Benthic N2 fixation in coral reefs and the potential effects of human‐induced environmental change

Tropical coral reefs are among the most productive and diverse ecosystems, despite being surrounded by ocean waters where nutrients are in short supply. Benthic dinitrogen (N₂) fixation is a significant internal source of “new” nitrogen (N) in reef ecosystems, but related information appears to be sparse. Here, we review the current state (and gaps) of knowledge on N₂ fixation associated with coral reef organisms and their ecosystems. By summarizing the existing literature, we show that benthic N₂ fixation is an omnipresent process in tropical reef environments. Highest N₂ fixation rates are detected in reef‐associated cyanobacterial mats and sea grass meadows, clearly showing the significance of these functional groups, if present, to the input of new N in reef ecosystems. Nonetheless, key benthic organisms such as hard corals also importantly contribute to benthic N₂ fixation in the reef. Given the usually high coral coverage of healthy reef systems, these results indicate that benthic symbiotic associations may be more important than previously thought. In fact, mutualisms between carbon (C) and N₂ fixers have likely evolved that may enable reef communities to mitigate N limitation. We then explore the potential effects of the increasing human interferences on the process of benthic reef N₂ fixation via changes in diazotrophic populations, enzymatic activities, or availability of benthic substrates favorable to these microorganisms. Current knowledge indicates positive effects of ocean acidification, warming, and deoxygenation and negative effects of increased ultraviolet radiation on the amount of N fixed in coral reefs. Eutrophication may either boost or suppress N₂ fixation, depending on the nutrient becoming limiting. As N₂ fixation appears to play a fundamental role in nutrient‐limited reef ecosystems, these assumptions need to be expanded and confirmed by future research efforts addressing the knowledge gaps identified in this review.     

Convergent photophysiology and prokaryotic assemblage structure in epilithic cyanobacterial tufts and algal turf communities

As global change spurs shifts in benthic community composition on coral reefs globally, a better understanding of the defining taxonomic and functional features that differentiate proliferating benthic taxa is needed to predict functional trajectories of reef degradation better. This is especially critical for algal groups, which feature dramatically on changing reefs. Limited attention has been given to characterizing the features that differentiate tufting epilithic cyanobacterial communities from ubiquitous turf algal assemblages. Here, we integrated an in situ assessment of photosynthetic yield with metabarcoding and shotgun metagenomic sequencing to explore photophysiology and prokaryotic assemblage structure within epilithic tufting benthic cyanobacterial communities and epilithic algal turf communities. Significant differences were not detected in the average quantum yield. However, variability in yield was significantly higher in cyanobacterial tufts. Neither prokaryotic assemblage diversity nor structure significantly differed between these functional groups. The sampled cyanobacterial tufts, predominantly built by Okeania sp., were co-dominated by members of the Proteobacteria, Firmicutes, and Bacteroidota, as were turf algal communities. Few detected ASVs were significantly differentially abundant between functional groups and consisted exclusively of taxa belonging to the phyla Proteobacteria and Firmicutes. Assessment of the distribution of recovered cyanobacterial amplicons demonstrated that alongside sample-specific cyanobacterial diversification, the dominant cyanobacterial members were conserved across tufting cyanobacterial and turf algal communities. Overall, these data suggest a convergence in taxonomic identity and mean photosynthetic potential between tufting epilithic cyanobacterial communities and algal turf communities, with numerous implications for consumer-resource dynamics on future reefs and trajectories of reef functional ecology.     

Black reefs: iron-induced phase shifts on coral reefs

The Line Islands are calcium carbonate coral reef platforms located in iron-poor regions of the central Pacific. Natural terrestrial run-off of iron is non-existent and aerial deposition is extremely low. However, a number of ship groundings have occurred on these atolls. The reefs surrounding the shipwreck debris are characterized by high benthic cover of turf algae, macroalgae, cyanobacterial mats and corallimorphs, as well as particulate-laden, cloudy water. These sites also have very low coral and crustose coralline algal cover and are call black reefs because of the dark-colored benthic community and reduced clarity of the overlying water column. Here we use a combination of benthic surveys, chemistry, metagenomics and microcosms to investigate if and how shipwrecks initiate and maintain black reefs. Comparative surveys show that the live coral cover was reduced from 40 to 60% to <10% on black reefs on Millennium, Tabuaeran and Kingman. These three sites are relatively large (>0.75 km²). The phase shift occurs rapidly; the Kingman black reef formed within 3 years of the ship grounding. Iron concentrations in algae tissue from the Millennium black reef site were six times higher than in algae collected from reference sites. Metagenomic sequencing of the Millennium Atoll black reef-associated microbial community was enriched in iron-associated virulence genes and known pathogens. Microcosm experiments showed that corals were killed by black reef rubble through microbial activity. Together these results demonstrate that shipwrecks and their associated iron pose significant threats to coral reefs in iron-limited regions.     

Framework of barrier reefs threatened by ocean acidification

To date, studies of ocean acidification (OA) on coral reefs have focused on organisms rather than communities, and the few community effects that have been addressed have focused on shallow back reef habitats. The effects of OA on outer barrier reefs, which are the most striking of coral reef habitats and are functionally and physically different from back reefs, are unknown. Using 5‐m long outdoor flumes to create treatment conditions, we constructed coral reef communities comprised of calcified algae, corals, and reef pavement that were assembled to match the community structure at 17 m depth on the outer barrier reef of Moorea, French Polynesia. Communities were maintained under ambient and 1200 μatm pCO₂ for 7 weeks, and net calcification rates were measured at different flow speeds. Community net calcification was significantly affected by OA, especially at night when net calcification was depressed ~78% compared to ambient pCO₂. Flow speed (2–14 cm s^?1) enhanced net calcification only at night under elevated pCO₂. Reef pavement also was affected by OA, with dissolution ~86% higher under elevated pCO₂ compared to ambient pCO₂. These results suggest that net accretion of outer barrier reef communities will decline under OA conditions predicted within the next 100 years, largely because of increased dissolution of reef pavement. Such extensive dissolution poses a threat to the carbonate foundation of barrier reef communities.     

Ecophysiology of stromatolitic microbial mats,Stocking Island,exuma cays,Bahamas

Intertidal stromatolites, covered by cyanobacterial mats, were recently discovered at Stocking Island, Exuma Cays, Bahamas. Ecophysiological responses (CO₂ fixation, N₂ fixation, and photoacclimation) of these cyanobacterial mats to experimental manipulations were examined to identify potential environmental variables controlling community structure and function. The mats exhibit horizontal zonation that shifts from soft to crusty to hard in a seaward direction. Cluster analysis of chemotaxonomic photopigments (chlorophylls and carotenoids) revealed that visually distinct mat types are composed of distinct phototrophic assemblages. Under reduced irradiance, diatoms within the mats photoacclimated by increasing accessory photopigments (diadinoxanthin, fucoxanthin, and chlorophyll c ₁ c ₂) and cyanobacteria reduced the photoprotective carotenoid echinenone. In a 4-day nutrient addition bioassay experiment, nitrate, phosphate, dissolved organic carbon, and trace metal enrichments did not enhance CO₂ fixation, but phosphate enrichments tripled N₂ fixation rates. The addition of DCMU increased N₂ fixation rates relative to nonamended light and dark rates, indicating light (photosystem I) enhanced nitrogenase activity. Soft mats appear to represent the early stages of colonization and stabilization of mat communities. Active growth following stabilization results in the formation of partially-lithified crusty mats, which eventually become highly-lithified and form hard mats. Collectively, our results suggest that Stocking Island stromatolitic mats have low growth rates and consequently exhibit slow responses to increased nutrient availability and changes in ambient irradiance. In general, intertidal stromatolitic mats at Stocking Island appear to exhibit low rates of CO₂ and N₂ fixation relative to nonlithifying temperate cyanobacteral mats. Although production is low, respiration is likewise low, leading to the suggestion that high production to respiration ratios (P:R) may be necessary for lithification of intertidal stromatolitic mats.     

Heterogeneous dissolved organic nitrogen supply over a coral reef: first evidence from nitrogen stable isotope ratios

Dissolved organic nitrogen (DON) potentially plays a major role in sustaining the high productivity and biological diversity of coral reefs. However, data are scarce regarding sources and sinks of DON. This study, for the first time, determined the ¹⁵N isotopic composition of total dissolved nitrogen (δ¹⁵N_TDN), reflecting the isotopic signature of DON, in the water column over a coral reef. The uniformity in δ¹⁵N_TDN during high tide (3.2 ± 0.3 ‰) indicated that the DON was mainly derived from offshore waters. In contrast, higher spatial heterogeneity of δ¹⁵N_TDN (3.1 ± 0.9 ‰) and DON concentrations during low tide indicated the existence of local DON sources patchily distributed over the reef. Low δ¹⁵N_TDN values located mid-reef were indicative of DON release from organisms that obtained their N via N₂ fixation, whereas high δ¹⁵N_TDN appeared to reflect localized release of DON by organisms exposed to dissolved inorganic nitrogen with elevated ¹⁵N, such as from terrestrial and offshore inputs. Collectively, the results highlight the importance of spatial patterns in DON release from reef communities in the N cycling of coral reefs.     

Dinitrogen fixation by exposed communities on the rim of Tikehau atoll (Tuamotu Archipelago, French Polynesia)

Various types of sub-aerially exposed microbial mats, including emergent mats, beach sand, beach rock and Kopara mats, are widespread on the 78 km (25 km²) of rim surrounding the Tikehau atoll lagoon. These mats form laminated accretions or diffuse microbial communities growing under high insolation and temperatures, and are therefore subject to desiccation. Both heterocystous and non-heterocystous cyanobacteria occur in these mats. Using acetylene reduction techniques, nitrogenase activity was observed at all sites over a period of 5 years and was 3–17 times higher during daylight than at night in all communities except for beach rock. ¹⁵N₂ measurements indicated a molar ratio of acetylene reduction to N₂ fixed of 1.6 for all exposed communities. Estimated N₂ fixation ranged from 1.44 to 8.0 mg N m⁻² day⁻¹ in these exposed communities (mean of 4.66 mg N m⁻² day⁻¹) with beachrock showing the highest rates. For the whole reef rim, daily N₂ fixation amounted to 98.42 kg N day⁻¹ which represents 28% of the rate of fixation in the entire lagoon (area 400 km²).     

Extreme spatial heterogeneity in carbonate accretion potential on a Caribbean fringing reef linked to local human disturbance gradients

The capacity of coral reefs to maintain their structurally complex frameworks and to retain the potential for vertical accretion is vitally important to the persistence of their ecological functioning and the ecosystem services they sustain. However, datasets to support detailed along‐coast assessments of framework production rates and accretion potential do not presently exist. Here, we estimate, based on gross bioaccretion and bioerosion measures, the carbonate budgets and resultant estimated accretion rates (EAR) of the shallow reef zone of leeward Bonaire – between 5 and 12 m depth – at unique fine spatial resolution along this coast (115 sites). Whilst the fringing reef of Bonaire is often reported to be in a better ecological condition than most sites throughout the wider Caribbean region, our data show that the carbonate budgets of the reefs and derived EAR varied considerably across this ~58 km long fringing reef complex. Some areas, in particular the marine reserves, were indeed still dominated by structurally complex coral communities with high net carbonate production (>10 kg CaCO₃ m^?2 year^?1), high live coral cover and complex structural topography. The majority of the studied sites, however, were defined by relatively low budget states (<2 kg CaCO₃ m^?2 year^?1) or were in a state of net erosion. These data highlight the marked spatial heterogeneity that can occur in budget states, and thus in reef accretion potential, even between quite closely spaced areas of individual reef complexes. This heterogeneity is linked strongly to the degree of localized land‐based impacts along the coast, and resultant differences in the abundance of reef framework building coral species. The major impact of this variability is that those sections of reef defined by low‐accretion rates will have limited capacity to maintain their structural integrity and to keep pace with current projections of climate change induced sea‐level rise (SLR), thus posing a threat to reef functioning and biodiversity, potentially leading to trophic cascades. Since many Caribbean reefs are more severely degraded than those found around Bonaire, it is to be expected that the findings presented here are rather the rule than the exception, but the study also highlights the need for similar high spatial resolution (along‐coast) assessments of budget states and accretion rates to meaningfully explore increasing coastal risk at the country level. The findings also more generally underline the significance of reducing local anthropogenic disturbance and restoring framework building coral assemblages. Appropriately focussed local preservation efforts may aid in averting future large‐scale above reef water depth increases on Caribbean coral reefs and will limit the social and economic implications associated with the loss of reef goods and services.     

Coral-associated nitrogen fixation rates and diazotrophic diversity on a nutrient-replete equatorial reef

The role of diazotrophs in coral physiology and reef biogeochemistry remains poorly understood, in part because N₂ fixation rates and diazotrophic community composition have only been jointly analyzed in the tissue of one tropical coral species. We performed field-based ¹⁵N₂ tracer incubations during nutrient-replete conditions to measure diazotroph-derived nitrogen (DDN) assimilation into three species of scleractinian coral (Pocillopora acuta, Goniopora columna, Platygyra sinensis). Using multi-marker metabarcoding (16S rRNA, nifH, 18S rRNA), we analyzed DNA- and RNA-based communities in coral tissue and skeleton. Despite low N₂ fixation rates, DDN assimilation supplied up to 6% of the holobiont’s N demand. Active coral-associated diazotrophs were chiefly Cluster I (aerobes or facultative anaerobes), suggesting that oxygen may control coral-associated diazotrophy. Highest N₂ fixation rates were observed in the endolithic community (0.20 µg N cm⁻² per day). While the diazotrophic community was similar between the tissue and skeleton, RNA:DNA ratios indicate potential differences in relative diazotrophic activity between these compartments. In Pocillopora, DDN was found in endolithic, host, and symbiont compartments, while diazotrophic nifH sequences were only observed in the endolithic layer, suggesting a possible DDN exchange between the endolithic community and the overlying coral tissue. Our findings demonstrate that coral-associated diazotrophy is significant, even in nutrient-rich waters, and suggest that endolithic microbes are major contributors to coral nitrogen cycling on reefs.Subject terms: Microbial ecology, Biogeochemistry, Stable isotope analysis     

Depth-dependent indicators of algal turf herbivory throughout the Main Hawaiian Islands

Herbivorous fish are key to maintaining a balance between coral and algae on reefs, where reefs with greater herbivore biomass often show lower algal cover. For reefs worldwide, algal turf cover is expanding and is increasingly used as an indicator of disturbance. Water depth affects reef fish composition; thus, it may be expected that herbivory could also differ by depth. We examined relationships between algal turf cover and biomass (g m⁻²), density (# m⁻²) and size (cm) of herbivore groups (grazers, browsers and scrapers) across shallow (< 6 m), mid (6–18 m) and deep (18–30 m) coral reefs in the Main Hawaiian Islands. We find that across all depth classes, algal turf cover decreased with increasing grazer and scraper density, with steeper relationships observed at mid and deep reefs than in shallow reefs. In contrast, algal turf cover slightly increased with increasing grazer and browser biomass at deep reefs. Considering fish size, algal turf cover increased with larger grazer and scrapers at mid and deep reefs. The results indicate that herbivorous fish density, rather than biomass, is a better indicator of reductions in algal turf cover and resulting coral-algal balance on Hawaiian reefs, where smaller fish exert greater top-down control on cover than larger fish. Despite significant differences in herbivorous fish compositions, length-frequency distributions and fishing intensities across depth, algal turf cover remains similar across depths. Increases in fishing would have a disproportionately negative impact in deep than shallow reefs due to a lower overall fish density, where grazing functions in deep reefs are maintained by significantly fewer and smaller grazers and browsers, and larger scrapers, than in shallow reefs. Developing an understanding of patterns of algal turf herbivory by depth is important to understanding the spatial scale at which herbivory and regime shifts operate.

     

Effects of coral transplantation and giant clam restocking on the structure of fish communities on degraded patch reefs

Active restoration is being practiced to supplement conservation activities for the purpose of reversing the trend of reef degradation. In the last decade, the feasibility of different restoration approaches such as coral transplantation and restocking of other marine biota has been the focus of research and relatively few have examined experimentally its effects on the resultant communities. In this study, coral transplantation and giant clam restocking were applied on 25 degraded patch reefs (~ 25 m²) inside a marine sanctuary in Pangasinan, northwestern Philippines to examine their effects on the community structure of reef fishes. Five interventions or treatments were employed: 1) “coral” consisted of transplantation of a combination of Acropora spp. and Pocillopora spp. on concrete blocks; 2) “clam” consisted of restocking of Tridacna gigas; 3) “clam+coral” consisted of restocking of T. gigas with Acropora spp. transplanted on their shells; 4) “shell” consisted of deployment of T. gigas shells; and 5) “control” consisted of no intervention. Fish communities on the patch reefs were monitored monthly for 3 months before the intervention and were monitored further for 11 months after the intervention, including 1 recruitment season. After the intervention, the coral cover and the “other biota” category increased in the coral and clam+coral treatments, due to the transplanted corals and deployed giant clams. Consequently, the complexity of the substrate was enhanced. A month after the intervention, a rapid increase in the abundance and species richness of reef fishes on the coral, clam+coral and clam treatments was observed compared to the shell and control treatments. A change in species composition of reef fish assemblage was also apparent in the coral and clam+coral treatments relative to the clam, shell and control, especially 4 months after the intervention. The present experiment demonstrates the feasibility of improving the condition of degraded patch reefs, which can subsequently enhance the fish community. Results also show the importance of the underlying substratum and the abundance of live corals and clams to reef fishes.     

Differential thermal tolerance between algae and corals may trigger the proliferation of algae in coral reefs

Marine heatwaves can lead to rapid changes in entire communities, including in the case of shallow coral reefs the potential overgrowth of algae. Here we tested experimentally the differential thermal tolerance between algae and coral species from the Red Sea through the measurement of thermal performance curves and the assessment of thermal limits. Differences across functional groups (algae vs. corals) were apparent for two key thermal performance metrics. First, two reef‐associated algae species (Halimeda tuna and Turbinaria ornata) had higher lethal thermal limits than two coral species (Pocillopora verrucosa and Stylophora pistillata) conferring those species of algae with a clear advantage during heatwaves by surpassing the thermal threshold of coral survival. Second, the coral species had generally greater deactivation energies for net and gross primary production rates compared to the algae species, indicating greater thermal sensitivity in corals once the optimum temperature is exceeded. Our field surveys in the Red Sea reefs before and after the marine heatwave of 2015 show a change in benthic cover mainly in the southern reefs, where there was a decrease in coral cover and a concomitant increase in algae abundance, mainly turf algae. Our laboratory and field observations indicate that a proliferation of algae might be expected on Red Sea coral reefs with future ocean warming.     

Estimation of photosynthesis and calcification rates at a fringing reef by accounting for diurnal variations and the zonation of coral reef communities on reef flat and slope: a case study for the Shiraho reef, Ishigaki Island, southwest Japan

Seven coral reef communities were defined on Shiraho fringing reef, Ishigaki Island, Japan. Net photosynthesis and calcification rates were measured by in situ incubations at 10 sites that included six of the defined communities, and which occupied most of the area on the reef flat and slope. Net photosynthesis on the reef flat was positive overall, but the reef flat acts as a source for atmospheric CO₂, because the measured calcification/photosynthesis ratio of 2.5 is greater than the critical ratio of 1.67. Net photosynthesis on the reef slope was negative. Almost all excess organic production from the reef flat is expected to be effused to the outer reef and consumed by the communities there. Therefore, the total net organic production of the whole reef system is probably almost zero and the whole reef system also acts as a source for atmospheric CO₂. Net calcification rates of the reef slope corals were much lower than those of the branching corals. The accumulation rate of the former was approximately 0.5 m kyr⁻¹ and of the latter was ~0.7–5 m kyr⁻¹. Consequently, reef slope corals could not grow fast enough to keep up with or catch up to rising sea levels during the Holocene. On the other hand, the branching corals grow fast enough to keep up with this rising sea level. Therefore, a transition between early Holocene and present-day reef communities is expected. Branching coral communities would have dominated while reef growth kept pace with sea level rise, and the reef was constructed with a branching coral framework. Then, the outside of this framework was covered and built up by reef slope corals and present-day reefs were constructed.     

Coral frameworks revisited–reefs and coral carpets in the northern Red Sea

 Coral communities were investigated in the northern Red Sea, in the Gulfs of Suez and Aqaba, for their framework building potential. Five types of coral frameworks were differentiated: Acropora reef framework, Porites reef framework, Porites carpet, faviid carpet, and Stylophora carpet. Two non-framework community types were found: the Stylophora-Acropora community, and soft coral communities. Reef frameworks show a clear ecological zonation along depth and hydrodynamic exposure gradients, with clear indicator communities for each zone. By definition, coral carpets build a framework but lack distinct zonation patterns since they grow only in areas without pronounced gradients. In the northern Red Sea they show a gradual change with depth from Porites to faviid dominance. A Stylophora carpet is restricted to shallow water in the northern Gulf of Suez. Although growth rates of carpets may be somewhat less than those of reefs, the carbonate accumulation is considered to be higher in carpet areas due to their significantly higher areal extension. In addition, reefs and carpets have different sediment retention characteristics – the carpet retains, the reef exports. The in situ fossilization potential of coral carpets is expected to be higher than that of reef frameworks. Accepted: 25 May 1999     

Large‐scale coral reef rehabilitation after blast fishing in Indonesia

The severely degraded condition of many coral reefs worldwide calls for active interventions to rehabilitate their physical and biological structure and function, in addition to effective management of fisheries and no‐take reserves. Rehabilitation efforts to stabilize reef substratum sufficiently to support coral growth have been limited in size. We documented a large coral reef rehabilitation in Indonesia aiming to restore ecosystem functions by increasing live coral cover on a reef severely damaged by blast fishing and coral mining. The project deployed small, modular, open structures to stabilize rubble and to support transplanted coral fragments. Between 2013 to 2015, approximately 11,000 structures covering 7,000 m² were deployed over 2 ha of a reef at a cost of US$174,000. Live coral cover on the structures increased from less than 10% initially to greater than 60% depending on depth, deployment date and location, and disturbances. The mean live coral cover in the rehabilitation area in October 2017 was higher than reported for reefs in many other areas in the Coral Triangle, including marine protected areas, but lower than in the no‐take reference reef. At least 42 coral species were observed growing on the structures. Surprisingly, during the massive coral bleaching in other regions during the 2014–2016 El Niño–Southern Oscillation event, bleaching in the rehabilitation area was less than 5% cover despite warm water (≥30°C). This project demonstrates that coral rehabilitation is achievable over large scales where coral reefs have been severely damaged and are under continuous anthropogenic disturbances in warming waters.     

Inventory of the Maldives’ coral reefs using morphometrics generated from Landsat ETM+ imagery

In this study, we present exact measures of the number, area, and basic morphometric statistics for every single reef of the Maldivian archipelago, as derived from the interpretation of remotely sensed data collected by the Landsat-7 ETM+ earth-observing satellite sensor. We classified and mapped seven morphological attributes of reefs (six marine habitats and reef-top islands) to 30-m depth at 30×30 m spatial resolution (pixel size) for the entire archipelago. The total archipelagic area (all coral reef and lagoon habitats) of the 16 atolls, five oceanic faros, and four oceanic platform reefs which comprise the Maldives is 21,372.72±1,068.64 km² (approx. 20% of the Maldives Territorial Sea). A total of 2,041±10 distinct coral reef structures larger than 0.01 km² occur in the Maldives, covering an area of 4,493.85 km² (including enclosed reef lagoons and islands) to 30-m depth. Smaller areas of coral reef substratum cover another 19.29 km², bringing the total area of Maldivian coral reefs to 4,513.14±225.65 km². Shallow coral platforms thus occupy 21.1% of the total area of the archipelago (0.0052% of the EEZ area of the Maldives). Of these reefs, 538 are rim and oceanic reefs, covering 3,701.93 km² (82.5% of the total reef area), and 1,503 are patch reefs within the atoll lagoons, covering 791.92 km² (17.5% of the total reef area). Islands occupy only 5.1% of the total reef area. Mapping the Maldives coral reefs at high spatial resolution is only possible with remote sensing and spatial analysis technologies. These greatly reduce the large uncertainty around current estimates of reef area. Our accurate measure of total reef area is only 50.6% of the current best estimate, a result having significant implications for predictions of the Maldives reef productivity and response to global climate change. Here we present current best practice and compare the methods and measures with previous approaches.     

Holocene growth history of an eastern Pacific fringing reef,Punta Islotes,Costa Rica

Rock and sediment cores reveal that a well-developed fringing reef in Golfo Dulce, Pacific Costa Rica, up to 9 m thick was established on Cretaceous basalt about 5500 y BP. It is presently being smothered with fine sediments and is almost completely dead. This reef is made up of three main facies that are represented by comparable extant reef zones: reef-flat branching coral, fore-reef slope massive coral, and fore-reef talus sediment facies. Reef growth began with the establishment of small patch reefs dominantly formed by the branching coral Pocillopora damicornis. P. damicornis spread across the basalt bench and massive colonies of Porites lobata grew on the outer slopes, eventually blocking the seaward transport of Pocillopora fragments to the fore-reef talus sediments. The reef flourished until 500 years ago. Lower accumulation rates during the past 500 years may be due to deteriorating environmental conditions rather than slower growth after the reef reached sea level. Present-day reef communities are severely degraded with less than 2% living coral cover. The increased turbidity associated with the final stage of degradation of this reef is probably related to human activity on the adjacent shores, including deforestation, mining, and road construction.     

Coral recruitment and juvenile mortality as structuring factors for reef benthic communities in Biscayne National Park, USA

Coral communities of Biscayne National Park (BNP) on offshore linear bank-barrier reefs are depauperate of reef corals and have little topographic relief, while those on lagoonal patch reefs have greater coral cover and species richness despite presumably more stressful environmental regimes closer to shore. We hypothesized that differences in rates of coral recruitment and/or of coral survivorship were responsible for these differences in community structure. These processes were investigated by measuring: (1) juvenile and adult coral densities, and (2) size-frequency distributions of smaller coral size classes, at three pairs of bank- and patch-reefs distributed along the north-south range of coral reefs within the Park. In addition, small quadrats (0.25 m²) were censused for colonies <2 cm in size on three reefs (one offshore and one patch reef in the central park, and one intermediate reef at the southern end), and re-surveyed after 1 year. Density and size frequency data confirmed that large coral colonies were virtually absent from the offshore reefs, but showed that juvenile corals were common and had similar densities to those of adjacent bank and patch reefs. Large coral colonies were more common on inshore patch reefs, suggesting lower survivorship (higher mortality) of small and intermediate sized colonies on the offshore reefs. The more limited small-quadrat data showed similar survivorship rates and initial and final juvenile densities at all three sites, but a higher influx of new recruits to the patch reef site during the single annual study period. We consider the size-frequency data to be a better indicator of juvenile coral dynamics, since it is a more time-integrated measurement and was replicated at more sites. We conclude that lack of recruitment does not appear to explain the impoverished coral communities on offshore bank reefs in BNP. Instead, higher juvenile coral mortality appears to be a dominant factor structuring these communities. Accepted: 9 September 1999     

Top-heavy trophic structure within benthic viral dark matter

A better understanding of system-specific viral ecology in diverse environments is needed to predict patterns of virus–host trophic structure in the Anthropocene. This study characterised viral-host trophic structure within coral reef benthic cyanobacterial mats—a globally proliferating cause and consequence of coral reef degradation. We employed deep longitudinal multi-omic sequencing to characterise the viral assemblage (ssDNA, dsDNA, and dsRNA viruses) and profile lineage-specific host–virus interactions within benthic cyanobacterial mats sampled from Bonaire, Caribbean Netherlands. We recovered 11,012 unique viral populations spanning at least 10 viral families across the orders Caudovirales, Petitvirales, and Mindivirales. Gene-sharing network analyses provided evidence for extensive genomic novelty of mat viruses from reference and environmental viral sequences. Analysis of coverage ratios of viral sequences and computationally predicted hosts spanning 15 phyla and 21 classes revealed virus–host abundance (from DNA) and activity (from RNA) ratios consistently exceeding 1:1, suggesting a top-heavy intra-mat trophic structure with respect to virus–host interactions. Overall, our article contributes a curated database of viral sequences found in Caribbean coral reef benthic cyanobacterial mats (vMAT database) and provides multiple lines of field-based evidence demonstrating that viruses are active members of mat communities, with broader implications for mat functional ecology and demography.     

Isotopic analysis of cyanobacterial nitrogen fixation associated with subarctic lichen and bryophyte species

Dinitrogen fixation by cyanobacteria is of particular importance for the nutrient economy of cold biomes, constituting the main pathway for new N supplies to tundra ecosystems. It is prevalent in cyanobacterial colonies on bryophytes and in obligate associations within cyanolichens. Recent studies, applying interspecific variation in plant functional traits to upscale species effects on ecosystems, have all but neglected cryptogams and their association with cyanobacteria. Here we looked for species-specific patterns that determine cryptogam-mediated rates of N₂ fixation in the Subarctic. We hypothesised a contrast in N₂ fixation rates (1) between the structurally and physiologically different lichens and bryophytes, and (2) within bryophytes based on their respective plant functional types. Throughout the survey we supplied ¹⁵N-labelled N₂ gas to quantify fixation rates for monospecific moss, liverwort and lichen turfs. We sampled fifteen species in a design that captures spatial and temporal variations during the growing season in Abisko region, Sweden. We measured N₂ fixation potential of each turf in a common environment and in its field sampling site, in order to embrace both comparativeness and realism. Cyanolichens and bryophytes differed significantly in their cyanobacterial N₂ fixation capacity, which was not driven by microhabitat characteristics, but rather by morphology and physiology. Cyanolichens were much more prominent fixers than bryophytes per unit dry weight, but not per unit area due to their low specific thallus weight. Mosses did not exhibit consistent differences in N₂ fixation rates across species and functional types. Liverworts did not fix detectable amounts of N₂. Despite the very high rates of N₂ fixation associated with cyanolichens, large cover of mosses per unit area at the landscape scale compensates for their lower fixation rates, thereby probably making them the primary regional atmospheric nitrogen sink.