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Temperate mesophotic reef ecosystems (TMREs) are among the least known marine habitats. Information on their diversity and ecology is geographically and temporally scarce, especially in highly productive large upwelling ecosystems. Lack of information remains an obstacle to understanding the importance of TMREs as habitats, biodiversity reservoirs and their connections with better-studied shallow reefs. Here, we use environmental DNA (eDNA) from water samples to characterize the community composition of TMREs on the central Chilean coast, generating the first baseline for monitoring the biodiversity of these habitats. We analyzed samples from two depths (30 and 60 m) over four seasons (spring, summer, autumn, and winter) and at two locations approximately 16 km apart. We used a panel of three metabarcodes, two that target all eukaryotes (18S rRNA and mitochondrial COI) and one specifically targeting fishes (16S rRNA). All panels combined encompassed eDNA assigned to 42 phyla, 90 classes, 237 orders, and 402 families. The highest family richness was found for the phyla Arthropoda, Bacillariophyta, and Chordata. Overall, family richness was similar between depths but decreased during summer, a pattern consistent at both locations. Our results indicate that the structure (composition) of the mesophotic communities varied predominantly with seasons. We analyzed further the better-resolved fish assemblage and compared eDNA with other visual methods at the same locations and depths. We recovered eDNA from 19 genera of fish, six of these have also been observed on towed underwater videos, while 13 were unique to eDNA. We discuss the potential drivers of seasonal differences in community composition and richness. Our results suggest that eDNA can provide valuable insights for monitoring TMRE communities but highlight the necessity of completing reference DNA databases available for this region.

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Ecological communities are structured by a range of processes that operate over a range of spatial scales. While our understanding of such biodiversity patterns in macro-communities is well studied, our understanding at the microbial level is still lacking. Bacteria can be free living or associated with host eukaryotes, forming part of a wider "microbiome," which is fundamental for host performance and health. For habitat forming foundation-species, host-bacteria relationships likely play disproportionate roles in mediating processes for the wider ecosystem. Here, we describe host-bacteria communities across multiple spatial scales (i.e., from 10s of m to 100s of km) in the understudied kelp, Eisenia cokeri, in Peru. We found that E. cokeri supports a distinct bacterial community compared to the surrounding seawater, but the structure of these communities varied markedly at the regional (~480 km), site (1-10 km), and individual (10s of m) scale. The marked regional-scale differences we observed may be driven by a range of processes, including temperature, upwelling intensity, or regional connectivity patterns. However, despite this variability, we observed consistency in the form of a persistent core community at the genus level. Here, the genera Arenicella, Blastopirellula, Granulosicoccus, and Litorimonas were found in >80% of samples and comprised ~53% of total sample abundance. These genera have been documented within bacterial communities associated with kelps and other seaweed species from around the world and may be important for host function and wider ecosystem health in general.

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This study summarises six years of spatio-temporal patterns of the discarded demersal community fauna recorded by onboard scientific observer program for both artisanal and industrial crustacean fisheries between 2014 and 2019, from mesophotic to aphotic depths (96 to 650 m) along the southern Humboldt Current System (28-38°S). In this period, one cold and two warm climatic events were observed during the austral summer 2014, 2015-2016 (ENSO Godzilla), and 2016-2017 (coastal ENSO), respectively. Satellite information showed that Chlorophyll-a concentration varied seasonally and latitudinally, associated with upwelling centres, while equatorial wind stress decreased southward of 36°S. Discards were composed of 108 species, dominated by finfish and molluscs. The Chilean hake Merluccius gayi was dominant and ubiquitous (occurrence, 95% of 9104 hauls), being the most vulnerable species of the bycatch. Three assemblages were identified: assemblage 1 (~200 m deep), dominated by flounders Hippoglossina macrops and lemon crabs Platymera gaudichaudii, assemblage 2 (~260 m deep), dominated by squat lobsters Pleuroncodes monodon and Cervimunida johni and assemblage 3 (~320 m depth), dominated by grenadiers Coelorinchus aconcagua and cardinalfish Epigonus crassicaudus. These assemblages were segregated by depth, and varied by year, and geographic zone. The latter represented changes in the width of the continental shelf, increasing southward of 36°S. Alpha-diversity indexes (richness, Shannon, Simpson, and Pielou) also varied with depth and latitude, with higher diversity in deeper continental waters (>300 m), between 2018-2019. Finally, at a spatial scale of tens of kilometres, and a monthly basis, interannual variations of biodiversity occurred in the demersal community. Surface sea temperature, chlorophyll-a, or wind stress did not correlate with discarded demersal fauna diversity of the crustacean fishery operating along central Chile.

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Top-down and bottom-up forces determine ecosystem function and dynamics. Fisheries as a top-down force can shorten and destabilize food webs, while effects driven by climate change can alter the bottom-up forces of primary productivity. We assessed the response of a highly-resolved intertidal food web to these two global change drivers, using network analysis and bioenergetic modelling. We quantified the relative importance of artisanal fisheries as another predator species, and evaluated the independent and combined effects of fisheries and changes in plankton productivity on food web dynamics. The food web was robust to the loss of all harvested species but sensitive to the decline in plankton productivity. Interestingly, fisheries dampened the negative impacts of decreasing plankton productivity on non-harvested species by reducing the predation pressure of harvested consumers on non-harvested resources, and reducing the interspecific competition between harvested and non-harvested basal species. In contrast, the decline in plankton productivity increased the sensitivity of harvested species to fishing by reducing the total productivity of the food web. Our results show that strategies for new scenarios caused by climate change are needed to protect marine ecosystems and the wellbeing of local communities dependent on their resources.

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Nibblers (family Girellidae) are reef fishes that are mostly distributed in the Indo-Pacific, with one exception: Girella stuebeli, which is found in the Cabo Verde Archipelago, in the Atlantic Ocean. We capitalized on this unusual distribution to study the evolutionary history of the girellids, and determine the relationship between G. stuebeli and the remaining nibbler taxa. Based on thousands of genomic markers (RAD sequences), we identified the closest relatives of G. stuebeli as being a clade of three species endemic to the northwestern Pacific, restricted to the Sea of Japan and vicinity. This clade diverged from G. stuebeli approximately 2.2 Mya. Two alternative potential routes of migration may explain this affinity: a western route, from the Tropical Eastern Pacific and the Tropical Western Atlantic, and an eastern route via the Indian Ocean and Southern Africa. The geological history and oceanography of the regions combined with molecular data presented here, suggest that the eastern route of invasion (via the Indian Ocean and Southern Africa) is a more likely scenario.

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Embryonic development and larval morphology of Chromis crusma was described from five nests sampled between 21 and 25 m depth in central Chile (33°S). From each nest, a set of c. 100 randomly selected eggs were hand-collected and transported in seawater to the laboratory. Subsets of c. 30 eggs per nest were maintained in 50 ml glass containers at a constant ambient temperature of c. 12°C (range 11.5-12.9°C). Egg length (L) and width (W) and larval notochordal length (LN ) were measured from photographs. Geometric morphometric analyses were performed in newly hatched and 1 week old larvae to quantify shape changes. Ellipsoid eggs had an average (mean ± SE) size of 1.12 ± 0.05 mm L and 0.67 ± 0.02 mm W, with volume being similar throughout 15 developmental stages (i.e., ellipsoid-shaped; 0.27 mm3 ). Planktonic larvae hatched between 5 and 11 days at 12°C and had a mean LN of 3.13 ± 0.25 mm, a yolk sack volume of 0.03 mm3 and an oil droplet volume of 0.005 mm3 . Morphological traits at hatching included: (a) lack of paired fins and jaws; (b) single medial fin fold; (c) lack of eye pigmentation; (d) yolk sac present near anterior tip; (e) melanophores distributed along ventral surface with one pair over the forehead. In order to generate an up-to-date summary of developmental traits within Pomacentridae, we reviewed literature on egg development (e.g., shape and number of oil droplets), hatching and larval traits (e.g., morphology, pigmentation patterns). Thirty-two publications accounting for 35 species were selected, where eggs, embryonic development, hatching and larval traits were found for 26, 21, 24 and 34 species, respectively. In order to evaluate potential phylogenetic and environmental relationships within the early stages of Pomacentridae, cluster analyses (Bray Curtis similarity, group average) were also performed on egg and larval traits of 22 species divided by subfamily (Stegastinae, Chrominae, Abudefdufinae, Pomacentrinae) and thermal ranges (i.e., low: 16.5°C (range: 12-21°C), medium: 24.5°C (range:21-28°C) and high: 27°C (range: 26-28°C)), suggesting that early developmental patterns can be segregated by both temperature and phylogenetic relationships.

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Ecosystem-based management implies understanding feedbacks between ecosystems and society. Such understanding can be approached with the Drivers-Pressures-State change-Impacts-Response framework (DPSIR), incorporating stakeholders' preferences for ecosystem services to assess impacts on society. This framework was adapted to six locations in the central coast of Chile, where artisanal fisheries coexist with an increasing influx of tourists, and a set of fisheries management areas alternate with open access areas and a no-take Marine Protected Area (MPA). The ecosystem services in the study area were quantified using biomass and species richness in intertidal and subtidal areas as biological indicators. The demand for ecosystem services was elicited by interviews to the principal groups of users. Our results evidenced decreasing landings and a negative perception of fishermen on temporal trends of catches. The occurrence of recreational fishing was negligible, although the consumption of seafood by tourists was relatively high. Nevertheless, the consumption of organisms associated to the study system was low, which could be linked, amongst other factors, to decreasing catches. The comparison of biological indicators between management regimens provided variable results, but a positive effect of management areas and the MPA on some of the metrics was observed. The prioritising of ecosystem attributes by tourists was highly homogenous across the six locations, with "scenic beauty" consistently selected as the preferred attribute, followed by "diversity". The DPSIR framework illustrated the complex interactions existing in these locations, with weak linkages between society's priorities, existing management objectives and the state of biological communities. Overall, this work improved our knowledge on relations between components of coastal areas in central Chile, of paramount importance to advance towards an ecosystem-based management in the area.

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Over-exploited fisheries are a common feature of the modern world and a range of solutions including area closures (marine reserves; MRs), effort reduction, gear changes, ecosystem-based management, incentives and co-management have been suggested as techniques to rebuild over-fished populations. Historic accounts of lobster (Jasus frontalis) on the Chilean Juan Fernández Archipelago indicate a high abundance at all depths (intertidal to approximately 165 m), but presently lobsters are found almost exclusively in deeper regions of their natural distribution. Fishers' ecological knowledge (FEK) tells a story of serial depletion in lobster abundance at fishing grounds located closest to the fishing port with an associated decline in catch per unit effort (CPUE) throughout recent history. We have re-constructed baselines of lobster biomass throughout human history on the archipelago using historic data, the fishery catch record and FEK to permit examination of the potential effects of MRs, effort reduction and co-management (stewardship of catch) to restore stocks. We employed a bioeconomic model using FEK, fishery catch and effort data, underwater survey information, predicted population growth and response to MR protection (no-take) to explore different management strategies and their trade-offs to restore stocks and improve catches. Our findings indicate that increased stewardship of catch coupled with 30% area closure (MR) provides the best option to reconstruct historic baselines. Based on model predictions, continued exploitation under the current management scheme is highly influenced by annual fluctuations and unsustainable. We propose a community-based co-management program to implement a MR in order to rebuild the lobster population while also providing conservation protection for marine species endemic to the Archipelago.

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