scholarly journals DNA barcoding enhances large-scale biodiversity initiatives for deep-pelagic crustaceans within the Gulf of Mexico and adjacent waters

2021 ◽  
Vol 41 (1) ◽  
Author(s):  
Carlos Varela ◽  
Charles Golightly ◽  
Laura E Timm ◽  
Blake Wilkins ◽  
Tamara Frank ◽  
...  
Keyword(s):  
Gulf Of Mexico ◽  
Dna Barcoding ◽  
Deep Sea ◽  
Large Scale ◽  
Oil Spills ◽  
Large Subunit ◽  
Evolutionary Relationships ◽  
Protein Coding ◽  
Molecular Approaches ◽  
Species Complexes

Abstract The application of DNA barcoding represents a complementary and efficient approach to identifying specimens at all stages of their life cycle when used in combination with traditional morphological methods. Due to difficulties obtaining samples from the deep sea (> 200 m), these methods have been less frequently applied to deep-water taxa. We used DNA-barcoding techniques to enhance large-scale biodiversity initiatives for deep-pelagic crustaceans within the Gulf of Mexico, a region that has recently been identified as one of the world’s four most hyperdiverse ocean ecosystems. This study was conceptualized in direct response to the Deepwater Horizon Oil Spill in 2010, which identified major knowledge gaps in our understanding of deep-sea biodiversity. We employed traditional Sanger sequencing and a genomic skimming approach to target the mitochondrial ribosomal large subunit 16S and the protein-coding cytochrome oxidase subunit 1 (COI). Alongside these molecular approaches, traditional taxonomic investigations allowed for advancements in biodiversity, evolutionary relationships, cryptic species complexes, and distributional records across four abundant and common deep-pelagic orders (Amphipoda, Euphausiacea, Lophogastrida, and Decapoda). DNA barcodes were successfully obtained from 82 species for a total of 158 and 169 new 16S and COI sequences, respectively. Evidence of cryptic diversity has been found in the genera EucopiaDana, 1852 (Lophogastrida) and Allosergestes Judkins & Kensley, 2008 (Decapoda). New records for the Gulf of Mexico of species of LanceolaSay, 1818 (Amphipoda), Eupasiphae Wood-Mason in Wood-Mason & Alcock, 1893, PasiphaeaSavigny, 1816, and MeningodoraSmith, 1882 (Caridea) are presented. Preliminary results allow us to reconsider the current classification and evolutionary relationships of several lineages. The urgency to document biodiversity in the deep-pelagic is pressing against a backdrop of future threats including oil spills and deep-sea drilling.

scholarly journals A Mysterious World Revealed: Larval-Adult Matching of Deep-Sea Shrimps from the Gulf of Mexico

Diversity ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 457
Author(s):  
Carlos Varela ◽  
Heather Bracken-Grissom
Keyword(s):  
Gulf Of Mexico ◽  
Dna Barcoding ◽  
Deep Sea ◽  
Phylogenetic Trees ◽  
Developmental Stages ◽  
Large Subunit ◽  
Morphological Diversity ◽  
Protein Coding ◽  
Larval Stages ◽  
Taxonomic Descriptions

The identification of deep-sea (>200 m) pelagic larvae is extremely challenging due to the morphological diversity across ontogeny and duration of larval phases. Within Decapoda, developmental stages often differ conspicuously from their adult form, representing a bizarre and mysterious world still left to be discovered. The difficulties with sampling and rearing deep-sea larvae, combined with the lack of taxonomic expertise, argues for the use of molecular methods to aid in identification. Here, we use DNA barcoding combined with morphological methods, to match larval stages with their adult counterpart from the northern Gulf of Mexico and adjacent waters. For DNA barcoding, we targeted the mitochondrial ribosomal large subunit 16S (16S) and the protein coding cytochrome oxidase subunit 1 (COI). These data were combined with previous sequences to generate phylogenetic trees that were used to identify 12 unknown larval and two juvenile species from the infraorder Caridea and the suborder Dendrobranchiata. Once identified, we provide taxonomic descriptions and illustrations alongside the current state of knowledge for all families. For many groups, larval descriptions are missing or non-existent, so this study represents a first step of many to advance deep-sea larval diversity.

scholarly journals Into the Benthos and Back: What have Infauna Taught Us

2021 ◽  
Vol 2021 (1) ◽  
Author(s):  
Paul A. Montagna
Keyword(s):  
Gulf Of Mexico ◽  
Mississippi River ◽  
Deep Sea ◽  
Oil Spills ◽  
Hydrocarbon Exploration ◽  
Biologically Active ◽  
River Outflow ◽  
Exploration And Production ◽  
Long Time ◽  
Hydrocarbon Exploration And Production

ABSTRACT ID 685153 Because of death and gravity, the bottom of the sea is the memory of the ecosystem, where a record of all past events can be found as you move into deeper layers of sediment. Thus, benthos are primary indicators for environmental assessments. As hydrocarbon exploration and production moved to deeper waters, so did environmental studies. But there were only a few Gulf-wide surveys in the deepest parts of the Gulf of Mexico, and our understanding of deep-sea processes was based primarily on other regions of the world. The intensive focus on deep-sea response during and after the Deepwater Horizon (DWH) accident increased our knowledge dramatically. We learned that the deep sea is dynamic, fragile, and will take a long time to recover. There was a 50% loss of biodiversity within 9 km diameter around the DWH site, and a 10% within a 17 km of the site. But there is still much to learn. The deep-sea is a reservoir of biodiversity on Earth, but about 60% of Gulf of Mexico taxa are still unknown, which is a major hinderance to understanding the effects of oil spills. The northern Gulf of Mexico is dominated by Mississippi River outflow, but exactly how it drives deep-sea dynamics needs better resolution. Two outcomes of the last decade of research is that we know benthos diversity is a sensitive indicator of environmental change and damage, the surface sediments are the biologically active zones, and the natural process of sinking particles will eventually cover the damaged sediment leading to natural recovery. This “restoration in place” strategy must be confirmed by future monitoring and assessment studies.

scholarly journals Two decades of DNA barcoding in the genus Usnea (Parmeliaceae): how useful and reliable is the ITS?

2020 ◽  
pp. 303-357
Author(s):  
Robert Lücking ◽  
Miko Nadel ◽  
Elena Araujo ◽  
Alice Gerlach
Keyword(s):  
North America ◽  
Gene Duplication ◽  
Dna Barcoding ◽  
Data Sampling ◽  
Protein Coding ◽  
Species Complexes ◽  
Accuracy And Precision ◽  
Geographic Coverage ◽  
Species Pairs ◽  
Voucher Specimens

We present an exhaustive analysis of the ITS barcoding marker in the genus Usnea s.lat., separated into Dolichousnea, Eumitria, and Usnea including the subgenus Neuropogon, analyzing 1,751 accessions. We found only a few low-quality accessions, whereas information on voucher specimens and accuracy and precision of identifications was of subpar quality for many accessions. We provide an updated voucher table, alignment and phylogenetic tree to facilitate DNA barcoding of Usnea, either locally or through curated databases such as UNITE. Taxonomic and geographic coverage was moderate: while Dolichousnea and subgenus Neuropogon were well-represented among ITS data, sampling for Eumitria and Usnea s.str. was sparse and biased towards certain lineages and geographic regions, such as Antarctica, Europe, and South America. North America, Africa, Asia and Oceania were undersampled. A peculiar situation arose with New Zealand, represented by a large amount of ITS accessions from across both major islands, but most of them left unidentified. The species pair Usnea antarctica vs. U. aurantiacoatra was the most sampled clade, including numerous ITS accessions from taxonomic and ecological studies. However, published analyses of highly resolved microsatellite and RADseq markers showed that ITS was not able to properly resolve the two species present in this complex. While lack of resolution appears to be an issue with ITS in recently evolving species complexes, we did not find evidence for gene duplication (paralogs) or hybridization for this marker. Comparison with other markers demonstrated that particularly IGS and RPB1 are useful to complement ITS-based phylogenies. Both IGS and RPB1 provided better backbone resolution and support than ITS; while IGS also showed better resolution and support at species level, RPB1 was less resolved and delineated for larger species complexes. The nuLSU was of limited use, providing neither resolution nor backbone support. The other three commonly employed protein-coding markers, TUB2, RPB2, and MCM7, showed variable evidence of possible gene duplication and paralog formation, particularly in the MCM7, and these markers should be used with care, especially in multimarker coalescence approaches. A substantial challenge was provided by difficult morphospecies that did not form coherent clades with ITS or other markers, suggesting various levels of cryptic speciation, the most notorious example being the U. cornuta complex. In these cases, the available data suggest that multimarker approaches using ITS, IGS and RPB1 help to assess distinct lineages. Overall, ITS was found to be a good first approximation to assess species delimitation and recognition in Usnea s.lat., as long as the data are carefully analyzed, and reference sequences are critically assessed and not taken at face value. In difficult groups, we recommend IGS as a secondary barcode marker, with the option to employ more resource-intensive approaches, such as RADseq, in species complexes involving so-called species pairs or other cases of disparate morphology not reflected in the ITS or IGS. Attempts should be made to close taxonomic and geographic gaps especially for the latter two markers, in particular in Eumitria and Usnea s.str. and in the highly diverse areas of North America and Central America, Africa, Asia, and Oceania.

scholarly journals Bacteria From the Southern Gulf of Mexico: Baseline, Diversity, Hydrocarbon-Degrading Potential and Future Applications

2021 ◽  
Vol 8 ◽  
Author(s):  
Julieta Rodríguez-Salazar ◽  
Antonio Loza ◽  
Katya Ornelas-Ocampo ◽  
Rosa Maria Gutierrez-Rios ◽  
Liliana Pardo-López
Keyword(s):  
Gulf Of Mexico ◽  
Large Scale ◽  
Oil Spills ◽  
Microbial Consortia ◽  
Biotechnological Potential ◽  
Consulting Services ◽  
Third Generation Sequencing ◽  
Southern Gulf Of Mexico ◽  
Southwest Region ◽  
Research Consortium

The Gulf of Mexico Research Consortium (Consorcio de Investigación del Golfo de México (CIGoM), 2020) was founded in 2015 as a consortium of scientific research and consulting services, specializing in multidisciplinary projects related to the potential environmental impacts of natural and human-induced oil spills in marine ecosystems, to understand and act in the case of possible large-scale oil spills in the Gulf of Mexico. CIGoM comprises more than 300 specialized researchers trained at the most recognized Mexican institutions. Among the main interests of CIGoM are developing the first baseline of the bacterial community inhabiting the southern Gulf of Mexico, investigating the natural degradation of hydrocarbons by bacterial communities and microbial consortia and identifying and characterizing industrially relevant enzymes. In this review, using third-generation sequencing methodologies coupled to function screening methodologies, we report the bacterial profile found in samples of water and sediments in Mexican regions that include the Perdido Fold Belt (northwest of Mexico), Campeche Knolls (in the southeast) and Southwest region of the Gulf of Mexico. We also highlight some examples of novel lipases and dioxygenases with high biotechnological potential and some culturable hydrocarbon-degrading strains used in diverse bioremediation processes.

scholarly journals Impact of Oil Spills on Marine Life in the Gulf of Mexico: Effects on Plankton, Nekton, and Deep-Sea Benthos

Oceanography ◽  
2016 ◽  
Vol 29 (3) ◽  
pp. 174-181 ◽  
Author(s):  
Edward Buskey ◽  
Helen White ◽  
Andrew Esbaugh
Keyword(s):  
Gulf Of Mexico ◽  
Deep Sea ◽  
Oil Spills ◽  
Marine Life

Restoring barrier habitat in Louisiana to compensate for natural resource injuries: Shell Island and Chenier Ronquille Barrier Restoration Projects

Shore & Beach ◽  
2020 ◽  
pp. 65-71
Author(s):  
Whitney Thompson ◽  
Christopher Paul ◽  
John Darnall
Keyword(s):  
Gulf Of Mexico ◽  
Natural Resource ◽  
Large Scale ◽  
Barrier Island ◽  
Deepwater Horizon ◽  
Coastal Protection ◽  
Restoration Project ◽  
Island Restoration ◽  
Barataria Basin ◽  
Outer Coast

Coastal Louisiana received significant funds tied to BP penalties as a result of the Deepwater Horizon incident. As it is widely considered that the State of Louisiana sustained most of the damage due to this incident, there has been a firm push to waste no time in implementing habitat restoration projects. Sustaining the land on the coast of Louisiana is vital to our nation’s economy, as several of the nation’s largest ports are located on the Gulf coast in Louisiana. In addition, the ecosystems making up the Louisiana coast are important to sustain some of the largest and most valuable fisheries in the nation. Funded by BP Phase 3 Early Restoration, the goals of the Natural Resource Damage Assessment (NRDA) Outer Coast Restoration Project are to restore beach, dune, and marsh habitats to help compensate spill-related injuries to habitats and species, specifically brown pelicans, terns, skimmers, and gulls. Four island components in Louisiana were funded under this project; Shell Island Barrier Restoration, Chenier Ronquille Barrier Island Restoration, Caillou Lake Headlands Barrier Island Restoration, and North Breton Island Restoration (https://www. gulfspillrestoration.noaa.gov/louisiana-outer-coast-restoration, NOAA 2018). Shell Island and Chenier Ronquille are critical pieces of barrier shoreline within the Barataria Basin in Plaquemines Parish, Louisiana. These large-scale restoration projects were completed in the years following the Deepwater Horizon incident, creating new habitat and reinforcing Louisiana’s Gulf of Mexico shoreline. The Louisiana Coastal Protection and Restoration Authority (CPRA) finished construction of the Shell Island NRDA Restoration Project in 2017, which restored two barrier islands in Plaquemines Parish utilizing sand hydraulically dredged from the Mississippi River and pumped via pipeline over 20 miles over levees and through towns, marinas, and marshes to the coastline. The National Marine Fisheries Service (NMFS) also completed the Plaquemines Parish barrier island restoration at Chenier Ronquille in 2017 utilizing nearshore Gulf of Mexico sediment, restoring wetland, coastal, and nearshore habitat in the Barataria Basin. A design and construction overview is provided herein.

scholarly journals Mutational patterns and clonal evolution from diagnosis to relapse in pediatric acute lymphoblastic leukemia

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shumaila Sayyab ◽  
Anders Lundmark ◽  
Malin Larsson ◽  
Markus Ringnér ◽  
Sara Nystedt ◽  
...  
Keyword(s):  
Acute Lymphoblastic Leukemia ◽  
Large Scale ◽  
Somatic Mutations ◽  
Lymphoblastic Leukemia ◽  
Clonal Evolution ◽  
Point Mutations ◽  
Driver Genes ◽  
Protein Coding ◽  
Pediatric Acute Lymphoblastic Leukemia ◽  
Evolutionary Trajectories

AbstractThe mechanisms driving clonal heterogeneity and evolution in relapsed pediatric acute lymphoblastic leukemia (ALL) are not fully understood. We performed whole genome sequencing of samples collected at diagnosis, relapse(s) and remission from 29 Nordic patients. Somatic point mutations and large-scale structural variants were called using individually matched remission samples as controls, and allelic expression of the mutations was assessed in ALL cells using RNA-sequencing. We observed an increased burden of somatic mutations at relapse, compared to diagnosis, and at second relapse compared to first relapse. In addition to 29 known ALL driver genes, of which nine genes carried recurrent protein-coding mutations in our sample set, we identified putative non-protein coding mutations in regulatory regions of seven additional genes that have not previously been described in ALL. Cluster analysis of hundreds of somatic mutations per sample revealed three distinct evolutionary trajectories during ALL progression from diagnosis to relapse. The evolutionary trajectories provide insight into the mutational mechanisms leading relapse in ALL and could offer biomarkers for improved risk prediction in individual patients.

scholarly journals Annelid Diversity: Historical Overview and Future Perspectives

Diversity ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 129
Author(s):  
María Capa ◽  
Pat Hutchings
Keyword(s):  
State Of The Art ◽  
Molecular Taxonomy ◽  
Evolutionary Relationships ◽  
Diverse Group ◽  
Future Perspectives ◽  
Special Issue ◽  
Species Numbers ◽  
Species Complexes ◽  
Taxonomic Groups ◽  
A New Species

Annelida is a ubiquitous, common and diverse group of organisms, found in terrestrial, fresh waters and marine environments. Despite the large efforts put into resolving the evolutionary relationships of these and other Lophotrochozoa, and the delineation of the basal nodes within the group, these are still unanswered. Annelida holds an enormous diversity of forms and biological strategies alongside a large number of species, following Arthropoda, Mollusca, Vertebrata and perhaps Platyhelminthes, among the species most rich in phyla within Metazoa. The number of currently accepted annelid species changes rapidly when taxonomic groups are revised due to synonymies and descriptions of a new species. The group is also experiencing a recent increase in species numbers as a consequence of the use of molecular taxonomy methods, which allows the delineation of the entities within species complexes. This review aims at succinctly reviewing the state-of-the-art of annelid diversity and summarizing the main systematic revisions carried out in the group. Moreover, it should be considered as the introduction to the papers that form this Special Issue on Systematics and Biodiversity of Annelids.

scholarly journals The Evolution of Life Modes in Stictidaceae, with Three Novel Taxa

2021 ◽  
Vol 7 (2) ◽  
pp. 105
Author(s):  
Vinodhini Thiyagaraja ◽  
Robert Lücking ◽  
Damien Ertz ◽  
Samantha C. Karunarathna ◽  
Dhanushka N. Wanasinghe ◽  
...  
Keyword(s):  
New Species ◽  
Large Scale ◽  
Sequence Data ◽  
Large Subunit ◽  
Monte Carlo Sampling ◽  
Small Subunit ◽  
Sensu Stricto ◽  
Internal Transcribed Spacers ◽  
Character State ◽  
Phenotypic Data

Ostropales sensu lato is a large group comprising both lichenized and non-lichenized fungi, with several lineages expressing optional lichenization where individuals of the same fungal species exhibit either saprotrophic or lichenized lifestyles depending on the substrate (bark or wood). Greatly variable phenotypic characteristics and large-scale phylogenies have led to frequent changes in the taxonomic circumscription of this order. Ostropales sensu lato is currently split into Graphidales, Gyalectales, Odontotrematales, Ostropales sensu stricto, and Thelenellales. Ostropales sensu stricto is now confined to the family Stictidaceae, which includes a large number of species that are poorly known, since they usually have small fruiting bodies that are rarely collected, and thus, their taxonomy remains partly unresolved. Here, we introduce a new genus Ostropomyces to accommodate a novel lineage related to Ostropa, which is composed of two new species, as well as a new species of Sphaeropezia, S. shangrilaensis. Maximum likelihood and Bayesian inference analyses of mitochondrial small subunit spacers (mtSSU), large subunit nuclear rDNA (LSU), and internal transcribed spacers (ITS) sequence data, together with phenotypic data documented by detailed morphological and anatomical analyses, support the taxonomic affinity of the new taxa in Stictidaceae. Ancestral character state analysis did not resolve the ancestral nutritional status of Stictidaceae with confidence using Bayes traits, but a saprotrophic ancestor was indicated as most likely in a Bayesian binary Markov Chain Monte Carlo sampling (MCMC) approach. Frequent switching in nutritional modes between lineages suggests that lifestyle transition played an important role in the evolution of this family.

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