ORCID Profile
0000-0003-1548-5429
Current Organisation
San Diego State University
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Marine and Estuarine Ecology (incl. Marine Ichthyology) | Gene Expression (incl. Microarray and other genome-wide approaches) | Microbial Ecology | Comparative Physiology | Ecological Impacts of Climate Change | Physical Chemistry not elsewhere classified | Ecological Applications | Microbiology | Biological Adaptation | Global Change Biology
ANZSRC Socio-Economic Objective (SEO)
Physical and Chemical Conditions of Water in Coastal and Estuarine Environments | Ecosystem Adaptation to Climate Change | Coastal and Estuarine Flora, Fauna and Biodiversity | Climate Variability (excl. Social Impacts) | Control of Animal Pests, Diseases and Exotic Species in Coastal and Estuarine Environments | Marine Flora, Fauna and Biodiversity |
Related Links
Publications
Viral and microbial community dynamics in four aquatic environments
Publisher: Springer Science and Business Media LLC
Date: 11-02-2010
DOI: 10.1038/ISMEJ.2010.1
Abstract: The species composition and metabolic potential of microbial and viral communities are predictable and stable for most ecosystems. This apparent stability contradicts theoretical models as well as the viral-microbial dynamics observed in simple ecosystems, both of which show Kill-the-Winner behavior causing cycling of the dominant taxa. Microbial and viral metagenomes were obtained from four human-controlled aquatic environments at various time points separated by one day to >1 year. These environments were maintained within narrow geochemical bounds and had characteristic species composition and metabolic potentials at all time points. However, underlying this stability were rapid changes at the fine-grained level of viral genotypes and microbial strains. These results suggest a model wherein functionally redundant microbial and viral taxa are cycling at the level of viral genotypes and virus-sensitive microbial strains. Microbial taxa, viral taxa, and metabolic function persist over time in stable ecosystems and both communities fluctuate in a Kill-the-Winner manner at the level of viral genotypes and microbial strains.
Global microbialization of coral reefs
Publisher: Springer Science and Business Media LLC
Date: 25-04-2016
DOI: 10.1038/NMICROBIOL.2016.42
Abstract: Microbialization refers to the observed shift in ecosystem trophic structure towards higher microbial biomass and energy use. On coral reefs, the proximal causes of microbialization are overfishing and eutrophication, both of which facilitate enhanced growth of fleshy algae, conferring a competitive advantage over calcifying corals and coralline algae. The proposed mechanism for this competitive advantage is the DDAM positive feedback loop (dissolved organic carbon (DOC), disease, algae, microorganism), where DOC released by ungrazed fleshy algae supports copiotrophic, potentially pathogenic bacterial communities, ultimately harming corals and maintaining algal competitive dominance. Using an unprecedented data set of >400 s les from 60 coral reef sites, we show that the central DDAM predictions are consistent across three ocean basins. Reef algal cover is positively correlated with lower concentrations of DOC and higher microbial abundances. On turf and fleshy macroalgal-rich reefs, higher relative abundances of copiotrophic microbial taxa were identified. These microbial communities shift their metabolic potential for carbohydrate degradation from the more energy efficient Embden-Meyerhof-Parnas pathway on coral-dominated reefs to the less efficient Entner-Doudoroff and pentose phosphate pathways on algal-dominated reefs. This 'yield-to-power' switch by microorganism directly threatens reefs via increased hypoxia and greater CO2 release from the microbial respiration of DOC.
Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters
Publisher: Proceedings of the National Academy of Sciences
Date: 19-10-2015
Abstract: Bacteriophages (phages) are viruses that infect and kill bacteria. Being inanimate, phages rely on diffusion to search for bacterial prey. Here we demonstrate that a phage that adheres weakly to mucus exhibits subdiffusive motion, not normal diffusion, in mucosal surfaces. Supporting theory and experiments revealed that subdiffusive motion increases bacterial encounter rates for phages when bacterial concentration is low. To the best of our knowledge, no other predator has been shown to effectively use a subdiffusive search mechanism. Mucosal surfaces are vulnerable to infection. Mucus-adherent phages reduce bacterial infection of lifelike mucosal surfaces more effectively than nonadherent phages. These findings provide a basis for engineering adherent phages to manipulate mucosal surface microbiomes for protection from infection and other purposes.
The Phage Proteomic Tree: a Genome-Based Taxonomy for Phage
Publisher: American Society for Microbiology
Date: 15-08-2002
DOI: 10.1128/JB.184.16.4529-4535.2002
Abstract: There are ∼10 31 phage in the biosphere, making them the most abundant biological entities on the planet. Despite their great numbers and ubiquitous presence, very little is known about phage bio ersity, biogeography, or phylogeny. Information is limited, in part, because the current ICTV taxonomical system is based on culturing phage and measuring physical parameters of the free virion. No sequence-based taxonomic systems have previously been established for phage. We present here the “Phage Proteomic Tree,” which is based on the overall similarity of 105 completely sequenced phage genomes. The Phage Proteomic Tree places phage relative to both their near neighbors and all other phage included in the analysis. This method groups phage into taxa that predicts several aspects of phage biology and highlights genetic markers that can be used for monitoring phage bio ersity. We propose that the Phage Proteomic Tree be used as the basis of a genome-based taxonomical system for phage.
Elucidating genomic gaps using phenotypic profiles
Publisher: F1000 Research Ltd
Date: 17-10-2016
DOI: 10.12688/F1000RESEARCH.5140.2
Abstract: Advances in genomic sequencing provide the ability to model the metabolism of organisms from their genome annotation. The bioinformatics tools developed to deduce gene function through homology-based methods are dependent on public databases thus, novel discoveries are not readily extrapolated from current analysis tools with a homology dependence. Multi-phenotype Assay Plates (MAPs) provide a high-throughput method to profile bacterial phenotypes by growing bacteria in various growth conditions, simultaneously. More robust and accurate computational models can be constructed by coupling MAPs with current genomic annotation methods. PMAnalyzer is an online tool that analyzes bacterial growth curves from the MAP system which are then used to optimize metabolic models during in silico growth simulations. Using Citrobacter sedlakii as a prototype, the Rapid Annotation using Subsystem Technology (RAST) tool produced a model consisting of 1,367 enzymatic reactions. After the optimization, 44 reactions were added to, or modified within, the model. The model correctly predicted the outcome on 93% of growth experiments.
A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage
Publisher: Springer Science and Business Media LLC
Date: 23-10-2018
Viral diversity and dynamics in an infant gut
Publisher: Elsevier BV
Date: 06-2008
DOI: 10.1016/J.RESMIC.2008.04.006
Abstract: Metagenomic sequencing of DNA viruses from the feces of a healthy week-old infant revealed a viral community with extremely low ersity. The identifiable sequences were dominated by phages, which likely influence the ersity and abundance of co-occurring microbes. The most abundant fecal viral sequences did not originate from breast milk or formula, suggesting a non-dietary initial source of viruses. Certain sequences were stable in the infant's gut over the first 3 months of life, but microarray experiments demonstrated that the overall viral community composition changed dramatically between 1 and 2 weeks of age.
The Marine Viromes of Four Oceanic Regions
Publisher: Public Library of Science (PLoS)
Date: 07-11-2006
The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes
Publisher: Public Library of Science (PLoS)
Date: 11-12-2009
Correction for Nguyen et al., “Bacteriophage Transcytosis Provides a Mechanism To Cross Epithelial Cell Layers”
Publisher: American Society for Microbiology
Date: 07-03-2018
The Lagoon at Caroline/Millennium Atoll, Republic of Kiribati: Natural History of a Nearly Pristine Ecosystem
Publisher: Public Library of Science (PLoS)
Date: 03-06-2010
Metagenomics and metatranscriptomics: Windows on CF-associated viral and microbial communities
Publisher: Elsevier BV
Date: 03-2013
Effects of Coral Reef Benthic Primary Producers on Dissolved Organic Carbon and Microbial Activity
Publisher: Public Library of Science (PLoS)
Date: 18-11-2011
Variability and host density independence in inductions-based estimates of environmental lysogeny
Publisher: Springer Science and Business Media LLC
Date: 28-04-2017
Innate and acquired bacteriophage-mediated immunity
Publisher: Informa UK Limited
Date: 11-07-2013
DOI: 10.4161/BACT.25857
Functional metagenomic profiling of nine biomes
Publisher: Springer Science and Business Media LLC
Date: 12-03-2008
DOI: 10.1038/NATURE06810
Abstract: Microbial activities shape the biogeochemistry of the planet and macroorganism health. Determining the metabolic processes performed by microbes is important both for understanding and for manipulating ecosystems (for ex le, disruption of key processes that lead to disease, conservation of environmental services, and so on). Describing microbial function is h ered by the inability to culture most microbes and by high levels of genomic plasticity. Metagenomic approaches analyse microbial communities to determine the metabolic processes that are important for growth and survival in any given environment. Here we conduct a metagenomic comparison of almost 15 million sequences from 45 distinct microbiomes and, for the first time, 42 distinct viromes and show that there are strongly discriminatory metabolic profiles across environments. Most of the functional ersity was maintained in all of the communities, but the relative occurrence of metabolisms varied, and the differences between metagenomes predicted the biogeochemical conditions of each environment. The magnitude of the microbial metabolic capabilities encoded by the viromes was extensive, suggesting that they serve as a repository for storing and sharing genes among their microbial hosts and influence global evolutionary and metabolic processes.
Can we measure beauty? Computational evaluation of coral reef aesthetics
Publisher: PeerJ
Date: 10-11-2015
DOI: 10.7717/PEERJ.1390
Abstract: The natural beauty of coral reefs attracts millions of tourists worldwide resulting in substantial revenues for the adjoining economies. Although their visual appearance is a pivotal factor attracting humans to coral reefs current monitoring protocols exclusively target biogeochemical parameters, neglecting changes in their aesthetic appearance. Here we introduce a standardized computational approach to assess coral reef environments based on 109 visual features designed to evaluate the aesthetic appearance of art. The main feature groups include color intensity and ersity of the image, relative size, color, and distribution of discernable objects within the image, and texture. Specific coral reef aesthetic values combining all 109 features were calibrated against an established biogeochemical assessment (NCEAS) using machine learning algorithms. These values were generated for ∼2,100 random photographic images collected from 9 coral reef locations exposed to varying levels of anthropogenic influence across 2 ocean systems. Aesthetic values proved accurate predictors of the NCEAS scores (root mean square error 5 for N ≥ 3) and significantly correlated to microbial abundance at each site. This shows that mathematical approaches designed to assess the aesthetic appearance of photographic images can be used as an inexpensive monitoring tool for coral reef ecosystems. It further suggests that human perception of aesthetics is not purely subjective but influenced by inherent reactions towards measurable visual cues. By quantifying aesthetic features of coral reef systems this method provides a cost efficient monitoring tool that targets one of the most important socioeconomic values of coral reefs directly tied to revenue for its local population.
Grinder: a versatile amplicon and shotgun sequence simulator
Publisher: Oxford University Press (OUP)
Date: 19-03-2012
DOI: 10.1093/NAR/GKS251
Metagenomic analysis of stressed coral holobionts
Publisher: Wiley
Date: 08-2009
DOI: 10.1111/J.1462-2920.2009.01935.X
Abstract: The coral holobiont is the community of metazoans, protists and microbes associated with scleractinian corals. Disruptions in these associations have been correlated with coral disease, but little is known about the series of events involved in the shift from mutualism to pathogenesis. To evaluate structural and functional changes in coral microbial communities, Porites compressa was exposed to four stressors: increased temperature, elevated nutrients, dissolved organic carbon loading and reduced pH. Microbial metagenomic s les were collected and pyrosequenced. Functional gene analysis demonstrated that stressors increased the abundance of microbial genes involved in virulence, stress resistance, sulfur and nitrogen metabolism, motility and chemotaxis, fatty acid and lipid utilization, and secondary metabolism. Relative changes in taxonomy also demonstrated that coral-associated microbiota (Archaea, Bacteria, protists) shifted from a healthy-associated coral community (e.g. Cyanobacteria, Proteobacteria and the zooxanthellae Symbiodinium) to a community (e.g. Bacteriodetes, Fusobacteria and Fungi) of microbes often found on diseased corals. Additionally, low-abundance Vibrio spp. were found to significantly alter microbiome metabolism, suggesting that the contribution of a just a few members of a community can profoundly shift the health status of the coral holobiont.
Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa
Publisher: Proceedings of the National Academy of Sciences
Date: 25-11-2008
Abstract: During the last several decades corals have been in decline and at least one-third of all coral species are now threatened with extinction. Coral disease has been a major contributor to this threat, but little is known about the responsible pathogens. To date most research has focused on bacterial and fungal diseases however, viruses may also be important for coral health. Using a combination of empirical viral metagenomics and real-time PCR, we show that Porites compressa corals contain a suite of eukaryotic viruses, many related to the Herpesviridae. This coral-associated viral consortium was found to shift in response to abiotic stressors. In particular, when exposed to reduced pH, elevated nutrients, and thermal stress, the abundance of herpes-like viral sequences rapidly increased in 2 separate experiments. Herpes-like viral sequences were rarely detected in apparently healthy corals, but were abundant in a majority of stressed s les. In addition, surveys of the Nematostella and Hydra genomic projects demonstrate that even distantly related Cnidarians contain numerous herpes-like viral genes, likely as a result of latent or endogenous viral infection. These data support the hypotheses that corals experience viral infections, which are exacerbated by stress, and that herpes-like viruses are common in Cnidarians.
A Distinct Contractile Injection System Found in a Majority of Adult Human Microbiomes
Publisher: Cold Spring Harbor Laboratory
Date: 05-12-2019
DOI: 10.1101/865204
Abstract: An imbalance of normal bacterial groups such as Bacteroidales within the human gut is correlated with diseases like obesity. A current grand challenge in the microbiome field is to identify factors produced by normal microbiome bacteria that cause these observed health and disease correlations. While identifying factors like a bacterial injection system could provide a missing explanation for why Bacteroidales correlates with host health, no such factor has been identified to date. The lack of knowledge about these factors is a significant barrier to improving therapies like fecal transplants that promote a healthy microbiome. Here we show that a previously ill-defined Contractile Injection System is carried in the gut microbiome of 99% of in iduals from the United States and Europe. This type of Contractile Injection System, we name here Bacteroidales Injection System (BIS), is related to the contractile tails of bacteriophage (viruses of bacteria) and have been described to mediate interactions between bacteria and erse eukaryotes like amoeba, insects and tubeworms. Our findings that BIS are ubiquitous within adult human microbiomes suggest that they shape host health by mediating interactions between Bacteroidales bacteria and the human host or its microbiome.
Phage and bacteria diversification through a prophage acquisition ratchet
Publisher: Cold Spring Harbor Laboratory
Date: 09-04-2020
DOI: 10.1101/2020.04.08.028340
Abstract: Lysogeny is prevalent in the microbial-dense mammalian gut. This contrasts the classical view of lysogeny as a refuge used by phages under poor host growth conditions. Here we hypothesize that as carrying capacity increases, lysogens escape phage top-down control through superinfection exclusion, overcoming the canonical trade-off between competition and resistance. This hypothesis was tested by developing an ecological model that combined lytic and lysogenic communities and a ersification model that estimated the accumulation of prophages in bacterial genomes. The ecological model s led phage-bacteria traits stochastically for communities ranging from 1 to 1000 phage-bacteria pairs, and it included a fraction of escaping lysogens proportional to the increase in carrying capacity. The ersification model introduced new prophages at each ersification step and estimated the distribution of prophages per bacteria using combinatorics. The ecological model recovered the range of abundances and sublinear relationship between phage and bacteria observed across eleven ecosystems. The ersification model predicted an increase in the number of prophages per genome as bacterial abundances increased, in agreement with the distribution of prophages on 833 genomes from marine and human-associated bacteria. The study of lysogeny presented here offers a framework to interpret viral and microbial abundances and reconciles the Kill-the-Winner and Piggyback-the-Winner paradigms in viral ecology.
Impact of bacteria motility in the encounter rates with bacteriophage in mucus
Publisher: Springer Science and Business Media LLC
Date: 11-11-2019
DOI: 10.1038/S41598-019-52794-2
Abstract: Bacteriophages—or phages—are viruses that infect bacteria and are present in large concentrations in the mucosa that cover the internal organs of animals. Immunoglobulin (Ig) domains on the phage surface interact with mucin molecules, and this has been attributed to an increase in the encounter rates of phage with bacteria in mucus. However, the physical mechanism behind this phenomenon remains unclear. A continuous time random walk (CTRW) model simulating the diffusion due to mucin-T4 phage interactions was developed and calibrated to empirical data. A Langevin stochastic method for Escherichia coli ( E. coli ) run-and-tumble motility was combined with the phage CTRW model to describe phage-bacteria encounter rates in mucus for different mucus concentrations. Contrary to previous theoretical analyses, the emergent subdiffusion of T4 in mucus did not enhance the encounter rate of T4 against bacteria. Instead, for static E. coli, the diffusive T4 mutant lacking Ig domains outperformed the subdiffusive T4 wild type. E. coli ’s motility dominated the encounter rates with both phage types in mucus. It is proposed, that the local fluid-flow generated by E. coli ’s motility combined with T4 interacting with mucins may be the mechanism for increasing the encounter rates between the T4 phage and E. coli bacteria.
Bacteriophage adhering to mucus provide a non–host-derived immunity
Publisher: Proceedings of the National Academy of Sciences
Date: 20-05-2013
Abstract: Mucosal surfaces are a main entry point for pathogens and the principal sites of defense against infection. Both bacteria and phage are associated with this mucus. Here we show that phage-to-bacteria ratios were increased, relative to the adjacent environment, on all mucosal surfaces s led, ranging from cnidarians to humans. In vitro studies of tissue culture cells with and without surface mucus demonstrated that this increase in phage abundance is mucus dependent and protects the underlying epithelium from bacterial infection. Enrichment of phage in mucus occurs via binding interactions between mucin glycoproteins and Ig-like protein domains exposed on phage capsids. In particular, phage Ig-like domains bind variable glycan residues that coat the mucin glycoprotein component of mucus. Metagenomic analysis found these Ig-like proteins present in the phages s led from many environments, particularly from locations adjacent to mucosal surfaces. Based on these observations, we present the bacteriophage adherence to mucus model that provides a ubiquitous, but non–host-derived, immunity applicable to mucosal surfaces. The model suggests that metazoan mucosal surfaces and phage coevolve to maintain phage adherence. This benefits the metazoan host by limiting mucosal bacteria, and benefits the phage through more frequent interactions with bacterial hosts. The relationships shown here suggest a symbiotic relationship between phage and metazoan hosts that provides a previously unrecognized antimicrobial defense that actively protects mucosal surfaces.
Metagenomic and Small-Subunit rRNA Analyses Reveal the Genetic Diversity of Bacteria, Archaea, Fungi, and Viruses in Soil
Publisher: American Society for Microbiology
Date: 11-2007
DOI: 10.1128/AEM.00358-07
Abstract: Recent studies have highlighted the surprising richness of soil bacterial communities however, bacteria are not the only microorganisms found in soil. To our knowledge, no study has compared the ersities of the four major microbial taxa, i.e., bacteria, archaea, fungi, and viruses, from an in idual soil s le. We used metagenomic and small-subunit RNA-based sequence analysis techniques to compare the estimated richness and evenness of these groups in prairie, desert, and rainforest soils. By grouping sequences at the 97% sequence similarity level (an operational taxonomic unit [OTU]), we found that the archaeal and fungal communities were consistently less even than the bacterial communities. Although total richness levels are difficult to estimate with a high degree of certainty, the estimated number of unique archaeal or fungal OTUs appears to rival or exceed the number of unique bacterial OTUs in each of the collected soils. In this first study to comprehensively survey viral communities using a metagenomic approach, we found that soil viruses are taxonomically erse and distinct from the communities of viruses found in other environments that have been surveyed using a similar approach. Within each of the four microbial groups, we observed minimal taxonomic overlap between sites, suggesting that soil archaea, bacteria, fungi, and viruses are globally as well as locally erse.
Metagenomic analysis of the microbial community associated with the coral Porites astreoides
Publisher: Wiley
Date: 21-07-2007
DOI: 10.1111/J.1462-2920.2007.01383.X
Abstract: The coral holobiont is a dynamic assemblage of the coral animal, zooxanthellae, endolithic algae and fungi, Bacteria,Archaea and viruses. Zooxanthellae and some Bacteria form relatively stable and species-specific associations with corals. Other associations are less specific coral-associated Archaea differ from those in the water column, but the same archaeal species may be found on different coral species. It has been hypothesized that the coral animal can adapt to differing ecological niches by 'switching' its microbial associates. In the case of corals and zooxanthellae, this has been termed adaptive bleaching and it has important implications for carbon cycling within the coral holobiont and ultimately the survival of coral reefs. However, the roles of other components of the coral holobiont are essentially unknown. To better understand these other coral associates, a fractionation procedure was used to separate the microbes, mitochondria and viruses from the coral animal cells and zooxanthellae. The resulting metagenomic DNA was sequenced using pyrosequencing. Fungi, Bacteria and phage were the most commonly identified organisms in the metagenome. Three of the four fungal phyla were represented, including a wide ersity of fungal genes involved in carbon and nitrogen metabolism, suggesting that the endolithic community is more important than previously appreciated. In particular, the data suggested that endolithic fungi could be converting nitrate and nitrite to ammonia, which would enable fixed nitrogen to cycle within the coral holobiont. The most prominent bacterial groups were Proteobacteria (68%), Firmicutes (10%), Cyanobacteria (7%) and Actinobacteria (6%). Functionally, the bacterial community was primarily heterotrophic and included a number of pathways for the degradation of aromatic compounds, the most abundant being the homogentisate pathway. The most abundant phage family was the ssDNA Microphage and most of the eukaryotic viruses were most closely related to those known to infect aquatic organisms. This study provides a metabolic and taxonomic snapshot of microbes associated with the reef-building coral Porites astreoides and presents a basis for understanding how coral-microbial interactions structure the holobiont and coral reefs.
Phylogenetic classification of short environmental DNA fragments
Publisher: Oxford University Press (OUP)
Date: 19-02-2008
DOI: 10.1093/NAR/GKN038
Genomic and ecological attributes of marine bacteriophages encoding bacterial virulence genes
Publisher: Springer Science and Business Media LLC
Date: 05-02-2020
DOI: 10.1186/S12864-020-6523-2
Abstract: Bacteriophages encode genes that modify bacterial functions during infection. The acquisition of phage-encoded virulence genes is a major mechanism for the rise of bacterial pathogens. In coral reefs, high bacterial density and lysogeny has been proposed to exacerbate reef decline through the transfer of phage-encoded virulence genes. However, the functions and distribution of these genes in phage virions on the reef remain unknown. Here, over 28,000 assembled viral genomes from the free viral community in Atlantic and Pacific Ocean coral reefs were queried against a curated database of virulence genes. The ersity of virulence genes encoded in the viral genomes was tested for relationships with host taxonomy and bacterial density in the environment. These analyses showed that bacterial density predicted the profile of virulence genes encoded by phages. The Shannon ersity of virulence-encoding phages was negatively related with bacterial density, leading to dominance of fewer genes at high bacterial abundances. A statistical learning analysis showed that reefs with high microbial density were enriched in viruses encoding genes enabling bacterial recognition and invasion of metazoan epithelium. Over 60% of phages could not have their hosts identified due to limitations of host prediction tools for those which hosts were identified, host taxonomy was not an indicator of the presence of virulence genes. This study described bacterial virulence factors encoded in the genomes of bacteriophages at the community level. The results showed that the increase in microbial densities that occurs during coral reef degradation is associated with a change in the genomic repertoire of bacteriophages, specifically in the ersity and distribution of bacterial virulence genes. This suggests that phages are implicated in the rise of pathogens in disturbed marine ecosystems.
A communal catalogue reveals Earth’s multiscale microbial diversity
Publisher: Springer Science and Business Media LLC
Date: 11-2017
DOI: 10.1038/NATURE24621
Abstract: Our growing awareness of the microbial world’s importance and ersity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community s les collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of ersity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial ersity.
Decoding diversity in a coral reef fish species complex with restricted range using metagenomic sequencing of gut contents
Publisher: Wiley
Date: 10-03-2020
DOI: 10.1002/ECE3.6138
Biodiversity and biogeography of phages in modern stromatolites and thrombolites
Publisher: Springer Science and Business Media LLC
Date: 03-2008
DOI: 10.1038/NATURE06735
Abstract: Viruses, and more particularly phages (viruses that infect bacteria), represent one of the most abundant living entities in aquatic and terrestrial environments. The biogeography of phages has only recently been investigated and so far reveals a cosmopolitan distribution of phage genetic material (or genotypes). Here we address this cosmopolitan distribution through the analysis of phage communities in modern microbialites, the living representatives of one of the most ancient life forms on Earth. On the basis of a comparative metagenomic analysis of viral communities associated with marine (Highborne Cay, Bahamas) and freshwater (Pozas Azules II and Rio Mesquites, Mexico) microbialites, we show that some phage genotypes are geographically restricted. The high percentage of unknown sequences recovered from the three metagenomes (>97%), the low percentage similarities with sequences from other environmental viral (n = 42) and microbial (n = 36) metagenomes, and the absence of viral genotypes shared among microbialites indicate that viruses are genetically unique in these environments. Identifiable sequences in the Highborne Cay metagenome were dominated by single-stranded DNA microphages that were not detected in any other s les examined, including sea water, fresh water, sediment, terrestrial, extreme, metazoan-associated and marine microbial mats. Finally, a marine signature was present in the phage community of the Pozas Azules II microbialites, even though this environment has not been in contact with the ocean for tens of millions of years. Taken together, these results prove that viruses in modern microbialites display biogeographical variability and suggest that they may be derived from an ancient community.
A Glimpse into the Expanded Genome Content of Vibrio cholerae through Identification of Genes Present in Environmental Strains
Publisher: American Society for Microbiology
Date: 05-2005
DOI: 10.1128/JB.187.9.2992-3001.2005
Abstract: Vibrio cholerae has multiple survival strategies which are reflected both in its broad distribution in many aquatic environments and its high genotypic ersity. To obtain additional information regarding the content of the V. cholerae genome, suppression subtractive hybridization (SSH) was used to prepare libraries of DNA sequences from two southern California coastal isolates which are ergent or absent in the clinical strain V. cholerae O1 El Tor N16961. More than 1,400 subtracted clones were sequenced. This revealed the presence of novel sequences encoding functions related to cell surface structures, transport, metabolism, signal transduction, luminescence, mobile elements, stress resistance, and virulence. Flanking sequence information was determined for loci of interest, and the distribution of these sequences was assessed for a collection of V. cholerae strains obtained from southern California and Mexican environments. This led to the surprising observation that sequences related to the toxin genes toxA , cnf1 , and exoY are widespread and more common in these strains than those of the cholera toxin genes which are a hallmark of the pandemic strains of V. cholerae . Gene transfer among these strains could be facilitated by a 4.9-kbp plasmid discovered in one isolate, which possesses similarity to plasmids from other environmental vibrios. By investigating some of the nucleotide sequence basis for V. cholerae genotypic ersity, DNA fragments have been uncovered which could promote survival in coastal environments. Furthermore, a set of genes has been described which could be involved in as yet undiscovered interactions between V. cholerae and eukaryotic organisms.
A Distinct Contractile Injection System Gene Cluster Found in a Majority of Healthy Adult Human Microbiomes
Publisher: American Society for Microbiology
Date: 25-08-2020
DOI: 10.1128/MSYSTEMS.00648-20
Abstract: To engage with host cells, erse pathogenic bacteria produce syringe-like structures called contractile injection systems (CIS). CIS are evolutionarily related to the contractile tails of bacteriophages and are specialized to puncture membranes, often delivering effectors to target cells. Although CIS are key for pathogens to cause disease, paradoxically, similar injection systems have been identified within healthy human microbiome bacteria. Here, we show that gene clusters encoding a predicted CIS, which we term Bacteroidales injection systems (BIS), are present in the microbiomes of nearly all adult humans tested from Western countries. BIS genes are enriched within human gut microbiomes and are expressed both in vitro and in vivo . Further, a greater abundance of BIS genes is present within healthy gut microbiomes than in those humans with with inflammatory bowel disease (IBD). Our discovery provides a potentially distinct means by which our microbiome interacts with the human host or its microbiome.
Development and Use of Personalized Bacteriophage-Based Therapeutic Cocktails To Treat a Patient with a Disseminated Resistant Acinetobacter baumannii Infection
Publisher: American Society for Microbiology
Date: 10-2017
DOI: 10.1128/AAC.00954-17
Abstract: Widespread antibiotic use in clinical medicine and the livestock industry has contributed to the global spread of multidrug-resistant (MDR) bacterial pathogens, including Acinetobacter baumannii . We report on a method used to produce a personalized bacteriophage-based therapeutic treatment for a 68-year-old diabetic patient with necrotizing pancreatitis complicated by an MDR A. baumannii infection. Despite multiple antibiotic courses and efforts at percutaneous drainage of a pancreatic pseudocyst, the patient deteriorated over a 4-month period. In the absence of effective antibiotics, two laboratories identified nine different bacteriophages with lytic activity for an A. baumannii isolate from the patient. Administration of these bacteriophages intravenously and percutaneously into the abscess cavities was associated with reversal of the patient's downward clinical trajectory, clearance of the A. baumannii infection, and a return to health. The outcome of this case suggests that the methods described here for the production of bacteriophage therapeutics could be applied to similar cases and that more concerted efforts to investigate the use of therapeutic bacteriophages for MDR bacterial infections are warranted.
Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition
Publisher: PeerJ
Date: 19-08-2014
DOI: 10.7717/PEERJ.520
Mechanistic Model of Rothia mucilaginosa Adaptation toward Persistence in the CF Lung, Based on a Genome Reconstructed from Metagenomic Data
Publisher: Public Library of Science (PLoS)
Date: 30-05-2013
Viral metagenomics
Publisher: Springer Science and Business Media LLC
Date: 10-05-2005
DOI: 10.1038/NRMICRO1163
Abstract: Viruses, most of which infect microorganisms, are the most abundant biological entities on the planet. Identifying and measuring the community dynamics of viruses in the environment is complicated because less than one percent of microbial hosts have been cultivated. Also, there is no single gene that is common to all viral genomes, so total uncultured viral ersity cannot be monitored using approaches analogous to ribosomal DNA profiling. Metagenomic analyses of uncultured viral communities circumvent these limitations and can provide insights into the composition and structure of environmental viral communities.
Bacteriophage transcytosis provides a mechanism to cross epithelial cell layers
Publisher: American Society for Microbiology
Date: 29-12-2017
Abstract: Bacterial viruses are among the most numerous biological entities within the human body. These viruses are found within regions of the body that have conventionally been considered sterile, including the blood, lymph, and organs. However, the primary mechanism that bacterial viruses use to bypass epithelial cell layers and access the body remains unknown. Here, we used in vitro studies to demonstrate the rapid and directional transcytosis of erse bacteriophages across confluent cell layers originating from the gut, lung, liver, kidney, and brain. Bacteriophage transcytosis across cell layers had a significant preferential directionality for apical-to-basolateral transport, with approximately 0.1% of total bacteriophages applied being transcytosed over a 2-h period. Bacteriophages were capable of crossing the epithelial cell layer within 10 min with transport not significantly affected by the presence of bacterial endotoxins. Microscopy and cellular assays revealed that bacteriophages accessed both the vesicular and cytosolic compartments of the eukaryotic cell, with phage transcytosis suggested to traffic through the Golgi apparatus via the endomembrane system. Extrapolating from these results, we estimated that 31 billion bacteriophage particles are transcytosed across the epithelial cell layers of the gut into the average human body each day. The transcytosis of bacteriophages is a natural and ubiquitous process that provides a mechanistic explanation for the occurrence of phages within the body. IMPORTANCE Bacteriophages (phages) are viruses that infect bacteria. They cannot infect eukaryotic cells but can penetrate epithelial cell layers and spread throughout sterile regions of our bodies, including the blood, lymph, organs, and even the brain. Yet how phages cross these eukaryotic cell layers and gain access to the body remains unknown. In this work, epithelial cells were observed to take up and transport phages across the cell, releasing active phages on the opposite cell surface. Based on these results, we posit that the human body is continually absorbing phages from the gut and transporting them throughout the cell structure and subsequently the body. These results reveal that phages interact directly with the cells and organs of our bodies, likely contributing to human health and immunity.
Oxygen minimum zones harbour novel viral communities with low diversity
Publisher: Wiley
Date: 05-10-2012
DOI: 10.1111/J.1462-2920.2012.02891.X
Abstract: Oxygen minimum zones (OMZs) are oceanographic features that affect ocean productivity and bio ersity, and contribute to ocean nitrogen loss and greenhouse gas emissions. Here we describe the viral communities associated with the Eastern Tropical South Pacific (ETSP) OMZ off Iquique, Chile for the first time through abundance estimates and viral metagenomic analysis. The viral-to-microbial ratio (VMR) in the ETSP OMZ fluctuated in the oxycline and declined in the anoxic core to below one on several occasions. The number of viral genotypes (unique genomes as defined by sequence assembly) ranged from 2040 at the surface to 98 in the oxycline, which is the lowest viral ersity recorded to date in the ocean. Within the ETSP OMZ viromes, only 4.95% of genotypes were shared between surface and anoxic core viromes using reciprocal BLASTn sequence comparison. ETSP virome comparison with surface marine viromes (Sargasso Sea, Gulf of Mexico, Kingman Reef, Chesapeake Bay) revealed a dissimilarity of ETSP OMZ viruses to those from other oceanic regions. From the 1.4 million non-redundant DNA sequences s led within the altered oxygen conditions of the ETSP OMZ, more than 97.8% were novel. Of the average 3.2% of sequences that showed similarity to the SEED non-redundant database, phage sequences dominated the surface viromes, eukaryotic virus sequences dominated the oxycline viromes, and phage sequences dominated the anoxic core viromes. The viral community of the ETSP OMZ was characterized by fluctuations in abundance, taxa and ersity across the oxygen gradient. The ecological significance of these changes was difficult to predict however, it appears that the reduction in oxygen coincides with an increased shedding of eukaryotic viruses in the oxycline, and a shift to unique viral genotypes in the anoxic core.
TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets
Publisher: Springer Science and Business Media LLC
Date: 23-06-2010
Using viromes to predict novel immune proteins in non-model organisms
Publisher: The Royal Society
Date: 31-08-2016
Abstract: Immunity is mostly studied in a few model organisms, leaving the majority of immune systems on the planet unexplored. To characterize the immune systems of non-model organisms alternative approaches are required. Viruses manipulate host cell biology through the expression of proteins that modulate the immune response. We hypothesized that metagenomic sequencing of viral communities would be useful to identify both known and unknown host immune proteins. To test this hypothesis, a mock human virome was generated and compared to the human proteome using tBLASTn, resulting in 36 proteins known to be involved in immunity. This same pipeline was then applied to reef-building coral, a non-model organism that currently lacks traditional molecular tools like transgenic animals, gene-editing capabilities, and in vitro cell cultures. Viromes isolated from corals and compared with the predicted coral proteome resulted in 2503 coral proteins, including many proteins involved with pathogen sensing and apoptosis. There were also 159 coral proteins predicted to be involved with coral immunity but currently lacking any functional annotation. The pipeline described here provides a novel method to rapidly predict host immune components that can be applied to virtually any system with the potential to discover novel immune proteins.
Structure and function of a cyanophage-encoded peptide deformylase
Publisher: Springer Science and Business Media LLC
Date: 14-02-2013
DOI: 10.1038/ISMEJ.2013.4
Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
Publisher: MyJove Corporation
Date: 11-06-2015
DOI: 10.3791/52854
Sequencing at sea: Challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition
Publisher: PeerJ
Date: 11-07-2014
DOI: 10.7287/PEERJ.PREPRINTS.433V1
Abstract: Genomics and metagenomics have revolutionized our understanding of marine microbial ecology and the importance of microbes in global geochemical cycles. However, the process of DNA sequencing has always been an abstract extension of the research expedition, completed once the s les were returned to the laboratory. During the 2013 Southern Line Islands Research Expedition, we started the first effort to bring next generation sequencing to some of the most remote locations on our planet. We successfully sequenced twenty six marine microbial genomes, and two marine microbial metagenomes using the Ion Torrent PGM platform on the Merchant Yacht Hanse Explorer. Onboard sequence assembly, annotation, and analysis enabled us to investigate the role of the microbes in the coral reef ecology of these islands and atolls. This analysis identified phospohonate as an important phosphorous source for microbes growing in the Line Islands and reinforced the importance of L-serine in marine microbial ecosystems. Sequencing in the field allowed us to propose hypotheses and conduct experiments and further s ling based on the sequences generated. By eliminating the delay between s ling and sequencing, we enhanced the productivity of the research expedition. By overcoming the hurdles associated with sequencing on a boat in the middle of the Pacific Ocean we proved the flexibility of the sequencing, annotation, and analysis pipelines.
Correction: Corrigendum: Lytic to temperate switching of viral communities
Publisher: Springer Science and Business Media LLC
Date: 24-08-2016
DOI: 10.1038/NATURE19335
Widespread association of a Rickettsiales-like bacterium with reef-building corals
Publisher: Wiley
Date: 23-08-2004
DOI: 10.1111/J.1462-2920.2004.00647.X
Abstract: White band disease type I (WBD I) has been a major cause of the dramatic decline of Acroporid coral populations throughout the Caribbean during the last two decades, yet the aetiological agent of this disease is unknown. In this study, the bacterial communities associated with both healthy and diseased Acropora species were compared by 16S rDNA analyses. The bacterial communities of both healthy and diseased Acropora spp. were dominated by a single ribotype with 90% identity to a bacterium in the order Rickettsiales. Screening by nested PCR specific to the coral-associated Rickettsiales 1 (CAR1) bacterium showed that this microbe was widespread in both healthy and diseased A. cervicornis and A. palmata corals from 'healthy' (i.e. low WBD I incidence) and 'stressed' reefs (i.e. high WBD I incidence). These results indicate that there were no dramatic changes in the composition of the microbial community associated with WBD I. CAR1 was also associated with non-Acroporid corals of the Caribbean, as well as with two Acroporid corals native to the Pacific. CAR1 was not present in the water column. This bacterium was also absent from preserved Caribbean Acroporid s les collected between 1937 and 1980 before the outbreak of WBD I. These results suggest CAR1 is a relatively new bacterial associate of Acroporids and that a non-bacterial pathogen might be the cause of WBD I.
Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information
Publisher: American Society for Microbiology
Date: 30-04-2019
Abstract: Proper management of polymicrobial infections in patients with cystic fibrosis (CF) has extended their life span. Information about the composition and dynamics of each patient’s microbial community aids in the selection of appropriate treatment of pulmonary exacerbations. We propose the cystic fibrosis rapid response (CFRR) as a fast approach to determine viral and microbial community composition and activity during CF pulmonary exacerbations. The CFRR potential is illustrated with a case study in which a cystic fibrosis fatal exacerbation was characterized by the presence of shigatoxigenic Escherichia coli . The incorporation of the CFRR within the CF clinic could increase the life span and quality of life of CF patients.
Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics
Publisher: Proceedings of the National Academy of Sciences
Date: 27-12-2016
Abstract: We created a dataset of dinoflagellate transcriptomes to resolve internal phylogenetic relationships of the group. We show that the dinoflagellate theca originated once, through a process that likely involved changes in the metabolism of cellulose, and suggest that a late origin of dinosterol in the group is at odds with dinoflagellates being the source of this important biomarker before the Mesozoic. We also show that nonphotosynthetic dinoflagellates have retained nonphotosynthetic plastids with vital metabolic functions, and propose that one of these may be the evolutionary source of dinoflagellate bioluminescence. Finally, we reconstruct major molecular and morphological transitions in dinoflagellates and highlight the role of horizontal gene transfer in the origin of their unique nuclear architecture.
An application of statistics to comparative metagenomics
Publisher: Springer Science and Business Media LLC
Date: 20-03-2006
Abstract: Metagenomics, sequence analyses of genomic DNA isolated directly from the environments, can be used to identify organisms and model community dynamics of a particular ecosystem. Metagenomics also has the potential to identify significantly different metabolic potential in different environments. Here we use a statistical method to compare curated subsystems, to predict the physiology, metabolism, and ecology from metagenomes. This approach can be used to identify those subsystems that are significantly different between metagenome sequences. Subsystems that were overrepresented in the Sargasso Sea and Acid Mine Drainage metagenome when compared to non-redundant databases were identified. The methodology described herein applies statistics to the comparisons of metabolic potential in metagenomes. This analysis reveals those subsystems that are more, or less, represented in the different environments that are compared. These differences in metabolic potential lead to several testable hypotheses about physiology and metabolism of microbes from these ecosystems.
Finding novel genes in bacterial communities isolated from the environment
Publisher: Oxford University Press (OUP)
Date: 15-07-2006
DOI: 10.1093/BIOINFORMATICS/BTL247
Abstract: Motivation: Novel sequencing techniques can give access to organisms that are difficult to cultivate using conventional methods. When applied to environmental s les, the data generated has some drawbacks, e.g. short length of assembled contigs, in-frame stop codons and frame shifts. Unfortunately, current gene finders cannot circumvent these difficulties. At the same time, the automated prediction of genes is a prerequisite for the increasing amount of genomic sequences to ensure progress in metagenomics. Results: We introduce a novel gene finding algorithm that incorporates features overcoming the short length of the assembled contigs from environmental data, in-frame stop codons as well as frame shifts contained in bacterial sequences. The results show that by searching for sequence similarities in an environmental s le our algorithm is capable of detecting a high fraction of its gene content, depending on the species composition and the overall size of the s le. The method is valuable for hunting novel unknown genes that may be specific for the habitat where the s le is taken. Finally, we show that our algorithm can even exploit the limited information contained in the short reads generated by 454 technology for the prediction of protein coding genes. Availability: The program is freely available upon request. Contact: Lutz.Krause@CeBiTec.Uni-Bielefeld.DE
Clinical Insights from Metagenomic Analysis of Sputum Samples from Patients with Cystic Fibrosis
Publisher: American Society for Microbiology
Date: 02-2014
DOI: 10.1128/JCM.02204-13
Abstract: As DNA sequencing becomes faster and cheaper, genomics-based approaches are being explored for their use in personalized diagnoses and treatments. Here, we provide a proof of principle for disease monitoring using personal metagenomic sequencing and traditional clinical microbiology by focusing on three adults with cystic fibrosis (CF). The CF lung is a dynamic environment that hosts a complex ecosystem composed of bacteria, viruses, and fungi that can vary in space and time. Not surprisingly, the microbiome data from the induced sputum s les we collected revealed a significant amount of species ersity not seen in routine clinical laboratory cultures. The relative abundances of several species changed as clinical treatment was altered, enabling the identification of the climax and attack communities that were proposed in an earlier work. All patient microbiomes encoded a ersity of mechanisms to resist antibiotics, consistent with the characteristics of multidrug-resistant microbial communities that are commonly observed in CF patients. The metabolic potentials of these communities differed by the health status and recovery route of each patient. Thus, this pilot study provides an ex le of how metagenomic data might be used with clinical assessments for the development of treatments tailored to in idual patients.
Lytic to temperate switching of viral communities
Publisher: Springer Science and Business Media LLC
Date: 16-03-2016
DOI: 10.1038/NATURE17193
Abstract: Microbial viruses can control host abundances via density-dependent lytic predator-prey dynamics. Less clear is how temperate viruses, which coexist and replicate with their host, influence microbial communities. Here we show that virus-like particles are relatively less abundant at high host densities. This suggests suppressed lysis where established models predict lytic dynamics are favoured. Meta-analysis of published viral and microbial densities showed that this trend was widespread in erse ecosystems ranging from soil to freshwater to human lungs. Experimental manipulations showed viral densities more consistent with temperate than lytic life cycles at increasing microbial abundance. An analysis of 24 coral reef viromes showed a relative increase in the abundance of hallmark genes encoded by temperate viruses with increased microbial abundance. Based on these four lines of evidence, we propose the Piggyback-the-Winner model wherein temperate dynamics become increasingly important in ecosystems with high microbial densities thus 'more microbes, fewer viruses'.
Hyperspectral and Physiological Analyses of Coral-Algal Interactions
Publisher: Public Library of Science (PLoS)
Date: 26-11-2009
Some of the most interesting CASP 11 targets through the eyes of their authors
Publisher: Wiley
Date: 16-11-2015
DOI: 10.1002/PROT.24942
Viruses and the origin of microbiome selection and immunity
Publisher: Springer Science and Business Media LLC
Date: 16-12-2016
Viral communities associated with healthy and bleaching corals
Publisher: Wiley
Date: 12-08-2008
Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Ciénegas, Mexico
Publisher: Wiley
Date: 2009
Using pyrosequencing to shed light on deep mine microbial ecology
Publisher: Springer Science and Business Media LLC
Date: 20-03-2006
Abstract: Contrasting biological, chemical and hydrogeological analyses highlights the fundamental processes that shape different environments. Generating and interpreting the biological sequence data was a costly and time-consuming process in defining an environment. Here we have used pyrosequencing, a rapid and relatively inexpensive sequencing technology, to generate environmental genome sequences from two sites in the Soudan Mine, Minnesota, USA. These sites were adjacent to each other, but differed significantly in chemistry and hydrogeology. Comparisons of the microbes and the subsystems identified in the two s les highlighted important differences in metabolic potential in each environment. The microbes were performing distinct biochemistry on the available substrates, and subsystems such as carbon utilization, iron acquisition mechanisms, nitrogen assimilation, and respiratory pathways separated the two communities. Although the correlation between much of the microbial metabolism occurring and the geochemical conditions from which the s les were isolated could be explained, the reason for the presence of many pathways in these environments remains to be determined. Despite being physically close, these two communities were markedly different from each other. In addition, the communities were also completely different from other microbial communities sequenced to date. We anticipate that pyrosequencing will be widely used to sequence environmental s les because of the speed, cost, and technical advantages. Furthermore, subsystem comparisons rapidly identify the important metabolisms employed by the microbes in different environments.
Phage on tap–a quick and efficient protocol for the preparation of bacteriophage laboratory stocks
Publisher: PeerJ
Date: 26-07-2016
DOI: 10.7717/PEERJ.2261
Abstract: A major limitation with traditional phage preparations is the variability in titer, salts, and bacterial contaminants between successive propagations. Here we introduce the Phage On Tap (PoT) protocol for the quick and efficient preparation of homogenous bacteriophage (phage) stocks. This method produces homogenous, laboratory-scale, high titer (up to 10 10–11 PFU·ml −1 ), endotoxin reduced phage banks that can be used to eliminate the variability between phage propagations and improve the molecular characterizations of phage. The method consists of five major parts, including phage propagation, phage clean up by 0.22 μm filtering and chloroform treatment, phage concentration by ultrafiltration, endotoxin removal, and the preparation and storage of phage banks for continuous laboratory use. From a starting liquid lysate of 100 mL, the PoT protocol generated a clean, homogenous, laboratory phage bank with a phage recovery efficiency of 85% within just two days. In contrast, the traditional method took upwards of five days to produce a high titer, but lower volume phage stock with a recovery efficiency of only 4%. Phage banks can be further purified for the removal of bacterial endotoxins, reducing endotoxin concentrations by over 3,000-fold while maintaining phage titer. The PoT protocol focused on T-like phages, but is broadly applicable to a variety of phages that can be propagated to sufficient titer, producing homogenous, high titer phage banks that are applicable for molecular and cellular assays.
Microbial Ecology of Four Coral Atolls in the Northern Line Islands
Publisher: Public Library of Science (PLoS)
Date: 27-02-2008
Baselines and Degradation of Coral Reefs in the Northern Line Islands
Publisher: Public Library of Science (PLoS)
Date: 27-02-2008
Indirect effects of algae on coral: algae‐mediated, microbe‐induced coral mortality
Publisher: Wiley
Date: 05-06-2006
DOI: 10.1111/J.1461-0248.2006.00937.X
Abstract: Declines in coral cover are generally associated with increases in the abundance of fleshy algae. In many cases, it remains unclear whether algae are responsible, directly or indirectly, for coral death or whether they simply settle on dead coral surfaces. Here, we show that algae can indirectly cause coral mortality by enhancing microbial activity via the release of dissolved compounds. When coral and algae were placed in chambers together but separated by a 0.02 mum filter, corals suffered 100% mortality. With the addition of the broad-spectrum antibiotic icillin, mortality was completely prevented. Physiological measurements showed complementary patterns of increasing coral stress with proximity to algae. Our results suggest that as human impacts increase and algae become more abundant on reefs a positive feedback loop may be created whereby compounds released by algae enhance microbial activity on live coral surfaces causing mortality of corals and further algal growth.
Dissecting microbial employment
Publisher: Springer Science and Business Media LLC
Date: 09-2008
DOI: 10.1038/NBT0908-997
Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors
Publisher: Proceedings of the National Academy of Sciences
Date: 30-06-2014
Abstract: Microbial communities associated with coral reefs influence the health and sustenance of keystone benthic organisms (e.g., coral holobionts). The present study investigated the community structure and metabolic potential of microbes inhabiting coral reefs located across an extensive area in the central Pacific. We found that the taxa present correlated strongly with the percent coverage of corals and algae, while community metabolic potential correlated best with geographic location. These findings are inconsistent with prevailing biogeographic models of microbial ersity (e.g., distance decay) and metabolic potential (i.e., similar functional profiles regardless of phylogenetic variability). Based on these findings, we propose that the primary carbon sources determine community structure and that local biogeochemistry determines finer-scale metabolic function.
Black reefs: iron-induced phase shifts on coral reefs
Publisher: Springer Science and Business Media LLC
Date: 09-2011
Diel population and functional synchrony of microbial communities on coral reefs
Publisher: Springer Science and Business Media LLC
Date: 12-04-2019
DOI: 10.1038/S41467-019-09419-Z
Abstract: On coral reefs, microorganisms are essential for recycling nutrients to primary producers through the remineralization of benthic-derived organic matter. Diel investigations of reef processes are required to holistically understand the functional roles of microbial players in these ecosystems. Here we report a metagenomic analysis characterizing microbial communities in the water column overlying 16 remote forereef sites over a diel cycle. Our results show that microbial community composition is more dissimilar between day and night s les collected from the same site than between day or night s les collected across geographically distant reefs. Diel community differentiation is largely driven by the flux of Psychrobacter sp., which is two-orders of magnitude more abundant during the day. Nighttime communities are enriched with species of Roseobacter , Halomonas , and Alteromonas encoding a greater variety of pathways for carbohydrate catabolism, further illustrating temporal patterns of energetic provisioning between different marine microbes. Dynamic diel fluctuations of microbial populations could also support the efficient trophic transfer of energy posited in coral reef food webs.
Related Organisations
Related Funding Activities
Discovery Projects - Grant ID: DP110101679
Start Date: 05-2011
End Date: 12-2014
Amount: $300,000.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP140102776
Start Date: 2014
End Date: 03-2017
Amount: $458,000.00
Funder: Australian Research Council
View Funded Activity