Mangrove microbial community recovery and their role in early stages of forest recolonization within shrimp ponds.

Shrimp farming is blooming worldwide, posing a severe threat to mangroves and its multiple goods and ecosystem services. Several studies reported the impacts of aquaculture on mangrove biotic communities, including microbiomes. However, little is known about how mangrove soil microbiomes would change in response to mangrove forest recolonization. Using genome-resolved metagenomics, we compared the soil microbiome of mangrove forests (both with and without the direct influence of shrimp farming effluents) with active shrimp farms and mangroves under a recolonization process. We found that the structure and composition of active shrimp farms microbial communities differ from the control mangrove forests, mangroves under the impact of the shrimp farming effluents, and mangroves under recolonization. Shrimp farming ponds microbiomes have lower microbial diversity and are dominated by halophilic microorganisms, presenting high abundance of multiple antibiotic resistance genes. On the other hand, control mangrove forests, impacted mangroves (exposed to the shrimp farming effluents), and recolonization ponds were more diverse, with a higher abundance of genes related to carbon mobilization. Our data also indicated that the microbiome is recovering in the mangrove recolonization ponds, performing vital metabolic functions and functionally resembling microbiomes found in those soils of neighboring control mangrove forests. Despite highlighting the damage caused by the habitat changes in mangrove soil microbiome community and functioning, our study sheds light on these systems incredible recovery capacity. Our study shows the importance of natural mangrove forest recovery, enhancing ecosystem services by the soil microbial communities even in a very early development stage of mangrove forest, thus encouraging mangrove conservation and restoration efforts worldwide.

Habitat-specific fish fauna responses to different management regimes in the largest coral reef complex in the South Atlantic.

While marine protected areas (MPAs) are increasing worldwide, it is still needed to assess the effectiveness of those already consolidated. Methods and ecological assessments to understanding integrated and habitat-specific management regimes are still scarce and insufficient for policy implications and biodiversity conservation. Through Baited Remote Underwater Video (BRUV), we used fish assemblages as proxy of ecological and managerial status in two reef habitat types along three protection levels at Abrolhos Bank - the largest and most biodiverse coral reef complex of the South Atlantic. We found completely distinct responses in the fish fauna between the top (shallow) and bottom (deep) habitats of the unique "chapeirões" pinnacle reef formations. In the most protected zone (no-take), higher richness and abundance of commercial fish and more diverse trophic structure was observed. Particularly, large (sharks and groupers) and small carnivores (snappers) were more abundant and distributed more homogeneously over both reef habitats in the strictly enforced no-take zone. Abundance of these top-predators decreased from the low enforcement no-take zone to the multiple use area, where they were often absent while their typical preys (primary and secondary consumers) were thriving, notably in the top habitats. These outcomes highlight the importance to focus investigations not selectively on a single habitat type or depth zone in order to properly assess MPA effectiveness. Consequently, the monitoring and protection of fish species supported by marine spatial planning may benefit from an improved understanding of ecological functioning provided by MPA performance.

CPR and DPANN Have an Overlooked Role in Corals' Microbial Community Structure.

Understanding how microbial communities are structured in coral holobionts is important to estimate local and global impacts and provide efficient environment management strategies. Several studies investigated the relationship between corals and their microbial communities, including the environmental drivers of shifts in this relationship, associated with diseases and coral cover loss. However, these studies are often geographically or taxonomically restricted and usually focused on the most abundant microbial groups, neglecting the rare biosphere, including archaea in the group DPANN and the recently discovered bacterial members of the candidate phyla radiation (CPR). Although it is known that rare microbes can play essential roles in several environments, we still lack understanding about which taxa comprise the rare biosphere of corals' microbiome. Here, we investigated the host-related and technical factors influencing coral microbial community structure and the importance of CPR and DPANN in this context by analyzing more than a hundred coral metagenomes from independent studies worldwide. We show that coral genera are the main biotic factor shaping coral microbial communities. We also detected several CPR and DPANN phyla comprising corals' rare biosphere for the first time and showed that they significantly contribute to shaping coral microbial communities.

Structure of marginal coral reef assemblages under different turbidity regime.

Sediment load can influence both the population distribution and structures of coral reef communities. We investigated whether coral assemblages on inshore and more turbid reefs differ from those on offshore reefs in the largest coral reefs of the Southwest Atlantic. We compared inshore and offshore reefs (with different turbidity climatologies) in terms of benthic and coral assemblage structures, abundances and individual sizes of coral populations and recruitment patterns. Unexpectedly, the inshore reefs showed higher coral cover and abundance, larger colonies and more recruits. This finding is related to the predominance of sediment-tolerant species on the turbid reefs. In contrast, only Mussismilia braziliensis (main builder of Abrolhos) showed better performance (greater coverage, larger diameter and more recruits) on offshore reefs, apparently behaving as a strong competitor in less turbid environments. These results reinforce the recent thinking of coral reef of turbid environments as resistant ecosystems and potential refuges considering the unnatural increase of sediment supply.

Integrating Computational Methods to Investigate the Macroecology of Microbiomes.

Studies in microbiology have long been mostly restricted to small spatial scales. However, recent technological advances, such as new sequencing methodologies, have ushered an era of large-scale sequencing of environmental DNA data from multiple biomes worldwide. These global datasets can now be used to explore long standing questions of microbial ecology. New methodological approaches and concepts are being developed to study such large-scale patterns in microbial communities, resulting in new perspectives that represent a significant advances for both microbiology and macroecology. Here, we identify and review important conceptual, computational, and methodological challenges and opportunities in microbial macroecology. Specifically, we discuss the challenges of handling and analyzing large amounts of microbiome data to understand taxa distribution and co-occurrence patterns. We also discuss approaches for modeling microbial communities based on environmental data, including information on biological interactions to make full use of available Big Data. Finally, we summarize the methods presented in a general approach aimed to aid microbiologists in addressing fundamental questions in microbial macroecology, including classical propositions (such as "everything is everywhere, but the environment selects") as well as applied ecological problems, such as those posed by human induced global environmental changes.

Are Abrolhos no-take area sites of naïve fish? An evaluation using flight initiation distance of labrids

Fishing pressure affects the behavior of reef fish, especially of fishery-targeted species. In this context, it is critical to understand if fish behavior is preserved in no-take areas (NTAs), which are considered the best instrument for the recovery of fish stocks. Comparing the flight initiation distances (FIDs) of fish inhabiting multiple-use areas (MUAs), where fishing is allowed (including spearfishing), and NTAs is a useful approach to test whether NTAs can be effective as fish refuges. Here, we compared whether the FIDs of two target (Sparisoma axillare and Scarus trispinosus ) and one non-target (Halichoeres poeyi ) labrids are greater in the MUAs than in the NTAs. We also investigated whether group size (GS) and body size (BS) exert any effect on the FID. We sampled four MUAs and four NTAs in the Abrolhos Bank (Brazil). We found that only for the targeted species FID was shorter inside the NTAs and that the BS had a positive effect on the FID of all species. The GS and BS of the fish are greater in the NTAs than in the multiple-use areas only for S. trispinosus . Our study shows that fish, especially those species that are fishery targets, display an avoidance behavior against spearfishermen likely as a consequence of fishing pressure. We suggest that the NTAs in Abrolhos are not only important sites for the recovery of fish stocks but also possibly act as a repository area of naïve fish (fish that allow human approach), for reefs open for fishing.(AU)

A pressão pesqueira afeta o comportamento de peixes recifais, especialmente nas espécies alvo de pesca. Nesse contexto é importante entender se áreas fechadas a pesca ("no-take areas": NTAs), consideradas como melhor instrumento para recuperação dos estoques pesqueiros, garantem a integridade dos comportamentos dos peixes. Comparar distâncias iniciais de fuga ("fligth initiation distance": FIDs) de espécies entre recifes de uso múltiplos ("multiple-use areas": MUAs), onde a pesca é permitida (incluindo a pesca submarina), e as NTAs é uma abordagem útil para testar se as NTAs podem ser efetivas como refúgios para peixes recifais. Nesse trabalho FIDs de duas espécies alvo (Sparisoma axillare e Scarus trispinosus ) e uma não alvo (Halichoeres poeyi ) foram comparadas entre MUAs e NTAs. A possível influência do tamanho do grupo ("group size": GS) e o tamanho do corpo ("body size": BS) sobre FID também foram investigados. Foram amostradas quatro MUAs e quatro áreas NTAs no banco dos Abrolhos (Brasil). Nossos resultados mostraram que apenas FID das espécies alvo de pesca foi menor dentro de NTAs e que o BS teve um efeito positivo no FID de todas as espécies. Dentro da NTA, GS e BS foram maiores do que em recifes abertos à pesca apenas para S. trispinosus . Finalmente, sugerimos que NTAs em Abrolhos não são apenas importantes como recuperação dos estoques pesqueiros, mas estão possivelmente atuando como uma área repositória de peixes "ingênuos" (peixes que permitem aproximação humana) para os recifes onde a pesca é permitida.(AU)

Effect of phase shift from corals to Zoantharia on reef fish assemblages.

Consequences of reef phase shifts on fish communities remain poorly understood. Studies on the causes, effects and consequences of phase shifts on reef fish communities have only been considered for coral-to-macroalgae shifts. Therefore, there is a large information gap regarding the consequences of novel phase shifts and how these kinds of phase shifts impact on fish assemblages. This study aimed to compare the fish assemblages on reefs under normal conditions (relatively high cover of corals) to those which have shifted to a dominance of the zoantharian Palythoa cf. variabilis on coral reefs in Todos os Santos Bay (TSB), Brazilian eastern coast. We examined eight reefs, where we estimated cover of corals and P. cf. variabilis and coral reef fish richness, abundance and body size. Fish richness differed significantly between normal reefs (48 species) and phase-shift reefs (38 species), a 20% reduction in species. However there was no difference in fish abundance between normal and phase shift reefs. One fish species, Chaetodon striatus, was significantly less abundant on normal reefs. The differences in fish assemblages between different reef phases was due to differences in trophic groups of fish; on normal reefs carnivorous fishes were more abundant, while on phase shift reefs mobile invertivores dominated.

Tolerance of Brazilian brain coral Mussismilia braziliensis to sediment and organic matter inputs.

In Brazil, where reefs occur in markedly turbid environments, the relationship between sedimentation/organic matter and corals is poorly known. Thus, the ex situ effects of sediment with and without organic matter over the ΔF/Fm and physical state of Mussismilia braziliensis were analyzed. The ΔF/Fm and coral physical state, evaluated through the susceptibility index to sedimentation (SI), were measured in seven colonies exposed to sedimentation (0-450 mg cm(-2) day(-1)) free of organic matter after 45 days of exposure, and in 12 colonies exposed to sedimentation (0-500 mg cm(-2) day(-1)) with organic matter content (10%), in which case ΔF/Fm was measured after 72 h and SI after 120 h. In both cases there were effects of increasing sedimentation on the SI with no effect on ΔF/Fm. Despite the tolerance to high sedimentation rates shown by this coral, we noted that the presence of organic matter might reduce its tolerance to sedimentation stress.