Coral microbiome database: Integration of sequences reveals high diversity and relatedness of coral‐associated microbes DOI Creative Commons
Megan J. Huggett, Amy Apprill

Environmental Microbiology Reports, Journal Year: 2018, Volume and Issue: 11(3), P. 372 - 385

Published: Aug. 10, 2018

Coral-associated microorganisms are thought to play a fundamental role in the health and ecology of corals, but understanding specific coral-microbial interactions lacking. In order create framework examine specificity, we integrated phylogenetically compared 21,100 SSU rRNA gene Sanger-produced sequences from bacteria archaea associated with corals previous studies, accompanying host, location publication metadata, produce Coral Microbiome Database. From this database, identified 39 described candidate phyla Bacteria two Archaea demonstrating that one most diverse animal microbiomes. Secondly, new phylogenetic resource shows certain indeed including evolutionary distinct hosts. Specifically, 2-37 putative monophyletic, coral-specific sequence clusters within bacterial genera greatest number coral species (Vibrio, Endozoicomonas Ruegeria) as well functionally relevant microbial taxa ("Candidatus Amoebophilus", "Candidatus Nitrosopumilus" under recognized cyanobacteria). This provides for more targeted studies their associates, which is timely given escalated need understand microbiome its adaptability changing ocean reef conditions.

Language: Английский

Stress and stability: applying the Anna Karenina principle to animal microbiomes DOI
Jesse Zaneveld, Ryan McMinds, Rebecca Vega Thurber

et al.

Nature Microbiology, Journal Year: 2017, Volume and Issue: 2(9)

Published: Aug. 23, 2017

Language: Английский

Citations

784
The sponge holobiont in a changing ocean: from microbes to ecosystems DOI Creative Commons
Lucía Pita, Laura Rix, Beate M. Slaby

et al.

Microbiome, Journal Year: 2018, Volume and Issue: 6(1)

Published: March 9, 2018

The recognition that all macroorganisms live in symbiotic association with microbial communities has opened up a new field biology. Animals, plants, and algae are now considered holobionts, complex ecosystems consisting of the host, microbiota, interactions among them. Accordingly, ecological concepts can be applied to understand host-derived processes govern dynamics interactive networks within holobiont. In marine systems, holobionts further integrated into larger more ecosystems, concept referred as "nested ecosystems." this review, we discuss dynamic interact at multiple scales respond environmental change. We focus on symbiosis sponges their communities—a resulted one most diverse environment. recent years, sponge microbiology remarkably advanced terms curated databases, standardized protocols, information functions microbiota. Like Russian doll, these translated holobiont impact surrounding ecosystem. For example, sponge-associated metabolisms, fueled by high filtering capacity substantially affect biogeochemical cycling key nutrients like carbon, nitrogen, phosphorous. Since increasingly threatened anthropogenic stressors jeopardize stability ecosystem, link between perturbations, dysbiosis, diseases. Experimental studies suggest community composition is tightly linked health, but whether dysbiosis cause or consequence collapse remains unresolved. Moreover, potential role microbiome mediating for acclimate adapt change unknown. Future should aim identify mechanisms underlying scales, from develop management strategies preserve provided our present future oceans.

Language: Английский

Citations

495
Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations DOI
Cindy J. Castelle, Christopher T. Brown, Karthik Anantharaman

et al.

Nature Reviews Microbiology, Journal Year: 2018, Volume and Issue: 16(10), P. 629 - 645

Published: Sept. 4, 2018

Language: Английский

Citations

380
Enzymatic Halogenation and Dehalogenation Reactions: Pervasive and Mechanistically Diverse DOI
Vinayak Agarwal,

Zachary D. Miles,

Jaclyn M. Winter

et al.

Chemical Reviews, Journal Year: 2017, Volume and Issue: 117(8), P. 5619 - 5674

Published: Jan. 20, 2017

Naturally produced halogenated compounds are ubiquitous across all domains of life where they perform a multitude biological functions and adopt diversity chemical structures. Accordingly, diverse collection enzyme catalysts to install remove halogens from organic scaffolds has evolved in nature. Accounting for the different properties four halogen atoms (fluorine, chlorine, bromine, iodine) reactivity their substrates, enzymes performing biosynthetic degradative halogenation chemistry utilize numerous mechanistic strategies involving oxidation, reduction, substitution. Biosynthetic reactions range simple aromatic substitutions stereoselective C–H functionalizations on remote carbon centers can initiate formation complex ring Dehalogenating enzymes, other hand, best known removing man-made organohalogens, yet also function naturally, albeit rarely, metabolic pathways. This review details scope mechanism nature's dehalogenation enzymatic strategies, highlights gaps our understanding, posits new advances field might arise near future.

Language: Английский

Citations

367
Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny DOI Creative Commons
F. Joseph Pollock, Ryan McMinds,

S.J. Smith

et al.

Nature Communications, Journal Year: 2018, Volume and Issue: 9(1)

Published: Nov. 16, 2018

Scleractinian corals' microbial symbionts influence host health, yet how coral microbiomes assembled over evolution is not well understood. We survey bacterial and archaeal communities in phylogenetically diverse Australian corals representing more than 425 million years of diversification. show that are anatomically compartmentalized both modern ecology evolutionary assembly. Coral mucus, tissue, skeleton differ community composition, richness, response to vs. environmental drivers. also find evidence coral-microbe phylosymbiosis, which microbiome composition richness reflect phylogeny. Surprisingly, the represents most biodiverse microbiome, shows strongest phylosymbiosis. Interactions between phylogeny significantly abundance four groups bacteria-including Endozoicomonas-like bacteria, divide into host-generalist host-specific subclades. Together these results trace symbiosis across anatomy during a basal animal lineage.

Language: Английский

Citations

332
An introduction to phylosymbiosis DOI Open Access
Shen Jean Lim, Seth R. Bordenstein

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2020, Volume and Issue: 287(1922), P. 20192900 - 20192900

Published: March 4, 2020

Phylosymbiosis was recently formulated to support a hypothesis-driven framework for the characterization of new, cross-system trend in host-associated microbiomes. Defining phylosymbiosis as ‘microbial community relationships that recapitulate phylogeny their host’, we review relevant literature and data last decade, emphasizing frequently used methods regular patterns observed analyses. Quantitative is provided by statistical evaluating higher microbiome variation between host species than within species, topological similarities dendrogram, positive association genetic beta diversity. Significant degrees are prevalent, but not universal, microbiomes plants animals from terrestrial aquatic habitats. Consistent with natural selection shaping phylosymbiosis, transplant experiments demonstrate reduced performance and/or fitness upon host–microbiome mismatches. Hybridization can also disrupt phylosymbiotic cause hybrid pathologies. The pervasiveness carries several important implications advancing knowledge eco-evolutionary processes impact interactions future applications precision microbiology. Important steps will be examine beyond bacterial communities, apply evolutionary modelling an increasingly sophisticated understanding unravel microbial mechanisms contribute pattern. This serves gateway experimental, conceptual quantitative themes outlines opportunities ripe investigation diversity disciplines.

Language: Английский

Citations

246
The sponge microbiome project DOI Creative Commons
Lucas Moitinho‐Silva,

Shaun Nielsen,

Amnon Amir

et al.

GigaScience, Journal Year: 2017, Volume and Issue: 6(10)

Published: Aug. 16, 2017

Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial limited number sponge species, severely limiting comparative analyses diversity structure. Here, we provide an extensive standardised dataset that will facilitate microbiome comparisons across large spatial, temporal, environmental scales. Samples from marine (n = 3569 specimens), seawater 370), sediments 65) other environments 29) were collected locations globe. This incorporates at least 268 including several yet unidentified taxa. The V4 region was amplified sequenced extracted DNA using procedures. Raw sequences (total 1.1 billion sequences) processed clustered (i) standard protocol QIIME closed-reference picking resulting in 39 543 operational taxonomic units (OTU) 97% sequence identity, (ii) de novo clustering Mothur 518 246 OTUs, (iii) new high-resolution Deblur 83 908 unique bacterial sequences. Abundance tables, representative sequences, classifications, metadata provided. represents comprehensive resource sponge-associated based on can be used address overarching hypotheses regarding host-associated prokaryotes, host specificity, convergent evolution, drivers structure, rare biosphere.

Language: Английский

Citations

234
Metaorganisms in extreme environments: do microbes play a role in organismal adaptation? DOI Creative Commons
Corinna Bang, Tal Dagan, Peter Deines

et al.

Zoology, Journal Year: 2018, Volume and Issue: 127, P. 1 - 19

Published: Feb. 15, 2018

From protists to humans, all animals and plants are inhabited by microbial organisms. There is an increasing appreciation that these resident microbes influence the fitness of their plant animal hosts, ultimately forming a metaorganism consisting uni- or multicellular host community associated microorganisms. Research on host–microbe interactions has become emerging cross-disciplinary field. In both vertebrates invertebrates complex microbiome confers immunological, metabolic behavioural benefits; conversely, its disturbance can contribute development disease states. However, molecular cellular mechanisms controlling within poorly understood many key between organisms remain unknown. this perspective article, we outline some issues in interspecies particular address question how metaorganisms react adapt inputs from extreme environments such as deserts, intertidal zone, oligothrophic seas, hydrothermal vents.

Language: Английский

Citations

234
Marine Rare Actinomycetes: A Promising Source of Structurally Diverse and Unique Novel Natural Products DOI Creative Commons
Ramesh Subramani, Detmer Sipkema

Marine Drugs, Journal Year: 2019, Volume and Issue: 17(5), P. 249 - 249

Published: April 26, 2019

Rare actinomycetes are prolific in the marine environment; however, knowledge about their diversity, distribution and biochemistry is limited. Marine rare represent a rather untapped source of chemically diverse secondary metabolites novel bioactive compounds. In this review, we aim to summarize present on isolation, natural product discovery reported from mid-2013 2017. A total 97 new species, representing 9 genera belonging 27 families have been reported, with highest numbers isolates Pseudonocardiaceae, Demequinaceae, Micromonosporaceae Nocardioidaceae. Additionally, study reviewed 167 compounds produced by 58 different actinomycete species 24 genera. Most antibacterial, antifungal, antiparasitic, anticancer or antimalarial activities. The products were derived Nocardiopsis, Micromonospora, Salinispora Pseudonocardia. Members genus Micromonospora revealed be richest unique products.

Language: Английский

Citations

226
It’s the song, not the singer: an exploration of holobiosis and evolutionary theory DOI
W. Ford Doolittle,

Austin Booth

Biology & Philosophy, Journal Year: 2016, Volume and Issue: 32(1), P. 5 - 24

Published: Oct. 13, 2016

Language: Английский

Citations

203