disease events had higher bacterial diversity and abundance of disease-related bacteria, such as vibrios, than samples collected in pristine locations whilst showed a reduced dominance of Endozoicomonas spp. In contrast, bacterial symbionts exhibited remarkable stability in P. clavata collected both at euphotic and mesophotic depths in pristine locations suggesting that fluctuations in environmental parameters such as temperature have limited effect in structuring the bacterial holobiont. Interestingly the coral pathogen Vibrio coralliilyticus was not found on diseased corals collected during a deep mortality episode suggesting that neither temperature anomalies nor recognized microbial pathogens are solely sufficient to explain for the events. Overall our data suggest that anthropogenic influence may play a significant role in determining the coral health status by affecting the composition of the associated microbial community. Environmental stressful events and microbial infections may thus be superimposed to compromise immunity and trigger mortality outbreaks.
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57
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Kimes NE, Johnson WR, Torralba M, Nelson KE, Weil E, Morris PJ. The Montastraea faveolata microbiome: ecological and temporal influences on a Caribbean reef-building coral in decline. Environ Microbiol 2013; 15:2082-94. [PMID: 23750924 DOI: 10.1111/1462-2920.12130] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Accepted: 02/18/2013] [Indexed: 11/27/2022]
Abstract
Coral-associated microbial communities, including protists, bacteria, archaea and viruses, are important components of the coral holobiont that influence the health of corals and coral reef ecosystems. Evidence suggests that the composition of these microbial communities is affected by numerous parameters; however, little is known about the confluence of these ecological and temporal effects. In this study, we used ribosomal RNA gene sequencing to identify the zooxanthellae, bacteria and archaea associated with healthy and yellow band diseased (YBD) colonies in the Media Luna reef of La Parguera, Puerto Rico, in order to examine the influence of YBD on the Montastraea faveolata microbiome. In addition, we evaluated the influence of season on the differences between healthy and YBD M. faveolata microbiomes by sampling from the same tagged colonies in both March and September of 2007. To the best of our knowledge, this is the first coral microbiome study to examine sequences from the zooxanthellar, bacterial and archaeal communities simultaneously from individual coral samples. Our results confirm differences in the M. faveolata zooxanthellar, bacterial and archaeal communities between healthy and YBD colonies in March; however, the September communities do not exhibit the same differences. Moreover, we provide evidence that the differences in the M. faveolata microbiomes between March and September are more significant than those observed between healthy and YBD. This data suggest that the entire coral microbiome, not just the bacterial community, is a dynamic environment where both disease and season play important roles.
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Affiliation(s)
- Nikole E Kimes
- Belle W. Baruch Institute for Marine and Coastal Sciences, University of South Carolina, Georgetown, SC 29442, USA
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58
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Krediet CJ, Ritchie KB, Paul VJ, Teplitski M. Coral-associated micro-organisms and their roles in promoting coral health and thwarting diseases. Proc Biol Sci 2013; 280:20122328. [PMID: 23363627 DOI: 10.1098/rspb.2012.2328] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Over the last decade, significant advances have been made in characterization of the coral microbiota. Shifts in its composition often correlate with the appearance of signs of diseases and/or bleaching, thus suggesting a link between microbes, coral health and stability of reef ecosystems. The understanding of interactions in coral-associated microbiota is informed by the on-going characterization of other microbiomes, which suggest that metabolic pathways and functional capabilities define the 'core' microbiota more accurately than the taxonomic diversity of its members. Consistent with this hypothesis, there does not appear to be a consensus on the specificity in the interactions of corals with microbial commensals, even though recent studies report potentially beneficial functions of the coral-associated bacteria. They cycle sulphur, fix nitrogen, produce antimicrobial compounds, inhibit cell-to-cell signalling and disrupt virulence in opportunistic pathogens. While their beneficial functions have been documented, it is not certain whether or how these microbes are selected by the hosts. Therefore, understanding the role of innate immunity, signal and nutrient exchange in the establishment of coral microbiota and in controlling its functions will probably reveal ancient, evolutionarily conserved mechanisms that dictate the outcomes of host-microbial interactions, and impact the resilience of the host.
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Affiliation(s)
- Cory J Krediet
- Interdisciplinary Ecology, University of Florida-IFAS, Gainesville, FL 32610, USA
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59
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Bacterial colonization of Hydra hatchlings follows a robust temporal pattern. ISME JOURNAL 2013; 7:781-90. [PMID: 23344242 DOI: 10.1038/ismej.2012.156] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Animals are colonized by complex bacterial communities. The processes controlling community membership and influencing the establishment of the microbial ecosystem during development are poorly understood. Here we aimed to explore the assembly of bacterial communities in Hydra with the broader goal of elucidating the general rules that determine the temporal progression of bacterial colonization of animal epithelia. We profiled the microbial communities in polyps at various time points after hatching in four replicates. The composition and temporal patterns of the bacterial communities were strikingly similar in all replicates. Distinct features included high diversity of community profiles in the first week, a remarkable but transient adult-like profile 2 weeks after hatching, followed by progressive emergence of a stable adult-like pattern characterized by low species diversity and the preponderance of the Betaproteobacterium Curvibacter. Intriguingly, this process displayed important parallels to the assembly of human fecal communities after birth. In addition, a mathematical modeling approach was used to uncover the organizational principles of this colonization process, suggesting that both, local environmental or host-derived factor(s) modulating the colonization rate, as well as frequency-dependent interactions of individual bacterial community members are important aspects in the emergence of a stable bacterial community at the end of development.
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60
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Fan L, Liu M, Simister R, Webster NS, Thomas T. Marine microbial symbiosis heats up: the phylogenetic and functional response of a sponge holobiont to thermal stress. ISME JOURNAL 2013; 7:991-1002. [PMID: 23283017 DOI: 10.1038/ismej.2012.165] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Large-scale mortality of marine invertebrates is a major global concern for ocean ecosystems and many sessile, reef-building animals, such as sponges and corals, are experiencing significant declines through temperature-induced disease and bleaching. The health and survival of marine invertebrates is often dependent on intimate symbiotic associations with complex microbial communities, yet we have a very limited understanding of the detailed biology and ecology of both the host and the symbiont community in response to environmental stressors, such as elevated seawater temperatures. Here, we use the ecologically important sponge Rhopaloeides odorabile as a model to explore the changes in symbiosis during the development of temperature-induced necrosis. Expression profiling of the sponge host was examined in conjunction with the phylogenetic and functional structure and the expression profile of the symbiont community. Elevated temperature causes an immediate stress response in both the host and symbiont community, including reduced expression of functions that mediate their partnership. Disruption to nutritional interdependence and molecular interactions during early heat stress further destabilizes the holobiont, ultimately leading to the loss of archetypal sponge symbionts and the introduction of new microorganisms that have functional and expression profiles consistent with a scavenging lifestyle, a lack virulence functions and a high growth rate. Previous models have postulated various mechanisms of mortality and disease in marine invertebrates. Our study suggests that interruption of symbiotic interactions is a major determinant for mortality in marine sessile invertebrates. High symbiont specialization and low functional redundancy, thus make these holobionts extremely vulnerable to environmental perturbations, including climate change.
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Affiliation(s)
- Lu Fan
- Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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61
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Golberg K, Pavlov V, Marks RS, Kushmaro A. Coral-associated bacteria, quorum sensing disrupters, and the regulation of biofouling. BIOFOULING 2013; 29:669-82. [PMID: 23777289 DOI: 10.1080/08927014.2013.796939] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Marine biofouling, the settlement of microorganisms and macroorganisms on structures submerged in seawater, although economically detrimental, is a successful strategy for survival in hostile environments, where coordinated bacterial communities establish biofilms via the regulation of quorum sensing (QS) communication systems. The inhibition of QS activity among bacteria isolated from different coral species was investigated to gain further insight into its potency in the attenuation, or even the prevention, of undesirable biofouling on marine organisms. It is hypothesized that coral mucus/microorganism interactions are competitive, suggesting that the dominant communities secrete QS disruptive compounds. One hundred and twenty bacterial isolates were collected from healthy coral species and screened for their ability to inhibit QS using three bioreporter strains. Approximately 12, 11, and 24% of the isolates exhibited anti-QS activity against Escherichia coli pSB1075, Chromobacterium violaceum CV026, and Agrobacterium tumefaciens KYC55 indicator strains, respectively. Isolates with positive activity against the bioluminescent monitor strains were scanned via a cytotoxic/genotoxic, E. coli TV1061 and DPD2794 antimicrobial panel. Isolates detected by C. violaceum CV026 and A. tumefaciens KYC55 reporter strains were tested for their ability to inhibit the growth of these reporter strains, which were found to be unaffected. Tests of the Favia sp. coral isolate Fav 2-50-7 (>98% similarity to Vibrio harveyi) for its ability to attenuate the formation of biofilm showed extensive inhibitory activity against biofilms of Pseudomonas aeruginosa and Acinetobacter baumannii. To ascertain the stability and general structure of the active compound, cell-free culture supernatants exposed to an increasing temperature gradient or to digestion by proteinase K, were shown to maintain potent QS attenuation and the ability to inhibit the growth of biofilms. Mass spectrometry confirmed the presence of a low molecular mass compound. The anti-QS strategy exemplified in the coral mucus is a model with potentially wide applications, including countering the ecological threat posed by biofilms. Manipulating synchronized bacterial behavior by detecting new QS inhibitors will facilitate the discovery of new antifouling compounds.
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Affiliation(s)
- Karina Golberg
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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62
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Lins-de-Barros MM, Cardoso AM, Silveira CB, Lima JL, Clementino MM, Martins OB, Albano RM, Vieira RP. Microbial community compositional shifts in bleached colonies of the Brazilian reef-building coral Siderastrea stellata. MICROBIAL ECOLOGY 2013; 65:205-213. [PMID: 22864853 DOI: 10.1007/s00248-012-0095-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2012] [Accepted: 07/16/2012] [Indexed: 06/01/2023]
Abstract
The association of metazoan, protist, and microbial communities with Scleractinian corals forms the basis of the coral holobiont. Coral bleaching events have been occurring around the world, introducing changes in the delicate balance of the holobiont symbiotic interactions. In this study, Archaea, bacteria, and eukaryotic phototrophic plastids of bleached colonies of the Brazilian coral Siderastrea stellata were analyzed for the first time, using 16S rRNA gene libraries. Prokaryotic communities were slightly more diverse in healthy than in bleached corals. However, the eukaryotic phototrophic plastids community was more diverse in bleached corals. Archaea phylogenetic analyses revealed a high percentage of Crenarchaeota sequences, mainly related to Nitrosopumilus maritimus and Cenarchaeum symbiosum. Dramatic changes in bacterial community composition were observed in this bleaching episode. The dominant bacterial group was Alphaproteobacteria followed by Gammaproteobacteria in bleached and Betaproteobacteria in healthy samples. Plastid operational taxonomic units (OTUs) from both coral samples were mainly related to red algae chloroplasts (Florideophycea), but we also observed some OTUs related to green algae chloroplasts (Chlorophyta). There seems to be a strong relationship between the Bacillariophyta phylum and our bleached coral samples as clones related to members of the diatom genera Amphora and Nitzschia were detected. The present study reveals information from a poorly investigated coral species and improves the knowledge of coral microbial community shifts that could occur during bleaching episodes.
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Affiliation(s)
- Monica M Lins-de-Barros
- Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro (UFRJ), CCS, 21941-590, Rio de Janeiro, Brazil.
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63
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Shade A, Peter H, Allison SD, Baho DL, Berga M, Bürgmann H, Huber DH, Langenheder S, Lennon JT, Martiny JBH, Matulich KL, Schmidt TM, Handelsman J. Fundamentals of microbial community resistance and resilience. Front Microbiol 2012; 3:417. [PMID: 23267351 PMCID: PMC3525951 DOI: 10.3389/fmicb.2012.00417] [Citation(s) in RCA: 770] [Impact Index Per Article: 64.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 11/19/2012] [Indexed: 12/20/2022] Open
Abstract
Microbial communities are at the heart of all ecosystems, and yet microbial community behavior in disturbed environments remains difficult to measure and predict. Understanding the drivers of microbial community stability, including resistance (insensitivity to disturbance) and resilience (the rate of recovery after disturbance) is important for predicting community response to disturbance. Here, we provide an overview of the concepts of stability that are relevant for microbial communities. First, we highlight insights from ecology that are useful for defining and measuring stability. To determine whether general disturbance responses exist for microbial communities, we next examine representative studies from the literature that investigated community responses to press (long-term) and pulse (short-term) disturbances in a variety of habitats. Then we discuss the biological features of individual microorganisms, of microbial populations, and of microbial communities that may govern overall community stability. We conclude with thoughts about the unique insights that systems perspectives – informed by meta-omics data – may provide about microbial community stability.
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Affiliation(s)
- Ashley Shade
- Department of Molecular, Cellular and Developmental Biology, Yale University New Haven, CT, USA
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64
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Scheuring I, Yu DW. How to assemble a beneficial microbiome in three easy steps. Ecol Lett 2012; 15:1300-1307. [PMID: 22913725 PMCID: PMC3507015 DOI: 10.1111/j.1461-0248.2012.01853.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 05/14/2012] [Accepted: 07/24/2012] [Indexed: 12/31/2022]
Abstract
There is great interest in explaining how beneficial microbiomes are assembled. Antibiotic-producing microbiomes are arguably the most abundant class of beneficial microbiome in nature, having been found on corals, arthropods, molluscs, vertebrates and plant rhizospheres. An exemplar is the attine ants, which cultivate a fungus for food and host a cuticular microbiome that releases antibiotics to defend the fungus from parasites. One explanation posits long-term vertical transmission of Pseudonocardia bacteria, which (somehow) evolve new compounds in arms-race fashion against parasites. Alternatively, attines (somehow) selectively recruit multiple, non-coevolved actinobacterial genera from the soil, enabling a 'multi-drug' strategy against parasites. We reconcile the models by showing that when hosts fuel interference competition by providing abundant resources, the interference competition favours the recruitment of antibiotic-producing (and -resistant) bacteria. This partner-choice mechanism is more effective when at least one actinobacterial symbiont is vertically transmitted or has a high immigration rate, as in disease-suppressive soils.
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Affiliation(s)
- István Scheuring
- Research Group in Theoretical Biology and Evolutionary Ecology, Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös University and HAS, Pázmány P. sétány 1/C, H-1117, Budapest, Hungary
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR47TJ, UK
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65
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McDole T, Nulton J, Barott KL, Felts B, Hand C, Hatay M, Lee H, Nadon MO, Nosrat B, Salamon P, Bailey B, Sandin SA, Vargas-Angel B, Youle M, Zgliczynski BJ, Brainard RE, Rohwer F. Assessing coral reefs on a Pacific-wide scale using the microbialization score. PLoS One 2012; 7:e43233. [PMID: 22970122 PMCID: PMC3436891 DOI: 10.1371/journal.pone.0043233] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 07/18/2012] [Indexed: 11/21/2022] Open
Abstract
The majority of the world's coral reefs are in various stages of decline. While a suite of disturbances (overfishing, eutrophication, and global climate change) have been identified, the mechanism(s) of reef system decline remain elusive. Increased microbial and viral loading with higher percentages of opportunistic and specific microbial pathogens have been identified as potentially unifying features of coral reefs in decline. Due to their relative size and high per cell activity, a small change in microbial biomass may signal a large reallocation of available energy in an ecosystem; that is the microbialization of the coral reef. Our hypothesis was that human activities alter the energy budget of the reef system, specifically by altering the allocation of metabolic energy between microbes and macrobes. To determine if this is occurring on a regional scale, we calculated the basal metabolic rates for the fish and microbial communities at 99 sites on twenty-nine coral islands throughout the Pacific Ocean using previously established scaling relationships. From these metabolic rate predictions, we derived a new metric for assessing and comparing reef health called the microbialization score. The microbialization score represents the percentage of the combined fish and microbial predicted metabolic rate that is microbial. Our results demonstrate a strong positive correlation between reef microbialization scores and human impact. In contrast, microbialization scores did not significantly correlate with ocean net primary production, local chla concentrations, or the combined metabolic rate of the fish and microbial communities. These findings support the hypothesis that human activities are shifting energy to the microbes, at the expense of the macrobes. Regardless of oceanographic context, the microbialization score is a powerful metric for assessing the level of human impact a reef system is experiencing.
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Affiliation(s)
- Tracey McDole
- Biology Department, San Diego State University, San Diego, California, United States of America.
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66
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Barott KL, Rohwer FL. Unseen players shape benthic competition on coral reefs. Trends Microbiol 2012; 20:621-8. [PMID: 22944243 DOI: 10.1016/j.tim.2012.08.004] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 08/08/2012] [Accepted: 08/09/2012] [Indexed: 01/05/2023]
Abstract
Recent work has shown that hydrophilic and hydrophobic organic matter (OM) from algae disrupts the function of the coral holobiont and promotes the invasion of opportunistic pathogens, leading to coral morbidity and mortality. Here we refer to these dynamics as the (3)DAM [dissolved organic matter (DOM), direct contact, disease, algae and microbes] model. There is considerable complexity in coral-algae interactions; turf algae and macroalgae promote heterotrophic microbial overgrowth of coral, macroalgae also directly harm the corals via hydrophobic OM, whereas crustose coralline algae generally encourage benign microbial communities. In addition, complex flow patterns transport OM and pathogens from algae to downstream corals, and direct algal contact enhances their delivery. These invisible players (microbes, viruses, and OM) are important drivers of coral reefs because they have non-linear responses to disturbances and are the first to change in response to perturbations, providing near real-time trajectories for a coral reef, a vital metric for conservation and restoration.
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Affiliation(s)
- Katie L Barott
- Department of Biology, San Diego State University, San Diego, CA 92182, USA.
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67
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Sharp KH, Ritchie KB. Multi-partner interactions in corals in the face of climate change. THE BIOLOGICAL BULLETIN 2012; 223:66-77. [PMID: 22983033 DOI: 10.1086/bblv223n1p66] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Recent research has explored the possibility that increased sea-surface temperatures and decreasing pH (ocean acidification) contribute to the ongoing decline of coral reef ecosystems. Within corals, a diverse microbiome exerts significant influence on biogeochemical and ecological processes, including food webs, organismal life cycles, and chemical and nutrient cycling. Microbes on coral reefs play a critical role in regulating larval recruitment, bacterial colonization, and pathogen abundance under ambient conditions, ultimately governing the overall resilience of coral reef systems. As a result, microbial processes may be involved in reef ecosystem-level responses to climate change. Developments of new molecular technologies, in addition to multidisciplinary collaborative research on coral reefs, have led to the rapid advancement in our understanding of bacterially mediated reef responses to environmental change. Here we review new discoveries regarding (1) the onset of coral-bacterial associations; (2) the functional roles that bacteria play in healthy corals; and (3) how bacteria influence coral reef response to environmental change, leading to a model describing how reef microbiota direct ecosystem-level response to a changing global climate.
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Affiliation(s)
- Koty H Sharp
- Eckerd College, 4200 54th Avenue South, St. Petersburg, Florida 33711, USA.
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Abrolhos bank reef health evaluated by means of water quality, microbial diversity, benthic cover, and fish biomass data. PLoS One 2012; 7:e36687. [PMID: 22679480 PMCID: PMC3367994 DOI: 10.1371/journal.pone.0036687] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 04/04/2012] [Indexed: 12/31/2022] Open
Abstract
The health of the coral reefs of the Abrolhos Bank (southwestern Atlantic) was characterized with a holistic approach using measurements of four ecosystem components: (i) inorganic and organic nutrient concentrations, [1] fish biomass, [1] macroalgal and coral cover and (iv) microbial community composition and abundance. The possible benefits of protection from fishing were particularly evaluated by comparing sites with varying levels of protection. Two reefs within the well-enforced no-take area of the National Marine Park of Abrolhos (Parcel dos Abrolhos and California) were compared with two unprotected coastal reefs (Sebastião Gomes and Pedra de Leste) and one legally protected but poorly enforced coastal reef (the “paper park” of Timbebas Reef). The fish biomass was lower and the fleshy macroalgal cover was higher in the unprotected reefs compared with the protected areas. The unprotected and protected reefs had similar seawater chemistry. Lower vibrio CFU counts were observed in the fully protected area of California Reef. Metagenome analysis showed that the unprotected reefs had a higher abundance of archaeal and viral sequences and more bacterial pathogens, while the protected reefs had a higher abundance of genes related to photosynthesis. Similar to other reef systems in the world, there was evidence that reductions in the biomass of herbivorous fishes and the consequent increase in macroalgal cover in the Abrolhos Bank may be affecting microbial diversity and abundance. Through the integration of different types of ecological data, the present study showed that protection from fishing may lead to greater reef health. The data presented herein suggest that protected coral reefs have higher microbial diversity, with the most degraded reef (Sebastião Gomes) showing a marked reduction in microbial species richness. It is concluded that ecological conditions in unprotected reefs may promote the growth and rapid evolution of opportunistic microbial pathogens.
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Bucci V, Bradde S, Biroli G, Xavier JB. Social interaction, noise and antibiotic-mediated switches in the intestinal microbiota. PLoS Comput Biol 2012; 8:e1002497. [PMID: 22577356 PMCID: PMC3343147 DOI: 10.1371/journal.pcbi.1002497] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 03/12/2012] [Indexed: 11/19/2022] Open
Abstract
The intestinal microbiota plays important roles in digestion and resistance against entero-pathogens. As with other ecosystems, its species composition is resilient against small disturbances but strong perturbations such as antibiotics can affect the consortium dramatically. Antibiotic cessation does not necessarily restore pre-treatment conditions and disturbed microbiota are often susceptible to pathogen invasion. Here we propose a mathematical model to explain how antibiotic-mediated switches in the microbiota composition can result from simple social interactions between antibiotic-tolerant and antibiotic-sensitive bacterial groups. We build a two-species (e.g. two functional-groups) model and identify regions of domination by antibiotic-sensitive or antibiotic-tolerant bacteria, as well as a region of multistability where domination by either group is possible. Using a new framework that we derived from statistical physics, we calculate the duration of each microbiota composition state. This is shown to depend on the balance between random fluctuations in the bacterial densities and the strength of microbial interactions. The singular value decomposition of recent metagenomic data confirms our assumption of grouping microbes as antibiotic-tolerant or antibiotic-sensitive in response to a single antibiotic. Our methodology can be extended to multiple bacterial groups and thus it provides an ecological formalism to help interpret the present surge in microbiome data.
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Affiliation(s)
- Vanni Bucci
- Program in Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
- * E-mail: (VB); (SB); (JBX)
| | - Serena Bradde
- Program in Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
- * E-mail: (VB); (SB); (JBX)
| | - Giulio Biroli
- Institut Physique Théorique (IPhT) CEA Saclay, and CNRS URA, Gif Sur Yvette, France
| | - Joao B. Xavier
- Program in Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
- * E-mail: (VB); (SB); (JBX)
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70
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Bruce T, de Castro A, Kruger R, Thompson CC, Thompson FL. Microbial Diversity of Brazilian Biomes. ADVANCES IN MICROBIAL ECOLOGY 2012. [DOI: 10.1007/978-1-4614-2182-5_13] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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71
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Abstract
Microbial processes largely control the health and resilience of coral reef ecosystems, and new technologies have led to an exciting wave of discovery regarding the mechanisms by which microbial communities support the functioning of these incredibly diverse and valuable systems. There are three questions at the forefront of discovery: What mechanisms underlie coral reef health and resilience? How do environmental and anthropogenic pressures affect ecosystem function? What is the ecology of microbial diseases of corals? The goal is to understand the functioning of coral reefs as integrated systems from microbes and molecules to regional and ocean-basin scale ecosystems to enable accurate predictions of resilience and responses to perturbations such as climate change and eutrophication. This review outlines recent discoveries regarding the microbial ecology of different microenvironments within coral ecosystems, and highlights research directions that take advantage of new technologies to build a quantitative and mechanistic understanding of how coral health is connected through microbial processes to its surrounding environment. The time is ripe for natural resource managers and microbial ecologists to work together to create an integrated understanding of coral reef functioning. In the context of long-term survival and conservation of reefs, the need for this work is immediate.
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Affiliation(s)
- Melissa Garren
- Scripps Institution of Oceanography, Marine Biology Research Division, La Jolla, CA 92037, USA.
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72
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Galiana E, Marais A, Mura C, Industri B, Arbiol G, Ponchet M. Ecosystem screening approach for pathogen-associated microorganisms affecting host disease. Appl Environ Microbiol 2011; 77:6069-75. [PMID: 21742919 PMCID: PMC3165409 DOI: 10.1128/aem.05371-11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 06/28/2011] [Indexed: 12/25/2022] Open
Abstract
The microbial community in which a pathogen evolves is fundamental to disease outcome. Species interacting with a pathogen on the host surface shape the distribution, density, and genetic diversity of the inoculum, but the role of these species is rarely determined. The screening method developed here can be used to characterize pathogen-associated species affecting disease. This strategy involves three steps: (i) constitution of the microbial community, using the pathogen as a trap; (ii) community selection, using extracts from the pathogen as the sole nutrient source; and (iii) molecular identification and the screening of isolates focusing on their effects on the growth of the pathogen in vitro and host disease. This approach was applied to a soilborne plant pathogen, Phytophthora parasitica, structured in a biofilm, for screening the microbial community from the rhizosphere of Nicotiana tabacum (the host). Two of the characterized eukaryotes interfered with the oomycete cycle and may affect the host disease. A Vorticella species acted through a mutualistic interaction with P. parasitica, disseminating pathogenic material by leaving the biofilm. A Phoma species established an amensal interaction with P. parasitica, strongly suppressing disease by inhibiting P. parasitica germination. This screening method is appropriate for all nonobligate pathogens. It allows the definition of microbial species as promoters or suppressors of a disease for a given biotope. It should also help to identify important microbial relationships for ecology and evolution of pathogens.
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Affiliation(s)
- Eric Galiana
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1301 Interactions Biotiques et Santé Végétale, F-06903 Sophia Antipolis, France.
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73
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Bosch TCG, McFall-Ngai MJ. Metaorganisms as the new frontier. ZOOLOGY 2011; 114:185-90. [PMID: 21737250 DOI: 10.1016/j.zool.2011.04.001] [Citation(s) in RCA: 227] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2010] [Revised: 04/03/2011] [Accepted: 04/08/2011] [Indexed: 11/29/2022]
Abstract
Because it appears that almost all organisms are part of an interdependent metaorganism, an understanding of the underlying host-microbe species associations, and of evolution and molecular underpinnings, has become the new frontier in zoology. The availability of novel high-throughput sequencing methods, together with the conceptual understanding that advances mostly originate at the intersection of traditional disciplinary boundaries, enable biologists to dissect the mechanisms that control the interdependent associations of species. In this review article, we outline some of the issues in inter-species interactions, present two case studies illuminating the necessity of interfacial research when addressing complex and fundamental zoological problems, and show that an interdisciplinary approach that seeks to understand co-evolved multi-species relationships will connect genomes, phenotypes, ecosystems and the evolutionary forces that have shaped them. We hope that this article inspires other collaborations of a similar nature on the diverse landscape commonly referred to as "zoology".
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Affiliation(s)
- Thomas C G Bosch
- Zoological Institute, Christian-Albrechts-University Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany.
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74
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Galkiewicz JP, Pratte ZA, Gray MA, Kellogg CA. Characterization of culturable bacteria isolated from the cold-water coral Lophelia pertusa. FEMS Microbiol Ecol 2011; 77:333-46. [DOI: 10.1111/j.1574-6941.2011.01115.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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Coddeville B, Maes E, Ferrier-Pagès C, Guerardel Y. Glycan Profiling of Gel Forming Mucus Layer from the Scleractinian Symbiotic Coral Oculina arbuscula. Biomacromolecules 2011; 12:2064-73. [DOI: 10.1021/bm101557v] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Bernadette Coddeville
- Université de Lille1, Unité de Glycobiologie Structurale et Fonctionnelle, UGSF, F-59650 Villeneuve d'Ascq, France
- CNRS, UMR 8576, F-59650 Villeneuve d'Ascq, France
| | - Emmanuel Maes
- Université de Lille1, Unité de Glycobiologie Structurale et Fonctionnelle, UGSF, F-59650 Villeneuve d'Ascq, France
- CNRS, UMR 8576, F-59650 Villeneuve d'Ascq, France
| | - Christine Ferrier-Pagès
- Centre Scientifique de Monaco, c/o Musée Océanographique, Avenue Saint Martin, MC-98000 Monaco
| | - Yann Guerardel
- Université de Lille1, Unité de Glycobiologie Structurale et Fonctionnelle, UGSF, F-59650 Villeneuve d'Ascq, France
- CNRS, UMR 8576, F-59650 Villeneuve d'Ascq, France
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Alagely A, Krediet CJ, Ritchie KB, Teplitski M. Signaling-mediated cross-talk modulates swarming and biofilm formation in a coral pathogen Serratia marcescens. ISME JOURNAL 2011; 5:1609-20. [PMID: 21509042 DOI: 10.1038/ismej.2011.45] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Interactions within microbial communities associated with marine holobionts contribute importantly to the health of these symbiotic organisms formed by invertebrates, dinoflagellates and bacteria. However, mechanisms that control invertebrate-associated microbiota are not yet fully understood. Hydrophobic compounds that were isolated from surfaces of asymptomatic corals inhibited biofilm formation by the white pox pathogen Serratia marcescens PDL100, indicating that signals capable of affecting the associated microbiota are produced in situ. However, neither the origin nor structures of these signals are currently known. A functional survey of bacteria recovered from coral mucus and from cultures of the dinoflagellate Symbiodinium spp. revealed that they could alter swarming and biofilm formation in S. marcescens. As swarming and biofilm formation are inversely regulated, the ability of some native α-proteobacteria to affect both behaviors suggests that the α-proteobacterial signal(s) target a global regulatory switch controlling the behaviors in the pathogen. Isolates of Marinobacter sp. inhibited both biofilm formation and swarming in S. marcescens PDL100, without affecting growth of the coral pathogen, indicative of the production of multiple inhibitors, likely targeting lower level regulatory genes or functions. A multi-species cocktail containing these strains inhibited progression of a disease caused by S. marcescens in a model polyp Aiptasia pallida. An α-proteobacterial isolate 44B9 had a similar effect. Even though ∼4% of native holobiont-associated bacteria produced compounds capable of triggering responses in well-characterized N-acyl homoserine lactone (AHL) biosensors, there was no strong correlation between the production of AHL-like signals and disruption of biofilms or swarming in S. marcescens.
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Affiliation(s)
- Ali Alagely
- Soil and Water Science Department, University of Florida, Institute of Food and Agricultural Sciences, Gainesville, FL 32610, USA
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77
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Angermeier H, Kamke J, Abdelmohsen UR, Krohne G, Pawlik JR, Lindquist NL, Hentschel U. The pathology of sponge orange band disease affecting the Caribbean barrel sponge Xestospongia muta. FEMS Microbiol Ecol 2010; 75:218-30. [PMID: 21118276 DOI: 10.1111/j.1574-6941.2010.01001.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The aim of this study was to examine sponge orange band (SOB) disease affecting the prominent Caribbean sponge Xestospongia muta. Scanning and transmission electron microscopy revealed that SOB is accompanied by the massive destruction of the pinacoderm. Chlorophyll a content and the main secondary metabolites, tetrahydrofurans, characteristic of X. muta, were significantly lower in bleached than in healthy tissues. Denaturing gradient gel electrophoresis using cyanobacteria-specific 16S rRNA gene primers revealed a distinct shift from the Synechococcus/Prochlorococcus clade of sponge symbionts towards several clades of unspecific cyanobacteria, including lineages associated with coral disease (i.e. Leptolyngbya sp.). Underwater infection experiments were conducted by transplanting bleached cores into healthy individuals, but revealed no signs of SOB development. This study provided no evidence for the involvement of a specific microbial pathogen as an etiologic agent of disease; hence, the cause of SOB disease in X. muta remains unidentified.
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Affiliation(s)
- Hilde Angermeier
- Julius-von-Sachs-Institute for Biological Sciences, University of Wuerzburg, Wuerzburg, Germany
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Heron SF, Willis BL, Skirving WJ, Eakin CM, Page CA, Miller IR. Summer hot snaps and winter conditions: modelling white syndrome outbreaks on Great Barrier Reef corals. PLoS One 2010; 5:e12210. [PMID: 20808912 PMCID: PMC2923161 DOI: 10.1371/journal.pone.0012210] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 07/08/2010] [Indexed: 12/03/2022] Open
Abstract
Coral reefs are under increasing pressure in a changing climate, one such threat being more frequent and destructive outbreaks of coral diseases. Thermal stress from rising temperatures has been implicated as a causal factor in disease outbreaks observed on the Great Barrier Reef, Australia, and elsewhere in the world. Here, we examine seasonal effects of satellite-derived temperature on the abundance of coral diseases known as white syndromes on the Great Barrier Reef, considering both warm stress during summer and deviations from mean temperatures during the preceding winter. We found a high correlation (r2 = 0.953) between summer warm thermal anomalies (Hot Snap) and disease abundance during outbreak events. Inclusion of thermal conditions during the preceding winter revealed that a significant reduction in disease outbreaks occurred following especially cold winters (Cold Snap), potentially related to a reduction in pathogen loading. Furthermore, mild winters (i.e., neither excessively cool nor warm) frequently preceded disease outbreaks. In contrast, disease outbreaks did not typically occur following warm winters, potentially because of increased disease resistance of the coral host. Understanding the balance between the effects of warm and cold winters on disease outbreak will be important in a warming climate. Combining the influence of winter and summer thermal effects resulted in an algorithm that yields both a Seasonal Outlook of disease risk at the conclusion of winter and near real-time monitoring of Outbreak Risk during summer. This satellite-derived system can provide coral reef managers with an assessment of risk three-to-six months in advance of the summer season that can then be refined using near-real-time summer observations. This system can enhance the capacity of managers to prepare for and respond to possible disease outbreaks and focus research efforts to increase understanding of environmental impacts on coral disease in this era of rapidly changing climate.
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Affiliation(s)
- Scott F Heron
- Coral Reef Watch, National Oceanic and Atmospheric Administration, Townsville, Queensland, Australia.
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