Influence of coral and algal exudates on microbially mediated reef metabolism.

Benthic primary producers in tropical reef ecosystems can alter biogeochemical cycling and microbial processes in the surrounding seawater. In order to quantify these influences, we measured rates of photosynthesis, respiration, and dissolved organic carbon (DOC) exudate release by the dominant benthic primary producers (calcifying and non-calcifying macroalgae, turf-algae and corals) on reefs of Mo'orea French Polynesia. Subsequently, we examined planktonic and benthic microbial community response to these dissolved exudates by measuring bacterial growth rates and oxygen and DOC fluxes in dark and daylight incubation experiments. All benthic primary producers exuded significant quantities of DOC (roughly 10% of their daily fixed carbon) into the surrounding water over a diurnal cycle. The microbial community responses were dependent upon the source of the exudates and whether the inoculum of microbes included planktonic or planktonic plus benthic communities. The planktonic and benthic microbial communities in the unamended control treatments exhibited opposing influences on DO concentration where respiration dominated in treatments comprised solely of plankton and autotrophy dominated in treatments with benthic plus plankon microbial communities. Coral exudates (and associated inorganic nutrients) caused a shift towards a net autotrophic microbial metabolism by increasing the net production of oxygen by the benthic and decreasing the net consumption of oxygen by the planktonic microbial community. In contrast, the addition of algal exudates decreased the net primary production by the benthic communities and increased the net consumption of oxygen by the planktonic microbial community thereby resulting in a shift towards net heterotrophic community metabolism. When scaled up to the reef habitat, exudate-induced effects on microbial respiration did not outweigh the high oxygen production rates of benthic algae, such that reef areas dominated with benthic primary producers were always estimated to be net autotrophic. However, estimates of microbial consumption of DOC at the reef scale surpassed the DOC exudation rates suggesting net consumption of DOC at the reef-scale. In situ mesocosm experiments using custom-made benthic chambers placed over different types of benthic communities exhibited identical trends to those found in incubation experiments. Here we provide the first comprehensive dataset examining direct primary producer-induced, and indirect microbially mediated alterations of elemental cycling in both benthic and planktonic reef environments over diurnal cycles. Our results highlight the variability of the influence of different benthic primary producers on microbial metabolism in reef ecosystems and the potential implications for energy transfer to higher trophic levels during shifts from coral to algal dominance on reefs

Coral reef biofilm bacterial diversity and successional trajectories are structured by reef benthic organisms and shift under chronic nutrient enrichment

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Remple, K. L., Silbiger, N. J., Quinlan, Z. A., Fox, M. D., Kelly, L. W., Donahue, M. J., & Nelson, C. E. Coral reef biofilm bacterial diversity and successional trajectories are structured by reef benthic organisms and shift under chronic nutrient enrichment. Npj Biofilms and Microbiomes, 7(1), (2021): 84, https://doi.org/10.1038/s41522-021-00252-1.Work on marine biofilms has primarily focused on host-associated habitats for their roles in larval recruitment and disease dynamics; little is known about the factors regulating the composition of reef environmental biofilms. To contrast the roles of succession, benthic communities and nutrients in structuring marine biofilms, we surveyed bacteria communities in biofilms through a six-week succession in aquaria containing macroalgae, coral, or reef sand factorially crossed with three levels of continuous nutrient enrichment. Our findings demonstrate how biofilm successional trajectories diverge from temporal dynamics of the bacterioplankton and how biofilms are structured by the surrounding benthic organisms and nutrient enrichment. We identify a suite of biofilm-associated bacteria linked with the orthogonal influences of corals, algae and nutrients and distinct from the overlying water. Our results provide a comprehensive characterization of marine biofilm successional dynamics and contextualize the impact of widespread changes in reef community composition and nutrient pollution on biofilm community structure.This work was supported through grants from the National Science Foundation for Biological Oceanography (1923877 to C.E.N. and M.J.D., 1949033 to C.E.N. and 2118687 to L.W.K., and 1924281 to N.J.S.) and the National Fish and Wildlife Foundation (grant no. 44447 to C.E.N.). This paper is funded in part by the National Oceanic and Atmospheric Administration, Project A/AS-1, which is sponsored by the University of Hawaii Sea Grant College Program, SOEST, under Institutional Grant No. NA18OAR4170076 from NOAA Office of Sea Grant, Department of Commerce. This is CSUN marine biology contribution #365, UH Sea Grant contribution UNIHI-SEAGRANT-JC-21-06, and UH SOEST contribution 11435

Effects of Coral Reef Benthic Primary Producers on Dissolved Organic Carbon and Microbial Activity

Benthic primary producers in marine ecosystems may significantly alter biogeochemical cycling and microbial processes in their surrounding environment. To examine these interactions, we studied dissolved organic matter release by dominant benthic taxa and subsequent microbial remineralization in the lagoonal reefs of Moorea, French Polynesia. Rates of photosynthesis, respiration, and dissolved organic carbon (DOC) release were assessed for several common benthic reef organisms from the backreef habitat. We assessed microbial community response to dissolved exudates of each benthic producer by measuring bacterioplankton growth, respiration, and DOC drawdown in two-day dark dilution culture incubations. Experiments were conducted for six benthic producers: three species of macroalgae (each representing a different algal phylum: Turbinaria ornata – Ochrophyta; Amansia rhodantha – Rhodophyta; Halimeda opuntia – Chlorophyta), a mixed assemblage of turf algae, a species of crustose coralline algae (Hydrolithon reinboldii) and a dominant hermatypic coral (Porites lobata). Our results show that all five types of algae, but not the coral, exuded significant amounts of labile DOC into their surrounding environment. In general, primary producers with the highest rates of photosynthesis released the most DOC and yielded the greatest bacterioplankton growth; turf algae produced nearly twice as much DOC per unit surface area than the other benthic producers (14.0±2.8 µmol h−1 dm−2), stimulating rapid bacterioplankton growth (0.044±0.002 log10 cells h−1) and concomitant oxygen drawdown (0.16±0.05 µmol L−1 h−1 dm−2). Our results demonstrate that benthic reef algae can release a significant fraction of their photosynthetically-fixed carbon as DOC, these release rates vary by species, and this DOC is available to and consumed by reef associated microbes. These data provide compelling evidence that benthic primary producers differentially influence reef microbial dynamics and biogeochemical parameters (i.e., DOC and oxygen availability, bacterial abundance and metabolism) in coral reef communities

Variability and host density independence in inductions-based estimates of environmental lysogeny.

Temperate bacterial viruses (phages) may enter a symbiosis with their host cell, forming a unit called a lysogen. Infection and viral replication are disassociated in lysogens until an induction event such as DNA damage occurs, triggering viral-mediated lysis. The lysogen-lytic viral reproduction switch is central to viral ecology, with diverse ecosystem impacts. It has been argued that lysogeny is favoured in phages at low host densities. This paradigm is based on the fraction of chemically inducible cells (FCIC) lysogeny proxy determined using DNA-damaging mitomycin C inductions. Contrary to the established paradigm, a survey of 39 inductions publications found FCIC to be highly variable and pervasively insensitive to bacterial host density at global, within-environment and within-study levels. Attempts to determine the source(s) of variability highlighted the inherent complications in using the FCIC proxy in mixed communities, including dissociation between rates of lysogeny and FCIC values. Ultimately, FCIC studies do not provide robust measures of lysogeny or consistent evidence of either positive or negative host density dependence to the lytic-lysogenic switch. Other metrics are therefore needed to understand the drivers of the lytic-lysogenic decision in viral communities and to test models of the host density-dependent viral lytic-lysogenic switch

Coral Reef Microbes: The Influences of Benthic Primary Producers, Nutrient Availability, and Anthropogenic Stressors on Community Structure and Metabolism

Includes bibliographical referencesGenomic studies of marine microbes have advanced our understanding of community ecology and the vast array of metabolisms microbes utilize for acquiring energy and nutrients in the ocean. The structure of microbial communities overlying coral reefs have been shown to reflect ecosystem health. For example, algal-dominated reefs are inhabited by more pathogen-like microbes. The objective of my PhD thesis was to use metagenomics to investigate the microbial communities associated with the coral animal (Chapter 2) and coral reefs influenced by different nutrient regimes (Chapter 3) and anthropogenic disturbances (Chapter 4).\ud The Line Island archipelago consists of eleven atolls spanning a latitudinal gradient from 6o north to 11o south. Nutrient concentrations vary across the islands where inorganic nutrient concentrations are approximately five and two-times higher for nitrogen and phosphorus, respectively on Jarvis (located closest to the equator)\ud compared to Kingman and Flint (located furthest north and south). Bacterial metagenomes were constructed from 26 coral reefs to investigate community differences between reefs on uninhabited versus populated Line Islands and the influence of biogeochemistry on community structure. The distribution of microbial taxa was most strongly predicted by the composition of certain benthic functional groups. Where reefs with higher coral cover observed on Islands Malden, Flint, and\ud Vostok were associated with higher abundances of Sphingomonadales. In contrast, Kiritimati reefs which were dominated by turf algae, were associated with higher abundances of Bacteriodetes. The microbial community metabolism on LI reefs was shown to be most strongly influenced by geographic distance from the equator. This grouping of community metabolism based on geographic location occurred despite\ud differences in the distribution of taxa present a reef sites. Distance from the equator is strongly correlated with nitrogen and phosphorus concentrations suggesting that nutrient availability is an important driver for community metabolism on Line Island reefs. Metabolic pathways positively correlated with higher nutrients included conjugative transfer, chemotaxis, nitrate and nitrite ammonification, cobalt-zinccadmium\ud resistance, multidrug resistance efflux pumps, and ton and tol transport. Low nutrient availability was correlated with metabolic pathways involved in photosynthesis, such as chlorophyll biosynthesis and photosystems I and II. The results from this study suggest that selection of microbial taxa is based on carbon sources (benthic community composition) and subsequently, specific genes are incorporated for adaptations to nutrient availability in that region.\ud To better understand how microbial community structure changes in response to environmental perturbations, three reefs that had undergone a coral-algal phase shift in response to ship groundings were investigated. The Line Islands are calcium carbonate coral reef platforms located in an extremely iron-limited region of the central Pacific. Therefore it was hypothesized that iron leaching from the shipwreck\ud debris was enabling the benthic algae to outcompete and overgrow the corals. The reefs surrounding the shipwreck debris were characterized by high benthic cover of turf algae, macroalgae, cyanobacterial mats, and corallimorphs, as well as particulateladen, cloudy water. These sites also have very low coral and crustose coralline algal (CCA) cover and are call black reefs because of the dark colored benthic community and reduced clarity of the overlying water column. A combination of benthic surveys, chemistry, metagenomics, and microcosms were used to investigate if and how shipwrecks initiate and maintain black reefs. Iron concentrations in algae tissue from the Millennium black reef site were 6-times higher than in algae collected from reference sites. Metagenomic sequencing of the Millennium Atoll black reef-associated\ud microbial community was enriched in iron-associated virulence genes and known pathogens. Microcosm experiments showed that corals were killed by black reef rubble via microbial activity. Together these results demonstrate that shipwrecks and their associated iron pose significant threats to coral reefs in iron-limited regions

Ecosystem Microbiology of Coral Reefs: Linking Genomic, Metabolomic, and Biogeochemical Dynamics from Animal Symbioses to Reefscape Processes

Over the past 2 decades, molecular techniques have established the critical role of both free-living and host-associated microbial partnerships in the environment. Advancing research to link microbial community dynamics simultaneously to host physiology and ecosystem biogeochemistry is required to broaden our understanding of the ecological roles of environmental microbes. Studies on coral reefs are actively integrating these data streams at multiple levels, from the symbiotic habitat of the coral holobiont to microbially mediated interactions between corals and algae to the effects of these interactions on the microbial community structure, metabolism, and organic geochemistry of the reef ecosystem. Coral reefs endure multiple anthropogenic impacts, including pollution, overfishing, and global change. In this context, we must develop ecosystem microbiology with an eye to providing managers with microbial indicators of reef ecosystem processes, coral health, and resilience to both local and global stressors

ConCISE: Consensus Annotation Propagation of Ion Features in Untargeted Tandem Mass Spectrometry Combining Molecular Networking and In Silico Metabolite Structure Prediction

Recent developments in molecular networking have expanded our ability to characterize the metabolome of diverse samples that contain a significant proportion of ion features with no mass spectral match to known compounds. Manual and tool-assisted natural annotation propagation is readily used to classify molecular networks; however, currently no annotation propagation tools leverage consensus confidence strategies enabled by hierarchical chemical ontologies or enable the use of new in silico tools without significant modification. Herein we present ConCISE (Consensus Classifications of In Silico Elucidations) which is the first tool to fuse molecular networking, spectral library matching and in silico class predictions to establish accurate putative classifications for entire subnetworks. By limiting annotation propagation to only structural classes which are identical for the majority of ion features within a subnetwork, ConCISE maintains a true positive rate greater than 95% across all levels of the ChemOnt hierarchical ontology used by the ClassyFire annotation software (superclass, class, subclass). The ConCISE framework expanded the proportion of reliable and consistent ion feature annotation up to 76%, allowing for improved assessment of the chemo-diversity of dissolved organic matter pools from three complex marine metabolomics datasets comprising dominant reef primary producers, five species of the diatom genus Pseudo-nitzchia, and stromatolite sediment samples