A large patch of anomalously warm water (nicknamed "the Blob") appeared off the coast of Alaska in the winter of 2013–2014 and subsequently stretched south to Baja California. This northeastern ...Pacific warm-water anomaly persisted through the end of 2015. Scientists and the public alike noted widespread changes in the biological structure and composition of both open-ocean and coastal ecosystems. Changes included geographical shifts of species such as tropical copepods, pelagic red crabs, and tuna; closures of commercially important fisheries; and mass strandings of marine mammals and seabirds. The ecological responses to these physical changes have been sparsely quantified and are largely unknown. Here, we provide a bottom-up summary of some of the biological changes observed in and around the areas affected by the Blob.
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While the field of microbial biogeography has largely focused on the contributions of abiotic factors to community patterns, the potential influence of biotic interactions in structuring microbial ...communities, such as those mediated by the production of specialized metabolites, remains largely unknown. Here, we examined the relationship between microbial community structure and specialized metabolism at local spatial scales in marine sediment samples collected from the Long-Term Ecological Research (LTER) site in Moorea, French Polynesia. By employing a multi-omic approach to characterize the taxonomic, functional, and specialized metabolite composition within sediment communities, we find that biogeographic patterns were driven by local scale processes (e.g., biotic interactions) and largely independent of dispersal limitation. Specifically, we observed high variation in biosynthetic potential (based on Bray-Curtis dissimilarity) between samples, even within 1 m
plots, that reflected uncharacterized chemical space associated with site-specific metabolomes. Ultimately, connecting biosynthetic potential to community metabolomes facilitated the in situ detection of natural products and revealed new insights into the complex metabolic dynamics associated with sediment microbial communities. Our study demonstrates the potential to integrate biosynthetic genes and metabolite production into assessments of microbial community dynamics.
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Summary
The microbial communities associated with marine sediments are critical for ecosystem function yet remain poorly characterized. While culture‐independent (CI) techniques capture the broadest ...perspective on community composition, culture‐dependent (CD) methods can select for low abundance taxa that are missed using CI approaches. This study aimed to assess microbial diversity in tropical marine sediments at five shallow‐water sites in Belize using both CD and CI techniques. The CD methods captured approximately 3% of the >800 genera detected across all sites using the CI approach. Additionally, 39 genera were only detected in culture, revealing rare taxa that were missed with the CI approach. Significantly different communities were detected across sites, with rare taxa playing an important role in distinguishing among communities. This study provides important baseline data describing shallow‐water sediment microbial communities, evidence that standard cultivation techniques may be more effective than previously recognized, and the first steps towards identifying new taxa that are amenable to agar plate cultivation.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
The Natural Product Domain Seeker (NaPDoS) webtool detects and classifies ketosynthase (KS) and condensation domains from genomic, metagenomic, and amplicon sequence data. Unlike other tools, a ...phylogeny-based classification scheme is used to make broader predictions about the polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) genes in which these domains are found. NaPDoS is particularly useful for the analysis of incomplete biosynthetic genes or gene clusters, as are often observed in poorly assembled genomes and metagenomes, or when loci are not clustered, as in eukaryotic genomes. To help support the growing interest in sequence-based analyses of natural product biosynthetic diversity, here we introduce version 2 of the webtool, NaPDoS2, available at http://napdos.ucsd.edu/napdos2. This update includes the addition of 1417 KS sequences, representing a major expansion of the taxonomic and functional diversity represented in the webtool database. The phylogeny-based KS classification scheme now recognizes 41 class and subclass assignments, including new type II PKS subclasses. Workflow modifications accelerate run times, allowing larger datasets to be analyzed. In addition, default parameters were established using statistical validation tests to maximize KS detection and classification accuracy while minimizing false positives. We further demonstrate the applications of NaPDoS2 to assess PKS biosynthetic potential using genomic, metagenomic, and PCR amplicon datasets. These examples illustrate how NaPDoS2 can be used to predict biosynthetic potential and detect genes involved in the biosynthesis of specific structure classes or new biosynthetic mechanisms.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPUK, ZAGLJ, ZRSKP
Thousands of natural products have been identified from cultured microorganisms, yet evidence of their production in the environment has proven elusive. Technological advances in mass spectrometry, ...combined with public databases, now make it possible to address this disparity by detecting compounds directly from environmental samples. Here, we used adsorbent resins, tandem mass spectrometry, and next-generation sequencing to assess the metabolome of marine sediments and its relationship to bacterial community structure. We identified natural products previously reported from cultured bacteria, providing evidence they are produced
, and compounds of anthropogenic origin, suggesting this approach can be used as an indicator of environmental impact. The bacterial metabolite staurosporine was quantified and shown to reach physiologically relevant concentrations, indicating that it may influence sediment community structure. Staurosporine concentrations were correlated with the relative abundance of the staurosporine-producing bacterial genus
and production confirmed in strains cultured from the same location, providing a link between compound and candidate producer. Metagenomic analyses revealed numerous biosynthetic gene clusters related to indolocarbazole biosynthesis, providing evidence for noncanonical sources of staurosporine and a path forward to assess the relationships between natural products and the organisms that produce them. Untargeted environmental metabolomics circumvents the need for laboratory cultivation and represents a promising approach to understanding the functional roles of natural products in shaping microbial community structure in marine sediments.
Natural products are readily isolated from cultured bacteria and exploited for useful purposes, including drug discovery. However, these compounds are rarely detected in the environments from which the bacteria are obtained, thus limiting our understanding of their ecological significance. Here, we used environmental metabolomics to directly assess chemical diversity in marine sediments. We identified numerous metabolites and, in one case, isolated strains of bacteria capable of producing one of the compounds detected. Coupling environmental metabolomics with community and metagenomic analyses provides opportunities to link compounds and producers and begin to assess the complex interactions mediated by specialized metabolites in marine sediments.
Long-standing theory predicts that the intensity of consumer–prey interactions declines with increasing latitude, yet for plant–herbivore interactions, latitudinal changes in herbivory rates and ...plant palatability have received variable support. The topic is of growing interest given that lower-latitude species are moving poleward at an accelerating rate due to climate change, and predicting local interactions will depend partly on whether latitudinal gradients occur in these critical biotic interactions. Here, we assayed the palatability of 50 seaweeds collected from polar (Antarctica), temperate (northeastern Pacific; California), and tropical (central Pacific; Fiji) locations to two herbivores native to the tropical and subtropical Atlantic, the generalist crab Mithraculus sculptus and sea urchin Echinometra lucunter. Red seaweeds (Rhodophyta) of polar and temperate origin were more readily consumed by urchins than were tropical reds. The decline in palatability with decreasing latitude is explained by shifts in tissue organic content along with the quantity and quality of secondary metabolites, degree of calcification or both. We detected no latitudinal shift in palatability of red seaweeds to crabs, nor any latitudinal shifts in palatability of brown seaweeds (Phaeophyta) to either crabs or urchins. Our results suggest that evolutionary pressure from tropical herbivores favored red seaweeds with lower palatability, either through the production of greater levels of chemical defenses, calcification, or both. Moreover, our results tentatively suggest that the "tropicalization" of temperate habitats is facilitated by the migration of tropical herbivores into temperate areas dominated by weakly defended and more nutritious foods, and that the removal of these competing seaweeds may facilitate the invasion of better-defended tropical seaweeds.
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BFBNIB, FZAB, GIS, IJS, INZLJ, KILJ, NLZOH, NMLJ, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK, ZRSKP
Tetrabromopyrrole (TBP) is a readily biosynthesized marine proteobacterial compound that induces coral settlement (attachment and metamorphosis) at concentrations ranging from 50 – 250 ng ml
-1
(0.13 ...– 0.65 µM). This suggests a great potential for the use of this compound as a settlement inducer for restoration purposes. However, the applicability and optimal concentration of TBP for many coral species is not yet known. Furthermore, TBP is an unstable compound, which may present both challenges and benefits to its potential use for restoration purposes. In order to assess the utility of this compound for restoration, settlement induction by TBP was assessed among a wide range of Caribbean coral species. Additionally, a suite of halogenated compounds (tribromopyrrole, pentabromopseudolin, dibromophenol, tribromophenol, bromophene, n-methyl tetrabromopyrrole, tetrachloropyrrole, dibromoindole, n-methyl tetrachloropyrrole and dibromopyridine) that are related to TBP, some of which have similar antibiotic and antialgal properties, were also tested for settlement induction activity. These compounds were chosen based on their structural similarity to TBP or their identity as a product within the bacterial TBP biosynthetic pathway. TBP induced settlement in nine of ten coral species tested including seven not previously reported (
Dendrogyra cylindrus
,
Orbicella faveolata
,
Colpophyllia natans
,
Diploria labyrinthiformis, Pseudodiploria clivosa, Acropora cervicornis, Montastraea cavernosa
) at concentrations ranging from 0.375 – 1.5 µM. No other compound tested induced settlement, demonstrating a high degree of specificity for TBP.
Deoxygenation is emerging as a major threat to coral reefs where it can have catastrophic effects, including mass coral mortality. Some coral species cannot survive more than a few days of exposure ...to low oxygen conditions, while others can tolerate deoxygenation for weeks, suggesting that coral tolerance to lowered dissolved oxygen (DO) concentrations is species-specific. However, hypoxia thresholds for corals have not yet been fully defined, and more information is needed to understand if tolerance to deoxygenation is consistent across all life stages. In this study, we tested the influence of severe (1.5 mg L
-1
DO) and intermediate (3.5 mg L
-1
DO) deoxygenation on larval settlement and survival during the early recruitment life phase of
Colpophyllia natans
,
Orbicella faveolata
, and
Pseudodiploria strigosa.
Exposure to deoxygenation over a 3-day settlement period did not significantly impact larval survival nor settlement rates compared to ambient DO concentrations (6 mg L
-1
DO) for all three species. However, recruit survivorship in
C. natans
and
O. faveolata
after further exposure to severe deoxygenation was reduced compared to intermediate deoxygenation and control DO conditions. After 45 days of exposure to severe deoxygenation only 2.5 ± 2.5% of the initial
O. faveolata
had survived the larval and recruit stages compared to 22.5 ± 4.5% in control oxygen conditions. Similarly,
C. natans
survival was 13.5 ± 6.0% under severe deoxygenation, compared to 41.0 ± 4.4% in the control treatment. In contrast, survival of
P. strigosa
larvae and recruits was not different under deoxygenation treatments compared to the control, and higher overall, relative to the other species, indicating that
P. strigosa
is more resilient to severe deoxygenation conditions during its earliest life stages. This study provides unique insights into species-specific variation in the tolerance of coral recruits to deoxygenation with implications for whether this life history stage may be a demographic bottleneck for three ecologically important Caribbean coral species. Given the increasing frequency and severity of deoxygenation events in Caribbean coastal waters, these results are an important contribution to the growing body of research on deoxygenation as a threat to coral reef persistence in the Anthropocene, with implications for conservation and restoration efforts integrating coral recruitment into reef recovery efforts.
Abstract An important factor dictating coral fitness is the quality of bacteria associated with corals and coral reefs. One way that bacteria benefit corals is by stimulating the larval to juvenile ...life cycle transition of settlement and metamorphosis. Tetrabromopyrrole (TBP) is a small molecule produced by bacteria that stimulates metamorphosis with and without attachment in a range of coral species. A standing debate remains, however, about whether TBP biosynthesis from live Pseudoalteromonas bacteria is the primary stimulant of coral metamorphosis. In this study, we create a Pseudoalteromonas sp. PS5 mutant lacking the TBP brominase gene, bmp2. Using this mutant, we confirm that the bmp2 gene is critical for TBP biosynthesis in Pseudoalteromonas sp. PS5. Mutation of this gene ablates the bacterium’s ability in live cultures to stimulate the metamorphosis of the stony coral Porites astreoides. We further demonstrate that expression of TBP biosynthesis genes is strongest in stationary and biofilm modes of growth, where Pseudoalteromonas sp. PS5 might exist within surface-attached biofilms on the sea floor. Finally, we create a modular transposon plasmid for genomic integration and fluorescent labeling of Pseudoalteromonas sp. PS5 cells. Our results functionally link a TBP biosynthesis gene from live bacteria to a morphogenic effect in corals. The genetic techniques established here provide new tools to explore coral-bacteria interactions and could help to inform future decisions about utilizing marine bacteria or their products for coral restoration.
•First large-scale food composition analysis using mass spectral molecular networking.•A methodological pipeline for compound discovery applicable to diverse foods was generated.•Molecular networking ...and statistical analyses were combined to detect chemical changes in foods.•Brewing, roasting, fermenting, spoiling, and ripening were investigated in example foods.•Time-based chemical changes were detected in yogurt, tea, beef, turkey, and tomato samples.
In our daily lives, we consume foods that have been transported, stored, prepared, cooked, or otherwise processed by ourselves or others. Food storage and preparation have drastic effects on the chemical composition of foods. Untargeted mass spectrometry analysis of food samples has the potential to increase our chemical understanding of these processes by detecting a broad spectrum of chemicals. We performed a time-based analysis of the chemical changes in foods during common preparations, such as fermentation, brewing, and ripening, using untargeted mass spectrometry and molecular networking. The data analysis workflow presented implements an approach to study changes in food chemistry that can reveal global alterations in chemical profiles, identify changes in abundance, as well as identify specific chemicals and their transformation products. The data generated in this study are publicly available, enabling the replication and re-analysis of these data in isolation, and serve as a baseline dataset for future investigations.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPUK, ZAGLJ, ZRSKP
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