Laís Lima

• Doctor of Philosophy
• PostDoc Position at University of California, San Diego

Coral reef health is tightly connected to the coral holobiont, which is the association between the coral animal and a diverse microbiome functioning as a unit. The coral holobiont depends on key services such as nitrogen and sulfur cycling mediated by the associated bacteria. However, these microbial services may be impaired in response to environ...

Elasmobranch epidermal microbiomes are species-specific, yet microbial assembly and retainment drivers are mainly unknown. The contribution of host-derived factors in recruiting an associated microbiome is essential for understanding host-microbe interactions. Here, we focus on the physical aspect of the host skin in structuring microbial communiti...

Background: Modern sequencing technologies offer extraordinary opportunities for virus discovery and virome analysis. Annotation of viral sequences from metagenomic data requires a complex series of steps to ensure accurate annotation of individual reads and assembled contigs. In addition, varying study designs will require project-specific statis...

Microbiomes confer beneficial physiological traits to their host, but microbial diversity is inherently variable, challenging the relationship between microbes and their contribution to host health. Here, we compare the diversity and architectural complexity of the epidermal microbiome from 74 individual whale sharks (Rhincodon typus) across five a...

Marine host-associated microbiomes are affected by a combination of species-specific (e.g., host ancestry, genotype) and habitat-specific features (e.g., environmental physiochemistry and microbial biogeography). The stingray epidermis provides a gradient of characteristics from high dermal denticles coverage with low mucus to reduce dermal denticl...

Coral reef health is tightly connected to the coral microbiome. Coral bleaching and disease outbreaks have caused an unprecedented loss in coral cover worldwide, particularly correlated to a warming ocean. Coping mechanisms of the coral holobiont under high temperatures are not completely described, but the associated microbial community is a poten...

Characterizations of shark-microbe systems in wild environments have outlined patterns of species-specific microbiomes; however, whether captivity affects these trends has yet to be determined. We used high-throughput shotgun sequencing to assess the epidermal microbiome belonging to leopard sharks (Triakis semifasciata) in captive (Birch Aquarium,...

Microbiomes confer beneficial physiological traits to their host, but microbial diversity is inherently variable, challenging the relationship between microbes and their functional contribution to host health. Here, we compare diversity and architectural complexity of the epidermal microbiome from 74 individual whale sharks (Rhincodon typus) across...

The epidermal microbiome is a critical element of marine organismal immunity, but the epidermal virome of marine organisms remains largely unexplored. The epidermis of sharks represents a unique viromic ecosystem. Sharks secrete a thin layer of mucus which harbors a diverse microbiome, while their hydrodynamic dermal denticles simultaneously repel...

Caribbean reefs have undergone large-scale losses in coral cover in past decades, sparking a search for species that are resilient under stress. Porites astreoides has been considered a “winner” and a key player in sustaining coral cover in the Caribbean as more sensitive species struggle. However, P. astreoides has recently declined in abundance,...

The coral holobiont is comprised of a highly diverse microbial community that provides key services to corals such as protection against pathogens and nutrient cycling. The coral surface mucus layer (SML) microbiome is very sensitive to external changes, as it constitutes the direct interface between the coral host and the environment. Here, we inv...

Background Analysis of viral diversity using modern sequencing technologies offers extraordinary opportunities for discovery. However, these analyses present a number of bioinformatic challenges due to viral genetic diversity and virome complexity. Due to the lack of conserved marker sequences, metagenomic detection of viral sequences requires a no...

Characterizations of sharks-microbe systems in wild environments have outlined patterns of species-specific microbiomes; however, whether captivity affects these trends has yet to be determined. We used high-throughput shotgun sequencing to assess the epidermal microbiome belonging to leopard sharks ( Triakis semifasciata ) in captive (Birch Aquari...

The epidermis of Chondrichthyan fishes consists of dermal denticles with production of minimal but protein-rich mucus that collectively, influence the attachment and biofilm development of microbes, facilitating a unique epidermal microbiome. Here, we use metagenomics to provide the taxonomic and functional characterization of the epidermal microbi...

Background: Characterizations of sharks-microbe systems in wild environments have outlined patterns of species-specific microbiomes; however, whether captivity affects these trends has yet to be determined. We used high-throughput shotgun sequencing to assess the epidermal microbiome belonging to leopard sharks (Triakis semifasciata) in captive (Bi...

Background: The epidermis of Chondrichthyan fishes consists of dermal denticles with production of minimal but protein rich mucus that influence the attachment and biofilm development of microbes, facilitating a unique epidermal microbiome. Here, we use metagenomics to provide the taxonomic and functional characterization of the epidermal microbiom...

Background: The epidermis of Chondrichthyan fishes consists of dermal denticles with production of minimal but protein rich mucus that influence the attachment and biofilm development of microbes, facilitating a unique epidermal microbiome. Here, we use metagenomics to provide the taxonomic and functional characterization of the epidermal microbiom...

Background The coral holobiont is comprised of a highly diverse microbial community that provides key services to corals such as protection against pathogens and nutrient cycling. The coral surface mucus layer (SML) microbiome is very sensitive to external changes and tied to ecosystem functioning, as it constitutes the direct interface between the...

The coral holobiont is comprised of a highly diverse microbial community that provides key services to corals such as protection against pathogens and nutrient cycling. The coral surface mucus layer (SML) microbiome is very sensitive to external changes, as it constitutes the direct interface between the coral host and the environment. Here we inve...

Microbiomes share an intimate relationship with the organisms they colonize, even across evolutionary timescales. That’s the basis of a theory called phylosymbiosis. Phylosymbiosis holds that microbial communities evolve as their host evolves and has been confirmed to exist for certain insects and mammals. Researchers recently tested whether that r...

Background: The vertebrate clade diverged into Chondrichthyes (sharks, rays, and chimeras) and Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical and physiological differences, including skin properties. The skin of Chondrichthyes fishes is covered in dermal denticles, whereas Osteichthyes fishes...

O livro intitulado ‘Biodiversidade Marinha dos Costões Rochosos de Arraial do Cabo: Histórico, Ecologia e Conservação é composto por 14 capítulos, perfazendo um compilado do conhecimento sobre as características oceanográficas, ambientais e dos principais grupos que ocorrem nos costões rochosos da região: Macroalgas, Porifera, Cnidaria, Mollusca, C...

Background: The vertebrate clade diverged into Chondrichthyes (sharks, rays, and chimeras) and Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical and physiological differences, including skin properties. The skin of Chondrichthyes fishes is covered in dermal denticles, whereas Osteichthyes fishes a...

Coral microbiome dysbiosis (i.e., shifts in the microbial community structure or complete loss of microbial symbionts) caused by environmental changes is a key player in the decline of coral health worldwide. Multiple factors in the water column and the surrounding biological community influence the dynamics of the coral microbiome. However, by inc...

Background: The vertebrate clade diverged into Chondrichthyes (sharks, rays, and chimeras) and Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical and physiological differences, including skin properties. The skin of Chondrichthyes fishes is covered in dermal denticles, whereas Osteichthyes fishes a...

Toxic chemicals within and adsorbed to microplastics (0.05-5 mm) have the potential to biomagnify in food webs. However, microplastic concentrations in highly productive, coastal habitats are not well understood. Therefore, we quantified the presence of microplastics in a benthic community and surrounding environment of a remote marine reserve on t...

Thermal stress induced by low seawater temperatures is a primary factor restricting coral growth and distribution. High latitude reefs may support coral populations that are resilient to thermal stress since they are exposed to wide annual temperature ranges. In Bermuda, the northernmost Atlantic reef system (32°18′N 64°47′W), corals are subjected...

Marginal reef sites are typically characterized by a low diversity of coral species; however, they are considered high conservation priorities. Despite their importance, the ecology of edge populations is poorly known. Arraial do Cabo, which is located within an upwelling region, represents the southernmost limit of the reef coral Siderastrea stell...

Corbicula fluminea is native mollusk from China. In Brazil, this species was first recorded in Rio Grande do Sul state in the late 70’s, being also recorded in the Amazonia basin between 1997 and 1998. The present note reports the occurrence of C. fluminea for the first time in the Caatinga biome and extends considerably the geographical distributi...

Corbicula fluminea is native mollusk from China. In Brazil, this species was first recorded in Rio Grande do Sul state in the late 70’s, being also recorded in the Amazonia basin between 1997 and 1998. The present note reports the occurrence of C. fluminea for the first time in the Caatinga biome and extends considerably the geographical distributi...

Melanoides tuberculata (Müller, 1774) (Gastropoda: Thiaridae) is the exotic species with the widest distribution among the freshwater macrobenthos in Brazil. The snail is a threat to native species and has medical and economical importance. In this study the occurrence of M. tuberculata is recorded and reported in the São Francisco River Basin, alo...