Biology subjects

Vega Thurber, R.

Publications and source records attributed to Vega Thurber, R..

6 recordsLinked to original sources

bioRxiv2026

Diversity, host-specificity, and environmental drivers of the coral reef eukaryome

Coral reefs are among the most diverse ecosystems on Earth, yet the diversity and structure of their associated microeukaryotic communities remain poorly resolved. We characterized reef-associated eukaryomes across 113 reefs spanning the Pacific Ocean using more than 6,300 samples from corals, seawater, and sediments during the Tara Pacific expedition. We identified [~]121,000 eukaryotic ASVs, revealing one of Earths largest undocumented reservoirs of eukaryotic diversity; over 80% of the recovered diversity was previously undetected in global ocean surveys and fewer than 2% of sequences matched reference databases. Reef habitats supported highly distinct communities, with sediments and seawater harboring 20-40-fold higher richness than corals. Unexpectedly, coral-associated communities across 29 host lineages were consistently dominated by small metazoans, particularly demosponges and maxillopods, identifying these taxa as pervasive and previously unrecognized components of coral eukaryomes alongside Apicomplexa. Across the Pacific, eukaryome composition was strongly structured by environmental gradients, with thermal stress emerging as the primary driver of community turnover. Together, these results identify coral reefs as a globally important reservoir of hidden eukaryotic diversity and reveal the reef eukaryome as a sensitive indicator of ecosystem reorganization under climate change.

systems biology↗

bioRxiv2023

Transcriptomics Reveals Tumorigenesis and Pathogen Response in Scombrid Puffy Snout Syndrome

Scombrids represent some of the most economically important fisheries globally. However, increased interest in creating aquaculture systems for these fish has also increased the risk for disease emergence. One such disease, Puffy Snout Syndrome (PSS), causes collagenous tissue growths on the face in numerous scombrid taxa. PSS has mainly been documented in captive-held fish populations and can lead to high mortality rates. Despite this, little is known about the causative agent(s) of PSS and the immune response they elicit. Therefore, we leveraged transcriptomic data of PSS symptomatic-captive, asymptomatic-captive, and healthy-wild Pacific Mackerel (Scomber japonicus) to evaluate the physiological characteristics of PSS infections and identify a potential mechanism of disease. Captive symptomatic and asymptomatic mackerel showed distinct gene expression patterns from their wild counterparts. Genes involved in tumorigenesis, immune response, and tissue remodeling were overexpressed in captive-held fish. WNT9 was the most overexpressed gene in captive groups, and the WNT signaling pathway itself showed a [~]3 fold increase in KEGG pathway enrichment analysis in captive animals. When captive fish were compared, asymptomatic fish showed lower expression of inflammation genes, but high expression of tumor suppressor genes compared to symptomatic-captive fish. Together, these host pathophysiological data and our past visual identification of RNA virus-like particles in afflicted tissues suggest that viral-mediated oncogenesis may be driving PSS in captive mackerel.

genomics↗

bioRxiv2022

Disparate patterns of genetic divergence in three widespread corals across a pan-Pacific environmental gradient highlights species-specific adaptation trajectories.

Tropical coral reefs are among the worst affected ecosystems by climate change with predictions ranging between a 70-90% loss of reefs in the coming decades. Effective conservation strategies that maximize ecosystem resilience, and potential for recovery, must be informed by the accurate characterization of extant genetic diversity and population structure together with an understanding of the adaptive potential of keystone species. Here, we analyzed samples from the Tara Pacific Expedition (2016 to 2018) that completed an 18,000 km longitudinal transect of the Pacific Ocean sampling three widespread corals - Pocillopora meandrina, Porites lobata, and Millepora cf. platyphylla - across 33 sites from 11 islands. Using deep metagenomic sequencing of 269 colonies in conjunction with morphological analyses and climate variability data we can show that the sampled transect encompasses multiple morphologically cryptic species that exhibit disparate biogeographic patterns, and most importantly, distinct evolutionary patterns, despite exposure to identical environmental regimes. Our findings demonstrate on a basin-scale that evolutionary trajectories are species-specific and complex, and can only in part be predicted from the environment. This highlights that conservation strategies must integrate multi-species investigations to consider the distinct genomic footprints shaped by selection as well as the genetic potential for adaptive change.

genetics↗

bioRxiv2021

Inconsistent patterns of microbial diversity and composition between highly similar sequencing protocols: a case study with reef-building corals

16S rRNA gene profiling (amplicon sequencing) is a popular technique for understanding host-associated and environmental microbial communities. Most protocols for sequencing amplicon libraries follow a standardized pipeline that can differ slightly depending on laboratory facility and user. Given that the same variable region of the 16S gene is targeted, it is generally accepted that sequencing output from differing protocols are comparable and this assumption underlies our ability to identify universal patterns in microbial dynamics through meta-analyses. However, discrepant results from a combined 16S rRNA dataset prepared by two labs whose protocols differed only in DNA polymerase and sequencing platform led us to scrutinize the outputs and challenge the idea of confidently combining them for standard microbiome analysis. Using technical replicates of reef-building coral samples from two species, Montipora aequituberculata and Porites lobata, we evaluated the consistency of alpha and beta diversity metrics between data resulting from these highly similar protocols. While we found minimal variation in alpha diversity between platform, significant differences were revealed with most beta diversity metrics, dependent on host species. These inconsistencies persisted following removal of low abundance taxa and when comparing across higher taxonomic levels, suggesting that bacterial community differences associated with sequencing protocol are likely to be context dependent and difficult to correct without extensive validation work. The results of this study encourage caution in the statistical comparison and interpretation of studies that combine rRNA sequence data from distinct protocols and point to a need for further work identifying mechanistic causes of these observed differences. ImportanceAmplicon sequencing remains a popular technique for characterizing organism and environmental microbiomes. The publication of sequence data from microbiome studies on open-access repositories provides an opportunity to identify universal patterns in microbial dynamics. To this end, it has been widely accepted that sequencing output from differing protocols are comparable and can be combined for analysis, so long as the same gene region is targeted. While most protocols for amplicon sequencing follow standardized pipelines, they can differ slightly between laboratory facility and user. In this study, we compared technical replicates of coral samples to evaluate the efficacy of combining organism-associated microbial datasets derived from two differing protocols. We found inconsistencies in the differences between bacterial communities, which persisted following data manipulations intended to increase comparability. These results suggest caution must be taken in the statistical comparison and interpretation of studies that combine data derived from distinct protocols.

microbiology↗

bioRxiv2021

Evaluation of the effects of library preparation procedure and sample characteristics on the accuracy of metagenomic profiles

Shotgun metagenomic sequencing has transformed our understanding of microbial community ecology. However, preparing metagenomic libraries for high-throughput DNA sequencing remains a costly, labor-intensive, and time-consuming procedure, which in turn limits the utility of metagenomes. Several library preparation procedures have recently been developed to offset these costs, but it is unclear how these newer procedures compare to current standards in the field. In particular, it is not clear if all such procedures perform equally well across different types of microbial communities, or if features of the biological samples being processed (e.g., DNA amount) impact the accuracy of the approach. To address these questions, we assessed how five different shotgun DNA sequence library preparation methods, including the commonly used Nextera(R) Flex kit, perform when applied to metagenomic DNA. We measured each methods ability to produce metagenomic data that accurately represents the underlying taxonomic and genetic diversity of the community. We performed these analyses across a range of microbial community types (e.g., soil, coral-associated, mouse-gut-associated) and input DNA amounts. We find that the type of community and amount of input DNA influence each methods performance, indicating that careful consideration may be needed when selecting between methods, especially for low complexity communities. However, cost-effective preparation methods we assessed are generally comparable to the current gold standard Nextera(R) DNA Flex kit for high-complexity communities. Overall, the results from this analysis will help expand and even facilitate access to metagenomic approaches in future studies. IMPORTANCEMetagenomic library preparation methods and sequencing technologies continue to advance rapidly, allowing researchers to characterize microbial communities in previously underexplored environmental samples and systems. However, widely-accepted standardized library preparation methods can be cost-prohibitive. Newly available approaches may be less expensive, but their efficacy in comparison to standardized methods remains unknown. In this study, we compared five different metagenomic library preparation methods. We evaluated each method across a range of microbial communities varying in complexity and quantity of input DNA. Our findings demonstrate the importance of considering sample properties, including community type, composition, and DNA amount, when choosing the most appropriate metagenomic library preparation method.

microbiology↗

bioRxiv2021

The coral symbiont Candidatus Aquarickettsia is variably abundant in threatened Caribbean acroporids and transmitted horizontally.

The aquatic symbiont "Candidatus Aquarickettsia rohweri" infects a diversity of non-bilaterian metazoan phyla. In the threatened coral Acropora cervicornis, Aquarickettsia proliferates in response to increased nutrient exposure, resulting in suppressed growth and increased disease susceptibility and mortality. This study evaluated the extent, as well as the ecology and evolution of Aquarickettsia infecting the Caribbean corals: Ac. cervicornis and Ac. palmata and their hybrid ( Ac. prolifera). The bacterial parasite Aquarickettsia was found in all acroporids, with host and sampling location impacting infection magnitude. Phylogenomic and genome-wide single nucleotide variant analysis found Aquarickettsia clustering by region, not by coral taxon. Fixation analysis suggested within coral colonies, Aquarickettsia are genetically isolated to the extent that reinfection is unlikely. Relative to other Rickettsiales, Aquarickettsia is undergoing positive selection, with Florida populations experiencing greater positive selection relative to the other Caribbean locations. This may be due to Aquarickettsia response to increased nutrient stress in Florida, as indicated by greater in situ replication rates in these corals. Aquarickettsia did not significantly codiversify with either coral animal nor algal symbiont, and qPCR analysis of gametes and juveniles from susceptible coral genotypes indicated absence in early life stages. Thus, despite being an obligate parasite, Aquarickettsia must be horizontally transmitted via coral mucocytes, an unidentified secondary host, or a yet unexplored environmentally mediated mechanism. Importantly, the prevalence of Aquarickettsia in Ac. cervicornis and high abundance in Florida populations suggests that disease mitigation efforts in the US and Caribbean should focus on preventing early infection via horizontal transmission.

microbiology↗